1795
Pathway
Uracil Degradation III
E. coli is able to utilize pyrimidine nucleosides and bases as the sole source of nitrogen at room temperature. This novel pathway for pyrimidine degradation was discovered by a combination of functional and comparative genomics techniques including high-throughput microarray and phenotype analysis. The pathway depicted here represents a combination of experimental work and functional predictions based on the available evidence.
In the presence of a flavin reductase, pyrimidine oxygenase catalyzes the first step in this pathway, the ring opening of uracil at the C4 carbonyl by a novel flavin hydroperoxide-catalyzed mechanism. The initial product of the reaction appears to be (Z)-3-ureidoacrylate peracid, which is unstable and can be slowly reduced to ureidoacrylate. While the RutB enzyme is able to hydrolyze ureidoacrylate, it is thought to hydrolyze peroxyureidoacrylate in vivo, yielding carbamate and (Z)-3-peroxyaminoacrylate. In a spontaneous reaction, carbamate decomposes into one molecule each of ammonia and CO2. The aminoacrylate peracid is thought to be reduced to aminoacrylate by the predicted aminoacrylate peracid reductase. Aminoacrylate can then hydrolyze either spontaneously or enzymatically to 3-oxopropanoate and a second molecule of ammonia. Malonate semialdehyde appears to be toxic and can not be utilized further. The compound may be detoxified by one of two malonic semialdehyde reductases to 3-hydroxypropanoate, which is then excreted into the medium. The toxicity of malonic semialdehyde appears to limit growth on pyrimidines as the sole source of nitrogen. (EcoCyc)
Metabolic
PW002026
Center
PathwayVisualizationContext2313
1738
2049
#000099
PathwayVisualization1779
1795
Uracil Degradation III
E. coli is able to utilize pyrimidine nucleosides and bases as the sole source of nitrogen at room temperature. This novel pathway for pyrimidine degradation was discovered by a combination of functional and comparative genomics techniques including high-throughput microarray and phenotype analysis. The pathway depicted here represents a combination of experimental work and functional predictions based on the available evidence.
In the presence of a flavin reductase, pyrimidine oxygenase catalyzes the first step in this pathway, the ring opening of uracil at the C4 carbonyl by a novel flavin hydroperoxide-catalyzed mechanism. The initial product of the reaction appears to be (Z)-3-ureidoacrylate peracid, which is unstable and can be slowly reduced to ureidoacrylate. While the RutB enzyme is able to hydrolyze ureidoacrylate, it is thought to hydrolyze peroxyureidoacrylate in vivo, yielding carbamate and (Z)-3-peroxyaminoacrylate. In a spontaneous reaction, carbamate decomposes into one molecule each of ammonia and CO2. The aminoacrylate peracid is thought to be reduced to aminoacrylate by the predicted aminoacrylate peracid reductase. Aminoacrylate can then hydrolyze either spontaneously or enzymatically to 3-oxopropanoate and a second molecule of ammonia. Malonate semialdehyde appears to be toxic and can not be utilized further. The compound may be detoxified by one of two malonic semialdehyde reductases to 3-hydroxypropanoate, which is then excreted into the medium. The toxicity of malonic semialdehyde appears to limit growth on pyrimidines as the sole source of nitrogen. (EcoCyc)
Metabolic
3
109799
1651
SubPathway
109308
204
Compound
3872
13416173
CAMPBELL LL Jr: Reductive degradation of pyrimidines. I. The isolation and characterization of a uracil fermenting bacterium, Clostridium uracilicum nov. spec. J Bacteriol. 1957 Feb;73(2):220-4.
1795
Pathway
1
Cell
CL:0000000
5
Hepatocyte
CL:0000182
4
Cardiomyocyte
CL:0000746
3
Neuron
CL:0000540
7
Epithelial Cell
CL:0000066
2
Platelet
CL:0000233
1
Homo sapiens
9606
Eukaryote
Human
3
Escherichia coli
562
Prokaryote
12
Mus musculus
10090
Eukaryote
Mouse
2
Bacteria
2
Prokaryote
Bacteria
24
Solanum lycopersicum
4081
Eukaryote
Tomato
18
Saccharomyces cerevisiae
4932
Eukaryote
Yeast
21
Xenopus laevis
8355
Eukaryote
African clawed frog
4
Arabidopsis thaliana
3702
Eukaryote
Thale cress
6
Caenorhabditis elegans
6239
Eukaryote
Roundworm
25
Escherichia coli (strain K12)
83333
Prokaryote
23
Pseudomonas aeruginosa
287
Prokaryote
60
Nitzschia sp.
0001
Eukaryote
Nitzschia4
17
Rattus norvegicus
10116
Eukaryote
Rat
5
Bos taurus
9913
Eukaryote
Cattle
10
Drosophila melanogaster
7227
Eukaryote
Fruit fly
49
Bathymodiolus platifrons
220390
Eukaryote
Deep sea mussel
19
Schizosaccharomyces pombe
4896
Eukaryote
3
Mitochondrial Matrix
GO:0005759
5
Cytoplasm
GO:0005737
11
Extracellular Space
GO:0005615
2
Mitochondrion
GO:0005739
1
Cytosol
GO:0005829
7
Endoplasmic Reticulum Membrane
GO:0005789
12
Mitochondrial Inner Membrane
GO:0005743
14
Mitochondrial Outer Membrane
GO:0005741
24
Mitochondrial Intermembrane Space
GO:0005758
13
Endoplasmic Reticulum
GO:0005783
31
Periplasmic Space
GO:0005620
35
Chloroplast
GO:0009507
4
Peroxisome
GO:0005777
10
Cell Membrane
GO:0005886
36
Membrane
GO:0016020
53
Endoplasmic Reticulum Body
GO:0010168
34
Plant-Type Vacuole
GO:0000325
32
Inner Membrane
GO:0070258
25
Golgi apparatus
GO:0005794
6
Lysosome
GO:0005764
16
Lysosomal Lumen
GO:0043202
18
Melanosome Membrane
GO:0033162
20
Endoplasmic Reticulum Lumen
GO:0005788
21
Synapse
GO:0045202
15
Nucleus
GO:0005634
40
Periplasm
GO:0042597
19
sarcoplasmic reticulum
GO:0016529
1
Liver
BTO:0000759
72
9
28
Stomach
BTO:0001307
155
26
8
Blood Vessel
BTO:0001102
74
11
4
Adrenal Medulla
BTO:0000049
71
8
25
Intestine
BTO:0000648
7
Nervous System
BTO:0001484
11
Heart
BTO:0000562
73
10
5
cardiocyte
BTO:0001539
2
Endothelium
BTO:0000393
4
3
1
1
PW_BS000004
8
5
1
1
PW_BS000008
15
11
1
PW_BS000015
31
1
5
1
1
PW_BS000031
3
2
1
1
PW_BS000003
2
1
1
1
PW_BS000002
26
1
1
1
5
PW_BS000026
54
1
3
1
5
PW_BS000054
49
7
1
1
PW_BS000049
17
12
1
1
PW_BS000017
22
14
1
1
PW_BS000022
42
24
1
1
PW_BS000042
10
1
7
1
1
PW_BS000010
18
13
1
1
PW_BS000018
70
28
5
1
1
PW_BS000070
103
3
3
1
PW_BS000103
111
5
12
1
PW_BS000111
112
2
12
1
PW_BS000112
108
1
3
PW_BS000108
107
31
3
PW_BS000107
100
5
2
1
PW_BS000100
105
11
3
PW_BS000105
117
1
3
1
PW_BS000117
147
1
24
1
PW_BS000147
155
3
24
1
PW_BS000155
157
2
24
1
PW_BS000157
161
3
18
1
PW_BS000161
159
24
PW_BS000159
166
1
1
PW_BS000166
178
3
21
1
PW_BS000178
152
8
4
PW_BS000152
101
5
3
1
PW_BS000101
188
1
18
PW_BS000024
187
31
18
PW_BS000024
163
2
18
1
PW_BS000163
205
5
6
1
PW_BS000024
206
2
6
1
PW_BS000024
219
31
4
PW_BS000024
220
1
4
PW_BS000024
222
3
4
1
PW_BS000024
213
7
18
1
PW_BS000024
210
13
18
1
PW_BS000024
212
1
7
18
1
PW_BS000024
160
1
18
1
PW_BS000160
170
18
PW_BS000170
225
35
4
1
PW_BS000024
151
1
4
1
PW_BS000151
226
4
4
1
PW_BS000024
162
12
18
1
PW_BS000162
224
2
4
1
PW_BS000024
195
13
18
PW_BS000024
249
13
4
1
PW_BS000024
164
4
PW_BS000164
281
1
25
1
PW_BS000024
285
10
4
1
PW_BS000024
286
36
4
1
PW_BS000024
287
53
4
1
PW_BS000024
227
34
4
1
PW_BS000024
223
12
4
1
PW_BS000024
294
11
4
1
PW_BS000024
308
10
1
1
PW_BS000024
315
1
23
PW_BS000024
318
31
23
PW_BS000024
322
1
23
1
PW_BS000024
312
5
23
1
PW_BS000024
320
11
23
PW_BS000024
293
4
1
PW_BS000024
133
3
12
1
PW_BS000133
134
12
12
1
PW_BS000134
331
7
12
1
PW_BS000028
114
11
12
PW_BS000114
132
1
12
1
PW_BS000132
327
1
1
12
5
PW_BS000028
347
1
3
12
5
PW_BS000028
345
24
12
1
PW_BS000028
130
13
12
1
PW_BS000130
368
3
60
1
PW_BS000028
310
31
2
PW_BS000024
304
1
2
PW_BS000024
119
2
17
1
PW_BS000119
124
1
5
1
PW_BS000124
383
7
5
1
PW_BS000100
388
1
6
1
PW_BS000112
94
3
PW_BS000094
390
7
6
1
PW_BS000112
398
7
17
1
PW_BS000113
118
1
17
1
PW_BS000118
336
1
12
1
PW_BS000028
109
32
3
PW_BS000109
406
3
5
1
PW_BS000115
407
2
5
1
PW_BS000115
122
5
5
1
PW_BS000122
409
11
5
PW_BS000115
424
1
1
5
5
PW_BS000115
425
1
3
5
5
PW_BS000115
418
24
5
1
PW_BS000115
384
12
5
1
PW_BS000100
125
13
5
1
PW_BS000125
120
3
17
1
PW_BS000120
135
5
17
1
PW_BS000135
137
11
17
PW_BS000137
459
1
1
17
5
PW_BS000115
460
1
3
17
5
PW_BS000115
454
24
17
1
PW_BS000115
121
12
17
1
PW_BS000121
136
13
17
1
PW_BS000136
479
3
10
1
PW_BS000115
481
2
10
1
PW_BS000115
483
11
10
PW_BS000115
297
5
10
1
PW_BS000024
299
1
10
1
PW_BS000024
495
7
10
1
PW_BS000115
489
24
10
1
PW_BS000115
480
12
10
1
PW_BS000115
300
13
10
1
PW_BS000024
501
3
6
1
PW_BS000115
208
11
6
PW_BS000024
506
24
6
1
PW_BS000115
391
12
6
1
PW_BS000112
395
13
6
1
PW_BS000113
95
1
7
2
1
PW_BS000095
1
1
PW_BS000001
13
1
2
1
PW_BS000013
20
4
1
1
1
PW_BS000020
5
4
1
1
PW_BS000005
43
25
1
1
PW_BS000043
190
11
18
PW_BS000024
198
5
18
1
PW_BS000024
277
1
2
18
PW_BS000024
290
5
49
1
PW_BS000024
333
1
2
12
PW_BS000028
129
1
5
12
1
PW_BS000129
341
4
1
12
1
PW_BS000028
356
25
12
1
PW_BS000028
334
4
12
1
PW_BS000028
412
1
2
5
PW_BS000115
414
1
5
5
1
PW_BS000115
419
25
5
1
PW_BS000115
408
4
5
1
PW_BS000115
446
1
2
17
PW_BS000115
450
1
5
17
1
PW_BS000115
455
25
17
1
PW_BS000115
374
4
17
1
PW_BS000053
490
25
10
1
PW_BS000115
482
4
10
1
PW_BS000115
507
25
6
1
PW_BS000115
502
4
6
1
PW_BS000115
9
6
1
1
PW_BS000009
14
10
1
PW_BS000014
28
1
16
1
1
PW_BS000028
33
18
1
1
PW_BS000033
24
4
10
1
1
PW_BS000024
60
25
1
PW_BS000060
46
1
1
4
PW_BS000046
29
1
1
1
PW_BS000029
72
5
1
3
PW_BS000072
61
25
1
7
PW_BS000061
36
1
20
1
1
PW_BS000036
37
7
21
1
3
PW_BS000037
93
25
20
1
1
PW_BS000093
27
15
1
PW_BS000027
7
1
1
PW_BS000007
97
1
5
2
1
PW_BS000097
113
6
12
1
PW_BS000113
110
2
3
1
PW_BS000110
123
1
7
5
1
PW_BS000123
126
6
5
1
PW_BS000126
127
1
16
5
1
PW_BS000127
6
1
3
1
PW_BS000006
140
10
3
PW_BS000140
143
1
5
19
1
PW_BS000143
146
5
19
1
PW_BS000146
180
2
21
1
PW_BS000180
207
6
6
1
PW_BS000024
211
10
18
PW_BS000024
214
25
18
1
PW_BS000024
215
6
18
1
PW_BS000024
216
4
18
1
PW_BS000024
65
11
1
PW_BS000065
291
6
49
1
PW_BS000024
292
4
49
1
PW_BS000024
298
1
7
10
1
PW_BS000024
301
6
10
1
PW_BS000024
302
1
16
10
1
PW_BS000024
253
5
4
1
PW_BS000024
332
1
7
12
1
PW_BS000028
115
10
12
PW_BS000115
337
1
16
12
1
PW_BS000028
343
18
12
1
PW_BS000028
329
14
12
1
PW_BS000028
352
25
12
PW_BS000028
353
25
12
7
PW_BS000028
360
4
10
12
1
PW_BS000028
370
2
60
1
PW_BS000028
228
36
1
PW_BS000024
232
40
3
PW_BS000024
405
10
5
PW_BS000115
415
18
5
1
PW_BS000115
429
1
5
1
PW_BS000115
434
4
10
5
1
PW_BS000115
382
14
5
1
PW_BS000100
436
25
5
PW_BS000115
443
6
17
1
PW_BS000115
376
10
17
PW_BS000053
447
1
7
17
1
PW_BS000115
448
1
16
17
1
PW_BS000115
451
18
17
1
PW_BS000115
464
1
17
1
PW_BS000115
469
4
10
17
1
PW_BS000115
399
14
17
1
PW_BS000113
471
25
17
PW_BS000115
472
25
17
7
PW_BS000115
478
10
10
PW_BS000115
487
18
10
1
PW_BS000115
484
14
10
1
PW_BS000115
209
10
6
PW_BS000024
504
18
6
1
PW_BS000115
515
4
10
6
1
PW_BS000115
389
14
6
1
PW_BS000112
513
1
7
6
1
PW_BS000115
289
2
49
1
PW_BS000024
35
5
19
1
4
PW_BS000035
16
2
1
2
PW_BS000016
1922
Carbamic acid
HMDB0003551
Carbamic acid is occasionally found as carbamate in workers exposed to pesticides. Carbamates, particularly carbofuran, seem to be more associated with exuberant and diversified symptomatology of pesticide exposure than organophosphates. Neurological symptoms occur among farmers occupationally exposed to acetylcholinesterase-inhibiting insecticides such as carbamates. Carbamic acid products of several amines, such as beta-N-methylamino-L-alanine (BMAA), ethylenediamine, and L-cysteine have been implicated in toxicity. Studies suggested that a significant portion of amino-compounds in biological samples (that naturally contain CO2/bicarbonate) can be present as a carbamic acid. The formation of carbamate glucuronide metabolites has been described for numerous pharmaceuticals and they have been identified in all of the species commonly used in drug metabolism studies (rat, dog, mouse, rabbit, guinea pig, and human). There has been no obvious species specificity for their formation and no preference for 1 or 2 degree amines. Many biological reactions have also been described in the literature that involve the reaction of CO2 with amino groups of biomolecules. For example, CO2 generated from cellular respiration is expired in part through the reversible formation of a carbamate between CO2 and the -amino groups of the alpha and beta-chains of hemoglobin. Glucuronidation is an important mechanism used by mammalian systems to clear and eliminate both endogenous and foreign chemicals. Many functional groups are susceptible to conjugation with glucuronic acid, including hydroxyls, phenols, carboxyls, activated carbons, thiols, amines, and selenium. Primary and secondary amines can also react with carbon dioxide (CO2) via a reversible reaction to form a carbamic acid. The carbamic acid is also a substrate for glucuronidation and results in a stable carbamate glucuronide metabolite. The detection and characterization of these products has been facilitated greatly by the advent of soft ionization mass spectrometry techniques and high field NMR instrumentation. (PMID: 16268118, 17168688, 12929145).
463-77-4
C01563
277
28616
271
DB04261
NC(O)=O
CH3NO2
InChI=1S/CH3NO2/c2-1(3)4/h2H2,(H,3,4)
KXDHJXZQYSOELW-UHFFFAOYSA-N
carbamic acid
61.04
61.016378345
0.79
2
carbamic acid
0
-1
FDB023195
Aminoformate;Aminoformic acid;Carbamate;Carbamate ion;Chlorphenesin carbamate;Maolate;Aminoameisensaeure;Carbamidsaeure
PW_C001922
Maolate
40034
Hydrogen Ion
HMDB0059597
Hydrogen ion is recommended by IUPAC as a general term for all ions of hydrogen and its isotopes. Depending on the charge of the ion, two different classes can be distinguished: positively charged ions and negatively charged ions. Under aqueous conditions found in biochemistry, hydrogen ions exist as the hydrated form hydronium, H3O+, but these are often still referred to as hydrogen ions or even protons by biochemists. [WikiPedia])
C00080
1038
15378
1010
[H+]
H
InChI=1S/p+1
GPRLSGONYQIRFK-UHFFFAOYSA-N
hydron
1.0079
1.007825032
0
hydron
1
0
H+;H(+);Hydrogen cation;Hydron;Proton
PW_C040034
H+
215
4
670
8
753
15
788
31
848
3
1116
2
1463
26
1464
54
2231
49
2780
17
4250
22
4254
42
4547
10
4576
18
4694
70
5241
103
5327
111
5353
112
5626
108
5639
107
5699
100
5720
105
5742
117
5963
147
6037
155
6070
157
6093
161
6130
159
6232
166
6483
178
6601
152
6692
101
6843
188
6910
187
7100
163
7168
205
7191
206
7453
219
7454
220
7472
222
7525
213
7532
210
7558
212
7572
160
7590
170
8195
225
8218
151
8243
226
8413
162
8420
224
9139
195
9155
249
11915
164
12015
281
12181
285
12246
286
12266
287
12521
227
13257
223
13325
294
15330
308
42329
315
42354
318
42401
322
42405
312
42454
320
76912
293
77136
133
77210
134
77372
331
77804
114
77955
132
77990
327
77991
347
78379
345
79929
130
80019
368
80387
310
80388
304
80722
119
93823
124
94823
383
110550
388
112855
94
113280
390
115537
398
115539
118
115856
336
116205
109
119973
406
120193
407
120549
122
120593
409
121170
424
121171
425
122569
418
122615
384
122687
125
122758
120
123183
135
123218
137
123742
459
123743
460
125141
454
125188
121
125273
136
125359
479
125550
481
125730
483
125736
297
125809
299
126517
495
126717
489
126766
480
126823
300
126902
501
127213
208
128308
506
128361
391
128430
395
22608
Ammonium
HMDB0041827
Ammonium is an important source of nitrogen for many plant species, especially those growing on hypoxic soils. However, it is also toxic to most crop species and is rarely applied as a sole nitrogen source. The ammonium (more obscurely: aminium) cation is a positively charged polyatomic cation with the chemical formula NH4+. It is formed by the protonation of ammonia (NH3). Ammonium is also a general name for positively charged or protonated substituted amines and quaternary ammonium cations (NR4+), where one or more hydrogen atoms are replaced by organic radical groups (indicated by R).
14798-03-9
C01342
16741146
28938
218
[NH4+]
H4N
InChI=1S/H3N/h1H3/p+1
QGZKDVFQNNGYKY-UHFFFAOYSA-O
azanium
18.0385
18.034374133
1
azanium
1
1
Ammonium ion;Ammonia ion;Ammonium;Ammonium chloride;Ammonium(1+);Azanium;Nh4+;[nh4]+;[nh4](+);Nh4(+)
PW_C022608
Ammon
5751
108
5892
95
5969
100
6226
166
8273
151
8367
225
11909
170
12470
249
42627
315
116281
109
1316
Carbon dioxide
HMDB0001967
Carbon dioxide is a colorless, odorless gas that can be formed by the body and is necessary for the respiration cycle of plants and animals. Carbon dioxide is produced during respiration by all animals, fungi and microorganisms that depend on living and decaying plants for food, either directly or indirectly. It is, therefore, a major component of the carbon cycle. Additionally, carbon dioxide is used by plants during photosynthesis to make sugars which may either be consumed again in respiration or used as the raw material to produce polysaccharides such as starch and cellulose, proteins and the wide variety of other organic compounds required for plant growth and development. When inhaled at concentrations much higher than usual atmospheric levels, it can produce a sour taste in the mouth and a stinging sensation in the nose and throat. These effects result from the gas dissolving in the mucous membranes and saliva, forming a weak solution of carbonic acid. Carbon dioxide is used by the food industry, the oil industry, and the chemical industry. Carbon dioxide is used to produce carbonated soft drinks and soda water. Traditionally, the carbonation in beer and sparkling wine comes about through natural fermentation, but some manufacturers carbonate these drinks artificially.
124-38-9
C00011
280
16526
274
O=C=O
CO2
InChI=1S/CO2/c2-1-3
CURLTUGMZLYLDI-UHFFFAOYSA-N
methanedione
44.0095
43.989829244
0.63
0
carbon dioxide
0
0
DBMET00423
FDB014084
Carbon oxide;Carbon-12 dioxide;Carbonic acid anhydride;Carbonic acid gas;Carbonic anhydride;[co2];Co2;E 290;E-290;E290;R-744
PW_C001316
CO2
50
8
121
1
204
4
480
13
503
18
640
3
677
31
695
20
806
5
1133
43
1638
49
1745
2
2551
17
3144
70
5283
103
5320
111
5750
108
5771
101
5968
100
6026
155
6078
161
6471
178
6637
107
6922
190
7017
160
7035
163
7061
188
7163
205
7308
198
7333
213
7461
222
7530
210
8215
225
8223
151
9158
249
11849
277
11908
170
12464
226
12688
290
42626
315
43523
318
76994
293
77122
133
77170
132
77470
333
77739
112
77750
129
77763
341
78077
134
78405
356
78427
334
78941
331
79227
130
80008
368
80675
119
80717
135
94836
384
113291
391
115549
121
119954
406
120089
122
120155
407
120364
412
120556
414
120833
419
120922
124
120991
408
121284
125
121505
383
122744
120
123011
446
123190
450
123418
455
123489
118
123556
374
123855
136
124063
398
125344
479
125460
297
125516
481
125824
490
125870
299
125931
482
126280
480
126887
501
127052
206
127277
507
127331
388
127390
502
1938
2-Aminoacrylic acid
HMDB0003609
2-Aminoacrylic acid, also known as 2,3-didehydroalanine or 2-aminoacrylate, belongs to the class of organic compounds known as alpha amino acids. These are amino acids in which the amino group is attached to the carbon atom immediately adjacent to the carboxylate group (alpha carbon). 2-Aminoacrylic acid is soluble (in water) and a moderately acidic compound (based on its pKa). In humans, 2-aminoacrylic acid is involved in thyroid hormone synthesis pathway. Outside of the human body, 2-aminoacrylic acid can be found in a number of food items such as evergreen huckleberry, welsh onion, japanese pumpkin, and lemon grass. This makes 2-aminoacrylic acid a potential biomarker for the consumption of these food products. Dehydroalanine (or (alpha)-(beta)-di-dehydroalanine) is an uncommon amino acid found in peptides of microbial origin (an unsaturated amino acid).
1948-56-7
C02218
123991
17123
110510
DB02688
NC(=C)C(O)=O
C3H5NO2
InChI=1S/C3H5NO2/c1-2(4)3(5)6/h1,4H2,(H,5,6)
UQBOJOOOTLPNST-UHFFFAOYSA-N
2-aminoprop-2-enoic acid
87.0773
87.032028409
0.43
2
dehydroalanine
0
0
FDB023206
(alpha)-(beta)-di-dehydroalanine;2-aminoacrylate;2-aminoacrylic acid;Dehydroalanine;A-b-di-dehydroalanine;Alpha-beta-di-dehydroalanine;2-aminoprop-2-enoate;2-aminoprop-2-enoic acid
PW_C001938
2Amnaa
4537
2
79043
132
1420
Water
HMDB0002111
Water is a chemical substance that is essential to all known forms of life. It appears colorless to the naked eye in small quantities, though it is actually slightly blue in color. It covers 71% of Earth's surface. Current estimates suggest that there are 1.4 billion cubic kilometers (330 million m3) of it available on Earth, and it exists in many forms. It appears mostly in the oceans (saltwater) and polar ice caps, but it is also present as clouds, rain water, rivers, freshwater aquifers, lakes, and sea ice. Water in these bodies perpetually moves through a cycle of evaporation, precipitation, and runoff to the sea. Clean water is essential to human life. In many parts of the world, it is in short supply. From a biological standpoint, water has many distinct properties that are critical for the proliferation of life that set it apart from other substances. It carries out this role by allowing organic compounds to react in ways that ultimately allow replication. All known forms of life depend on water. Water is vital both as a solvent in which many of the body's solutes dissolve and as an essential part of many metabolic processes within the body. Metabolism is the sum total of anabolism and catabolism. In anabolism, water is removed from molecules (through energy requiring enzymatic chemical reactions) in order to grow larger molecules (e.g. starches, triglycerides and proteins for storage of fuels and information). In catabolism, water is used to break bonds in order to generate smaller molecules (e.g. glucose, fatty acids and amino acids to be used for fuels for energy use or other purposes). Water is thus essential and central to these metabolic processes. Water is also central to photosynthesis and respiration. Photosynthetic cells use the sun's energy to split off water's hydrogen from oxygen. Hydrogen is combined with CO2 (absorbed from air or water) to form glucose and release oxygen. All living cells use such fuels and oxidize the hydrogen and carbon to capture the sun's energy and reform water and CO2 in the process (cellular respiration). Water is also central to acid-base neutrality and enzyme function. An acid, a hydrogen ion (H+, that is, a proton) donor, can be neutralized by a base, a proton acceptor such as hydroxide ion (OH-) to form water. Water is considered to be neutral, with a pH (the negative log of the hydrogen ion concentration) of 7. Acids have pH values less than 7 while bases have values greater than 7. Stomach acid (HCl) is useful to digestion. However, its corrosive effect on the esophagus during reflux can temporarily be neutralized by ingestion of a base such as aluminum hydroxide to produce the neutral molecules water and the salt aluminum chloride. Human biochemistry that involves enzymes usually performs optimally around a biologically neutral pH of 7.4. (Wikipedia).
7732-18-5
C00001
962
15377
937
O
H2O
InChI=1S/H2O/h1H2
XLYOFNOQVPJJNP-UHFFFAOYSA-N
water
18.0153
18.010564686
1
water
0
0
FDB013390
Dihydrogen oxide;Steam;[oh2];Acqua;Agua;Aqua;Bound water;Dihydridooxygen;Eau;H2o;Hoh;Hydrogen hydroxide;Wasser
PW_C001420
H2O
55
8
94
9
109
5
139
4
151
3
162
14
481
13
526
15
624
28
652
10
691
20
770
33
823
18
838
2
1094
31
1377
49
1465
54
1590
43
2018
24
2532
22
2678
60
2727
46
2778
17
2805
29
3143
70
3164
72
3634
61
4598
36
4727
37
4941
93
5030
27
5156
7
5195
97
5214
100
5227
94
5236
103
5297
105
5319
111
5343
113
5355
112
5402
110
5470
123
5483
125
5492
126
5507
127
5534
130
5537
114
5541
129
5591
135
5608
118
5622
108
5691
6
5759
140
5778
101
5841
143
5853
146
5877
107
5890
95
5910
147
5940
151
6032
155
6059
157
6087
161
6123
163
6133
159
6215
1
6218
166
6477
178
6507
180
6600
152
6713
117
6840
188
6888
160
7162
205
7181
207
7193
206
7211
211
7228
213
7238
214
7243
215
7295
198
7350
216
7388
210
7401
212
7467
222
7492
224
7500
190
7588
170
8201
225
8237
226
8414
162
9265
26
11850
277
11922
164
12011
281
12213
285
12250
286
12264
287
12327
249
12520
227
12632
65
12693
290
12705
291
12715
292
13007
298
13019
300
13025
301
13037
302
13261
223
13327
294
15340
308
42327
315
42695
318
43691
322
76914
293
77019
253
77102
132
77131
133
77215
134
77378
331
77397
332
77471
333
77516
115
77536
334
77628
336
77722
337
77759
341
77816
343
77982
347
78071
329
78235
352
78242
353
78270
356
79113
360
80014
368
80039
370
80591
228
80656
119
93830
383
94794
384
110557
390
110639
391
115844
398
119879
232
119915
122
119963
406
120008
407
120046
408
120113
124
120365
412
120430
405
120438
409
120606
415
120794
414
121158
425
121240
429
121351
121
121381
419
121607
434
122118
382
122384
436
122753
120
122797
374
122804
443
123012
446
123064
376
123072
137
123131
447
123142
136
123162
448
123231
451
123384
450
123730
460
123810
464
123940
455
124165
469
124670
399
124938
471
124945
472
125305
297
125353
479
125386
481
125424
482
125480
299
125682
483
125707
478
125745
487
126054
490
126238
495
126273
484
126764
480
126896
501
126963
502
127017
388
127177
208
127199
209
127227
504
127506
507
127576
515
127836
389
128082
395
128176
513
6753
Malonic semialdehyde
HMDB0011111
Malonic semialdehyde is formed in the alternative pathway of propionate metabolism and in the catabolism of beta-alanine. Studies done on these pathways in cultured cells from a patient with mitochondrial malonyl-CoA decarboxylase deficiency show that malonic semialdehyde is directly converted into acetyl-CoA in man. (PMID: 6418146).
926-61-4
C00222
868
17960
845
OC(=O)CC=O
C3H4O3
InChI=1S/C3H4O3/c4-2-1-3(5)6/h2H,1H2,(H,5,6)
OAKURXIZZOAYBC-UHFFFAOYSA-N
3-oxopropanoic acid
88.0621
88.016043994
0.46
1
3-oxopropanoic acid
0
-1
C00222
3-oxopropanoate;3-oxopropanoic acid;3-oxopropionic acid;Formyl acetate;Formyl acetic acid;Formylacetic acid;Malonaldehydic acid;Malonate semialdehyde;Formylacetate
PW_C006753
MalSah
43
3
541
4
12682
289
77524
112
77591
133
120085
407
120456
406
122832
119
123090
120
125456
481
125700
479
126994
206
127192
501
146
NADPH
HMDB0000221
Nicotinamide adenine dinucleotide phosphate. A coenzyme composed of ribosylnicotinamide 5'-phosphate (NMN) coupled by pyrophosphate linkage to the 5'-phosphate adenosine 2',5'-bisphosphate. It serves as an electron carrier in a number of reactions, being alternately oxidized (NADP+) and reduced (NADPH). (Dorland, 27th ed.).
53-57-6
C00005
22833512
16474
NADPH
17215925
NC(=O)C1=CN(C=CC1)[C@H]1O[C@@H](COP(O)(=O)OP(O)(=O)OC[C@@H]2O[C@@H]([C@@H](OP(O)(O)=O)[C@H]2O)N2C=NC3=C(N)N=CN=C23)[C@H](O)[C@@H]1O
C21H30N7O17P3
InChI=1S/C21H30N7O17P3/c22-17-12-19(25-7-24-17)28(8-26-12)21-16(44-46(33,34)35)14(30)11(43-21)6-41-48(38,39)45-47(36,37)40-5-10-13(29)15(31)20(42-10)27-3-1-2-9(4-27)18(23)32/h1,3-4,7-8,10-11,13-16,20-21,29-31H,2,5-6H2,(H2,23,32)(H,36,37)(H,38,39)(H2,22,24,25)(H2,33,34,35)/t10-,11-,13-,14-,15-,16-,20-,21-/m0/s1
ACFIXJIJDZMPPO-NCHANQSKSA-N
{[(2S,3S,4S,5S)-2-(6-amino-9H-purin-9-yl)-5-[({[({[(2S,3R,4S,5S)-5-(3-carbamoyl-1,4-dihydropyridin-1-yl)-3,4-dihydroxyoxolan-2-yl]methoxy}(hydroxy)phosphoryl)oxy](hydroxy)phosphoryl}oxy)methyl]-4-hydroxyoxolan-3-yl]oxy}phosphonic acid
745.4209
745.091102105
-2.14
9
[(2S,3S,4S,5S)-2-(6-aminopurin-9-yl)-5-{[({[(2S,3R,4S,5S)-5-(3-carbamoyl-4H-pyridin-1-yl)-3,4-dihydroxyoxolan-2-yl]methoxy(hydroxy)phosphoryl}oxy(hydroxy)phosphoryl)oxy]methyl}-4-hydroxyoxolan-3-yl]oxyphosphonic acid
0
-4
FDB021909
2'-(dihydrogen phosphate) 5'-(trihydrogen pyrophosphate) adenosine 5'-ester with 1,4-dihydro-1-b-d-ribofuranosylnicotinamide;2'-(dihydrogen phosphate) 5'-(trihydrogen pyrophosphate) adenosine 5'-ester with 1,4-dihydro-1-beta-delta-ribofuranosylnicotinamide;Adenosine 5'-(trihydrogen diphosphate) 2'-(dihydrogen phosphate) p'-5'-ester with 1,4-dihydro-1-beta-d-ribofuranosyl-3-pyridinecarboxamide;Adenosine 5'-(trihydrogen diphosphate) 2'-(dihydrogen phosphate) p'-5'-ester with 1,4-dihydro-1-beta-delta-ribofuranosyl-3-pyridinecarboxamide;Dihydrocodehydrogenase ii;Dihydronicotinamide adenine dinucleotide phosphate;Dihydronicotinamide adenine dinucleotide-p;Dihydrotriphosphopyridine nucleotide reduced;Nadp-reduced;Nadph;Nicotinamide-adenine-dinucleotide-phosphorate;Nicotinamide-adenine-dinucleotide-phosphoric acid;Reduced codehydrase ii;Reduced coenzyme ii;Reduced cozymase ii;Reduced triphosphopyridine nucleotide;Triphosphopyridine nucleotide reduced;B-nadph;B-nicotinamide-adenine-dinucleotide-phosphorate;B-nicotinamide-adenine-dinucleotide-phosphoric acid;Beta-nadph;Beta-nicotinamide-adenine-dinucleotide-phosphorate;Beta-nicotinamide-adenine-dinucleotide-phosphoric acid;Nicotinamide adenine dinucleotide phosphate - reduced
PW_C000146
NADPH
185
8
190
3
778
10
796
5
821
18
837
2
1609
29
1615
49
4687
31
4793
14
4797
14
5310
111
5789
108
5972
147
6128
159
6271
35
6779
117
7068
188
7103
163
7154
205
7205
160
7315
213
7345
210
7559
212
7591
170
8194
225
8219
151
8421
224
11812
198
11893
211
12006
222
12150
164
12245
286
12596
226
12648
249
42343
315
43746
322
76911
293
77166
132
77385
331
77394
332
77460
130
77504
112
77511
115
77623
336
80712
119
113164
94
120105
407
120425
405
120452
122
120616
123
121141
125
121275
429
121402
124
121483
383
123059
376
123086
135
123241
447
123712
136
123846
464
123961
118
124041
398
125472
481
125696
297
126214
299
126529
495
127009
206
127572
388
128101
390
552
Hydroxypropionic acid
HMDB0000700
3-Hydroxypropionic acid is a carboxylic acid. It is an intermediate in the breakdown of branched-chain amino acids and propionic acid from the gut. Typically it originates from propionyl-CoA and a defect in the enzyme propionyl carboxylase. This leads to a buildup in propionyl-CoA in the mitochondria. Such a buildup can lead to a disruption of the esterified CoA:free CoA ratio and ultimately to mitochondrial toxicity. Detoxification of these metabolic end products occurs via the transfer of the propionyl moiety to carnitine-forming propionyl-carnitine, which is then transferred across the inner mitochondrial membrane. 3-Hydroxypropionic acid is then released as the free acid. As an industrial chemical, it is used in the production of various chemicals such as acrylates in industry. When present in sufficiently high levels, 3-hydroxypropionic acid can act as an acidogen and a metabotoxin. An acidogen is an acidic compound that induces acidosis, which has multiple adverse effects on many organ systems. A metabotoxin is an endogenously produced metabolite that causes adverse health effects at chronically high levels. Chronically high levels of hydroxypropionic acid are associated with many inborn errors of metabolism including biotinidase deficiency, malonic aciduria, methylmalonate semialdehyde dehydrogenase deficiency, methylmalonic aciduria, methylmalonic aciduria due to cobalamin-related disorders, and propionic acidemia. Hydroxypropionic acid is an organic acid. Abnormally high levels of organic acids in the blood (organic acidemia), urine (organic aciduria), the brain, and other tissues lead to general metabolic acidosis. Acidosis typically occurs when arterial pH falls below 7.35. Infants with acidosis have symptoms that include poor feeding, vomiting, loss of appetite, weak muscle tone (hypotonia), and lack of energy (lethargy). These can progress to heart, liver, and kidney abnormalities, seizures, coma, and possibly death. These are also the characteristic symptoms of the IEMs mentioned above. Many affected children with organic acidemias experience intellectual disability or delayed development. In adults, acidosis or acidemia is characterized by headaches, confusion, feeling tired, tremors, sleepiness, and seizures.
503-66-2
C01013
68152
33404
61460
DB03688
OCCC(O)=O
C3H6O3
InChI=1S/C3H6O3/c4-2-1-3(5)6/h4H,1-2H2,(H,5,6)
ALRHLSYJTWAHJZ-UHFFFAOYSA-N
3-hydroxypropanoic acid
90.0779
90.031694058
0.86
2
hydroxypropionic acid
0
-1
FDB022189
2-deoxyglycerate;2-deoxyglyceric acid;3-hydroxypropanoate;3-hydroxypropanoic acid;3-hydroxypropionate;3-hydroxypropionic acid;Ethylenelactate;Ethylenelactic acid;Hydracrylic acid;Hydroxypropionate;B-hydroxypropionate;B-hydroxypropionic acid;B-lactate;B-lactic acid;Beta-hydroxypropionate;Beta-hydroxypropionic acid;Beta-lactate;Beta-lactic acid;3-hydroxy-propanoic acid;3-hydroxy-propanoate;β-hydroxypropionate;β-hydroxypropionic acid;Hydracrylate
PW_C000552
3OH
2282
4
78635
133
122264
406
124817
120
126428
479
127996
501
143
NADP
HMDB0000217
Nicotinamide adenine dinucleotide phosphate. A coenzyme composed of ribosylnicotinamide 5-phosphate (NMN) coupled by pyrophosphate linkage to the 5-phosphate adenosine 2,5-bisphosphate. It serves as an electron carrier in a number of reactions, being alternately oxidized (NADP+) and reduced (NADPH). (Dorland, 27th ed.) Hydrogen carrier in biochemical redox systems. In the hexose monophosphoric acid system it is reduced to Dihydrocoenzyme II and reoxidation in the presence of flavoproteins (Dictionary of Organic Compounds).
53-59-8
C00006
5886
18009
NAD(P)
5675
NC(=O)C1=C[N+](=CC=C1)[C@@H]1O[C@H](CO[P@](O)(=O)O[P@](O)(=O)OC[C@H]2O[C@H]([C@H](OP(O)(O)=O)[C@@H]2O)N2C=NC3=C(N)N=CN=C23)[C@@H](O)[C@H]1O
C21H29N7O17P3
InChI=1S/C21H28N7O17P3/c22-17-12-19(25-7-24-17)28(8-26-12)21-16(44-46(33,34)35)14(30)11(43-21)6-41-48(38,39)45-47(36,37)40-5-10-13(29)15(31)20(42-10)27-3-1-2-9(4-27)18(23)32/h1-4,7-8,10-11,13-16,20-21,29-31H,5-6H2,(H7-,22,23,24,25,32,33,34,35,36,37,38,39)/p+1/t10-,11-,13-,14-,15-,16-,20-,21-/m1/s1
XJLXINKUBYWONI-NNYOXOHSSA-O
1-[(2R,3R,4S,5R)-5-[({[({[(2R,3R,4R,5R)-5-(6-amino-9H-purin-9-yl)-3-hydroxy-4-(phosphonooxy)oxolan-2-yl]methoxy}(hydroxy)phosphoryl)oxy](hydroxy)phosphoryl}oxy)methyl]-3,4-dihydroxyoxolan-2-yl]-3-carbamoyl-1lambda5-pyridin-1-ylium
744.4129
744.083277073
-2.27
9
1-[(2R,3R,4S,5R)-5-{[({[(2R,3R,4R,5R)-5-(6-aminopurin-9-yl)-3-hydroxy-4-(phosphonooxy)oxolan-2-yl]methoxy(hydroxy)phosphoryl}oxy(hydroxy)phosphoryl)oxy]methyl}-3,4-dihydroxyoxolan-2-yl]-3-carbamoyl-1lambda5-pyridin-1-ylium
1
-3
FDB021908
Adenine-nicotinamide dinucleotide phosphate;Codehydrase ii;Codehydrogenase ii;Coenzyme ii;Cozymase ii;Nad phosphate;Nadp;Nadp+;Nicotinamide adenine dinucleotide phosphate;Nicotinamide-adenine dinucleotide phosphate;Tpn;Triphosphopyridine nucleotide;B-nadp;B-nicotinamide adenine dinucleotide phosphate;B-tpn;Beta-nadp;Beta-nicotinamide adenine dinucleotide phosphate;Beta-tpn;Oxidized nicotinamide-adenine dinucleotide phosphate;B-nicotinamide adenine dinucleotide phosphoric acid;Beta-nicotinamide adenine dinucleotide phosphoric acid;β-nicotinamide adenine dinucleotide phosphate;β-nicotinamide adenine dinucleotide phosphoric acid
PW_C000143
NADP
183
8
191
3
768
5
780
10
824
18
839
2
1611
29
1617
49
4685
31
4796
14
4801
14
5308
111
5790
108
6017
147
6132
159
6273
35
6778
117
7069
188
7105
163
7152
205
7206
160
7317
213
7346
210
7562
212
7589
170
8197
225
8220
151
8419
224
11811
198
11897
211
12008
222
12152
164
12249
286
12597
226
12650
249
42344
315
43745
322
76913
293
77164
132
77384
331
77396
332
77461
130
77515
115
77624
336
77814
334
77870
112
80713
119
113165
94
120106
407
120429
405
120450
122
120604
408
120618
123
121142
125
121277
429
121401
124
121485
383
123063
376
123084
135
123229
374
123243
447
123713
136
123848
464
123960
118
124043
398
125473
481
125694
297
125743
482
126215
299
126528
495
127010
206
127225
502
127570
388
128100
390
44507
3-Aminoacrylate
3-aminoacrylate is a member of the chemical class known as Enones. These are compounds containing the enone functional group, with the structure RC(=O)CR'. Aminoacrylate is involved in amino acid metabolism. A new amino acid is formed when the nucleophiles add to the aminoacrylate. (PMID 8663055)
C20253
46173135
59894
N\C=C/C(O)=O
C3H5NO2
InChI=1S/C3H5NO2/c4-2-1-3(5)6/h1-2H,4H2,(H,5,6)/b2-1-
YTLYLLTVENPWFT-UPHRSURJSA-N
(2Z)-3-aminoprop-2-enoic acid
87.0773
87.032028409
0.53
2
aminoacrylic acid
0
-1
(2z)-3-aminoprop-2-enoate;(z)-3-aminoacrylate;3-aminoacrylate;Aminoacrylate;(2z)-3-aminoprop-2-enoic acid;(z)-3-aminoacrylic acid;Aminoacrylic acid;3-aminoacrylic acid
PW_C044507
3AmnAc
40969
an unknown reduced electron acceptor
In general, an electron acceptor is a chemical entity that can accept electrons from another chemical entity. By accepting the electrons, the acceptor is reduced, and thus prior to receiving the electrons the entity is called "an oxidized electron acceptor" and after receiving them it is called "a reduced electron acceptor".
Many reduced electron acceptors are able to transfer the electrons to other molecules, becoming oxidized in the process. Thus the distinction between an electron acceptor and an electron donor is often not determined by the actual chemical entity, but by the role it plays in a particular reaction. However, some acceptors in biological reactions only accept electrons and do not transfer them further. Those are often known as "terminal electron acceptors".
While in general every chemical reaction in which electrons are transferred includes an electron donor and an electron acceptor, several molecules are commonly used in metabolism solely for the purpose of electron transfer, and are referred to in biology as electron acceptors. Examples of biological electron acceptors include organic molecules (e.g. NAD+, FAD, quinones) and proteins (e.g. ferredoxins, flavodoxins, cytochromes, blue copper proteins). In addition, a number of inorganic small molecules (e.g. oxygen, nitrate, iron (III), manganese (IV), sulfate) are often used as terminal electron acceptors. Different electron acceptors differ in the number of electrons that they transfer and in their electron affinity.
This particular entry is used when the identity of the electron acceptor is not known or cannot be defined.
17499
PW_C040969
AUREA
5728
108
40968
an unknown oxidized electron acceptor
In general, an electron acceptor is a chemical entity that can accept electrons from another chemical entity. By accepting the electrons, the acceptor is reduced, and thus prior to receiving the electrons the entity is called "an oxidized electron acceptor" and after receiving them it is called "a reduced electron acceptor".
Many reduced electron acceptors are able to transfer the electrons to other molecules, becoming oxidized in the process. Thus the distinction between an electron acceptor and an electron donor is often not determined by the actual chemical entity, but by the role it plays in a particular reaction. However, some acceptors in biological reactions only accept electrons and do not transfer them further. Those are often known as "terminal electron acceptors".
While in general every chemical reaction in which electrons are transferred includes an electron donor and an electron acceptor, several molecules are commonly used in metabolism solely for the purpose of electron transfer, and are referred to in biology as electron acceptors. Examples of biological electron acceptors include organic molecules (e.g. NAD+, FAD, quinones) and proteins (e.g. ferredoxins, flavodoxins, cytochromes, blue copper proteins). In addition, a number of inorganic small molecules (e.g. oxygen, nitrate, iron (III), manganese (IV), sulfate) are often used as terminal electron acceptors. Different electron acceptors differ in the number of electrons that they transfer and in their electron affinity.
This particular entry is used when the identity of the electron acceptor is not known or cannot be defined.
15339
PW_C040968
AUOEA
5727
108
204
Uracil
HMDB0000300
Uracil is a common naturally occurring pyrimidine found in RNA, it base pairs with adenine and is replaced by thymine in DNA. Methylation of uracil produces thymine. Uracil's use in the body is to help carry out the synthesis of many enzymes necessary for cell function through bonding with riboses and phosphates. Uracil serves as allosteric regulator and coenzyme for many important biochemical reactions. UDP and UTP regulate CPSase II activity in animals. UDP-glucose regulates the conversion of glucose to galactose in the liver and other tissues in the process of carbohydrate metabolism. Uracil is also involved in the biosynthesis of polysaccharides and the transportation of sugars containing aldehydes.
66-22-8
C00106
1174
17568
URACIL
1141
DB03419
O=C1NC=CC(=O)N1
C4H4N2O2
InChI=1S/C4H4N2O2/c7-3-1-2-5-4(8)6-3/h1-2H,(H2,5,6,7,8)
ISAKRJDGNUQOIC-UHFFFAOYSA-N
1,2,3,4-tetrahydropyrimidine-2,4-dione
112.0868
112.027277382
-0.63
2
uracil
0
0
FDB006426
2,4-dihydroxypyrimidine;2,4-dioxopyrimidine;2,4-pyrimidinediol;2,4-pyrimidinedione;Hybar x;Pirod;Pyrod;Uracil;Sq-8493sid51088798;Sq-6201sq-7726sid70371;Bms-205603-01uracil
PW_C000204
Uracil
538
8
2741
2
77589
111
78739
132
120451
122
122220
124
123085
135
124772
118
125695
297
126383
299
127189
205
127943
388
891
FMNH2
HMDB0001142
FMNH2 is the reduced form of flavin mononucleotide. It is a substrate of the enzyme FMN reductase (EC 1.5.1.29), an enzyme that catalyzes the chemical reaction FMNH2 + NAD(P)+ <=> FMN + NAD(P)H + H+. Flavin mononucleotide (FMN), or riboflavin-5′-phosphate, is a biomolecule produced from riboflavin (vitamin B2) by the enzyme riboflavin kinase and functions as prosthetic group of various oxidoreductases including NADH dehydrogenase. During a catalytic cycle, the reversible interconversion of oxidized (FMN), semiquinone (FMNH•) and reduced (FMNH2) forms occurs in the various oxidoreductases. FMN is a stronger oxidizing agent than NAD and is particularly useful because it can take part in both one- and two-electron transfers.
5666-16-0
C01847
445395
16048
FMNH2
393046
CC1=CC2=C(C=C1C)N(C[C@H](O)[C@H](O)[C@H](O)COP(O)(O)=O)C1=C(N2)C(=O)NC(=O)N1
C17H23N4O9P
InChI=1S/C17H23N4O9P/c1-7-3-9-10(4-8(7)2)21(15-13(18-9)16(25)20-17(26)19-15)5-11(22)14(24)12(23)6-30-31(27,28)29/h3-4,11-12,14,18,22-24H,5-6H2,1-2H3,(H2,27,28,29)(H2,19,20,25,26)/t11-,12+,14-/m0/s1
YTNIXZGTHTVJBW-SCRDCRAPSA-N
{[(2R,3S,4S)-5-{7,8-dimethyl-2,4-dioxo-1H,2H,3H,4H,5H,10H-benzo[g]pteridin-10-yl}-2,3,4-trihydroxypentyl]oxy}phosphonic acid
458.3597
458.120264866
-2.85
8
fmnh(.)
0
-2
FDB022449
Fmnh2;Reduced fmn;Reduced flavin mononucleotide;1,5-dihydroriboflavin 5'-(dihydrogen phosphate);Flavin mononucleotide (reduced);Fmnh;1,5-dihydroriboflavin 5'-(dihydrogen phosphoric acid)
PW_C000891
FMNH2
11954
225
1065
Oxygen
HMDB0001377
Oxygen is the third most abundant element in the universe after hydrogen and helium and the most abundant element by mass in the Earth's crust. Diatomic oxygen gas constitutes 20.9% of the volume of air. All major classes of structural molecules in living organisms, such as proteins, carbohydrates, and fats, contain oxygen, as do the major inorganic compounds that comprise animal shells, teeth, and bone. Oxygen in the form of O2 is produced from water by cyanobacteria, algae and plants during photosynthesis and is used in cellular respiration for all living organisms. Green algae and cyanobacteria in marine environments provide about 70% of the free oxygen produced on earth and the rest is produced by terrestrial plants. Oxygen is used in mitochondria to help generate adenosine triphosphate (ATP) during oxidative phosphorylation. For animals, a constant supply of oxygen is indispensable for cardiac viability and function. To meet this demand, an adult human, at rest, inhales 1.8 to 2.4 grams of oxygen per minute. This amounts to more than 6 billion tonnes of oxygen inhaled by humanity per year. At a resting pulse rate, the heart consumes approximately 8-15 ml O2/min/100 g tissue. This is significantly more than that consumed by the brain (approximately 3 ml O2/min/100 g tissue) and can increase to more than 70 ml O2/min/100 g myocardial tissue during vigorous exercise. As a general rule, mammalian heart muscle cannot produce enough energy under anaerobic conditions to maintain essential cellular processes; thus, a constant supply of oxygen is indispensable to sustain cardiac function and viability. However, the role of oxygen and oxygen-associated processes in living systems is complex, and they and can be either beneficial or contribute to cardiac dysfunction and death (through reactive oxygen species). Reactive oxygen species (ROS) are a family of oxygen-derived free radicals that are produced in mammalian cells under normal and pathologic conditions. Many ROS, such as the superoxide anion (O2-)and hydrogen peroxide (H2O2), act within blood vessels, altering mechanisms mediating mechanical signal transduction and autoregulation of cerebral blood flow. Reactive oxygen species are believed to be involved in cellular signaling in blood vessels in both normal and pathologic states. The major pathway for the production of ROS is by way of the one-electron reduction of molecular oxygen to form an oxygen radical, the superoxide anion (O2-). Within the vasculature there are several enzymatic sources of O2-, including xanthine oxidase, the mitochondrial electron transport chain, and nitric oxide (NO) synthases. Studies in recent years, however, suggest that the major contributor to O2- levels in vascular cells is the membrane-bound enzyme NADPH-oxidase. Produced O2- can react with other radicals, such as NO, or spontaneously dismutate to produce hydrogen peroxide (H2O2). In cells, the latter reaction is an important pathway for normal O2- breakdown and is usually catalyzed by the enzyme superoxide dismutase (SOD). Once formed, H2O2 can undergo various reactions, both enzymatic and nonenzymatic. The antioxidant enzymes catalase and glutathione peroxidase act to limit ROS accumulation within cells by breaking down H2O2 to H2O. Metabolism of H2O2 can also produce other, more damaging ROS. For example, the endogenous enzyme myeloperoxidase uses H2O2 as a substrate to form the highly reactive compound hypochlorous acid. Alternatively, H2O2 can undergo Fenton or Haber-Weiss chemistry, reacting with Fe2+/Fe3+ ions to form toxic hydroxyl radicals (-.OH). (PMID: 17027622, 15765131).
7782-44-7
C00007
977
15379
CPD-6641
952
O=O
O2
InChI=1S/O2/c1-2
MYMOFIZGZYHOMD-UHFFFAOYSA-N
oxidanone
31.9988
31.989829244
0
singlet oxygen
0
0
FDB022589
Dioxygen;Molecular oxygen;O2;Oxygen;Oxygen molecule;[oo];Dioxygene;Disauerstoff;E 948;E-948;E948
PW_C001065
O2
95
9
110
5
245
16
500
18
505
8
549
14
625
28
638
3
649
10
674
31
688
20
754
15
763
4
769
33
836
2
1375
49
2016
24
2531
22
2803
29
4260
42
4747
13
5467
123
5480
125
5493
126
5508
127
5809
108
5973
147
6129
159
7006
188
7032
163
7050
160
7319
213
7533
210
7560
212
8395
151
11816
216
11864
198
11883
215
11894
211
12057
225
12063
164
12247
286
12279
226
12325
249
12706
291
12716
292
13004
298
13016
300
13026
301
13038
302
13260
223
42276
17
42657
315
76910
293
77044
294
77214
134
77350
111
77363
130
77377
331
77395
332
77497
113
77512
115
77537
334
77626
336
77723
337
77736
112
77747
129
77756
341
77805
114
77812
133
78070
329
78151
132
78381
345
78805
343
79111
360
120047
408
120383
122
120426
405
120542
407
120553
414
120594
409
120601
406
120883
415
121045
124
121104
383
121605
434
121656
429
122117
382
122573
418
122689
384
122798
374
122822
443
123027
135
123060
376
123128
447
123139
136
123163
448
123176
119
123187
450
123219
137
123226
120
123459
451
123609
118
123669
398
124163
469
124214
464
124669
399
125145
454
125275
121
125425
482
125706
478
125731
483
125737
297
125740
479
125884
481
126100
299
126272
484
126522
495
126721
489
126825
480
126964
502
126986
207
127198
209
127214
208
127219
205
127222
501
127305
504
127345
206
127557
388
127574
515
127835
389
128081
395
128095
390
128312
506
128432
391
41602
Peroxyaminoacrylate
Peroxyaminoacrylate, also known as aminoacrylate peracid, belongs to the class of organic compounds known as peroxycarboxylic acids. These are organic acids with the general formula [H]OOC(R)=O (R = H, organyl group). Peroxyaminoacrylate is soluble (in water) and a very weakly acidic compound (based on its pKa). Peroxyaminoacrylate may be a unique E.coli metabolite. Peroxyaminoacrylate participates in a number of enzymatic reactions. In particular, Peroxyaminoacrylate and flavin mononucleotide can be biosynthesized from uracil and FMNH2; which is catalyzed by the enzyme pyrimidine oxygenase. In addition, Peroxyaminoacrylate can be converted into 3-aminoacrylate and carbamic acid; which is catalyzed by the enzyme peroxyureidoacrylate / ureidoacrylate amido hydrolase.
46173085
59892
N\C=C/C(=O)OO
C3H5NO3
InChI=1S/C3H5NO3/c4-2-1-3(5)7-6/h1-2,6H,4H2/b2-1-
WQKGFGLGYOHJOG-UPHRSURJSA-N
(2Z)-3-aminoprop-2-eneperoxoic acid
103.0767
103.026943031
0.19
2
peroxyaminoacrylate
0
0
(2z)-3-aminoprop-2-eneperoxoate;(2z)-3-aminoprop-2-eneperoxoic acid;(z)-3-peroxyaminoacrylate;(z)-3-peroxyaminoacrylic acid;Aminoacrylate peracid;Aminoacrylic acid peracid;Peroxy aminoacrylate;Peroxy aminoacrylic acid;Peroxyaminoacrylate;Peroxyaminoacrylic acid
PW_C041602
Peroate
1170
Flavin Mononucleotide
HMDB0001520
Flavin mononucleotide (FMN), or riboflavin-5?-phosphate, is a biomolecule produced from riboflavin (vitamin B2) by the enzyme riboflavin kinase and functions as prosthetic group of various oxidoreductases including NADH dehydrogenase as well as cofactor in biological blue-light photo receptors. During the catalytic cycle, the reversible interconversion of oxidized (FMN), semiquinone (FMNH) and reduced (FMNH2) forms occurs in the various oxidoreductases. FMN is a stronger oxidizing agent than NAD and is particularly useful because it can take part in both one- and two-electron transfers. Flavin mononucleotide is also used as an orange-red food colour additive. It is the principal form in which riboflavin is found in cells and tissues.
146-17-8
C00061
643976
17621
FMN
559060
DB03247
CC1=CC2=C(C=C1C)N(C[C@H](O)[C@H](O)[C@H](O)COP(O)(O)=O)C1=NC(=O)NC(=O)C1=N2
C17H21N4O9P
InChI=1S/C17H21N4O9P/c1-7-3-9-10(4-8(7)2)21(15-13(18-9)16(25)20-17(26)19-15)5-11(22)14(24)12(23)6-30-31(27,28)29/h3-4,11-12,14,22-24H,5-6H2,1-2H3,(H,20,25,26)(H2,27,28,29)/t11-,12+,14-/m0/s1
FVTCRASFADXXNN-SCRDCRAPSA-N
{[(2R,3S,4S)-5-{7,8-dimethyl-2,4-dioxo-2H,3H,4H,10H-benzo[g]pteridin-10-yl}-2,3,4-trihydroxypentyl]oxy}phosphonic acid
456.3438
456.104614802
-2.83
6
riboflavin 5'-phosphate
0
-3
FDB001984
Fmn;Flanin;Flavine mononucleotide;Flavol;Riboflavin;Riboflavin 5'-monophosphate;Riboflavin 5'-phosphate;Riboflavin mononucleotide;Riboflavin monophosphate;Riboflavin phosphate;Riboflavin-5'-phosphate na;Riboflavin-5-phosphate;Riboflavine 5'-monophosphate;Riboflavine 5'-phosphate;Riboflavine dihydrogen phosphate;Riboflavine monophosphate;Riboflavine phosphate;Riboflavine-5'-phosphate;Vitamin b2 phosphate;Flavin mononucleotide;Riboflavin 5'-(dihydrogen phosphate)
PW_C001170
FlvnMnt
539
8
1190
14
1692
2
4961
31
5772
101
11900
211
12313
225
77519
115
77590
111
78730
132
120433
405
120454
122
121929
124
123067
376
123088
135
124482
118
125698
297
126104
299
127190
205
127312
209
127686
388
7491
Protein rutD
P75895
Involved in hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in linear amides. Makes part of the rut operon, which is required for the utilization of pyrimidines as sole nitrogen source.
rutD
b1009
AP009048
3
3.5.1.-
7343
NADP-dependent L-serine/L-allo-threonine dehydrogenase ydfG
P39831
Involved in oxidoreductase activity. Catalyzes the NADP-dependent oxidation of L-allo- threonine to L-2-amino-3-keto-butyrate, which is spontaneously decarboxylated into aminoacetone. Also acts on L-serine, D-serine, D-threonine, D-3-hydroxyisobutyrate, L-3-hydroxyisobutyrate, D- glycerate and L-glycerate.
ydfG
b1539
AP009048
3
1.1.1.-; 1.1.1.298
7255
Putative NADH dehydrogenase/NAD(P)H nitroreductase rutE
P75894
Involved in oxidoreductase activity. Makes part of the rut operon, which is required for the utilization of pyrimidines as sole nitrogen source.
rutE
b1008
AP009048
3
1.1.1.298
7211
UPF0076 protein rutC
P0AFQ5
Translation, ribosomal structure and biogenesis. Makes part of the rut operon, which is required for the utilization of pyrimidines as sole nitrogen source.
rutC
b1010
AP009048
3
1.-.-.-
7336
Putative monooxygenase rutA
P75898
Involved in oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen. Part of the rut operon, which is required for the utilization of pyrimidines as sole nitrogen source.
rutA
b1012
AP009048
3
1.14.99.46
7374
Putative isochorismatase family protein rutB
P75897
Involved in hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in linear amides. Makes part of the rut operon, which is required for the utilization of pyrimidines as sole nitrogen source.
rutB
b1011
AP009048
3
3.5.1.110
3979
predicted aminoacrylate hydrolase
25
PW_P003979
10967
7491
1
6685
117
3956
3-hydroxy acid dehydrogenase
3
PW_P003956
10936
7343
4
3980
predicted malonic semialdehyde reductase
25
PW_P003980
10968
7255
1
6686
117
3978
predicted aminoacrylate peracid reductase
25
PW_P003978
10966
7211
1
6684
117
3976
pyrimidine oxygenase
25
PW_P003976
10964
7336
1
6682
101
3977
peroxyureidoacrylate / ureidoacrylate amido hydrolase
25
PW_P003977
10965
7374
1
6683
117
5907
PW_R005907
Right
24093
1922
1
Compound
false
24094
40034
2
Compound
false
24095
22608
1
Compound
false
24096
1316
1
Compound
false
5909
false
PW_R005909
Right
24101
1938
1
Compound
false
24102
1420
1
Compound
false
24103
40034
1
Compound
false
24104
6753
1
Compound
false
24105
22608
1
Compound
false
5871
3979
3.5.1.-
5910
false
PW_R005910
Right
24106
6753
1
Compound
false
24107
146
1
Compound
false
24108
40034
1
Compound
false
24109
552
1
Compound
false
24110
143
1
Compound
false
5872
3956
1.1.1.-
5873
3980
1.1.1.298
5908
false
PW_R005908
Right
24097
44507
1
Compound
false
24098
40969
1
Compound
false
24099
1938
1
Compound
false
24100
40968
1
Compound
false
5870
3978
1.-.-.-
5905
false
PW_R005905
Right
24082
204
1
Compound
false
24083
891
1
Compound
false
24084
1065
1
Compound
false
24085
41602
1
Compound
false
24086
1170
1
Compound
false
24087
40034
1
Compound
false
5868
3976
1.14.99.46
5906
false
PW_R005906
Right
24088
41602
1
Compound
false
24089
1420
1
Compound
false
24090
44507
1
Compound
false
24091
1922
1
Compound
false
24092
40034
1
Compound
false
5869
3977
3.5.1.110
69487
1922
3
false
1324
600
10
regular
100
100
69489
40034
55
false
1236
706
10
regular
78
78
69490
22608
3
false
1325
930
10
regular
100
100
69491
1316
52
false
1235
866
10
regular
78
78
69496
1938
3
false
1554
1222
10
regular
100
110
69498
1420
49
false
1440
1161
10
regular
78
78
69499
40034
55
false
1450
1324
10
regular
78
78
69500
6753
3
false
1004
1218
10
regular
100
110
69501
22608
3
false
1129
1333
10
regular
100
100
69502
146
62
false
919
1190
10
regular
50
30
69503
40034
55
false
900
1315
10
regular
78
78
69504
552
3
false
314
1219
10
regular
100
110
69505
143
61
false
534
1199
10
regular
50
30
69852
44507
3
false
1551
615
10
regular
100
100
69854
40969
3
false
1666
725
10
regular
100
130
69855
40968
3
false
1669
947
10
regular
100
130
69856
204
3
false
641
367
10
regular
100
100
69857
891
3
false
771
282
10
regular
100
100
69858
1065
65
false
761
463
10
regular
78
78
69859
41602
3
false
1186
367
10
regular
100
100
69860
1170
3
false
1066
477
10
regular
100
110
69861
40034
55
false
1086
298
10
regular
78
78
69865
1420
49
false
1418
298
10
regular
78
78
69866
40034
55
false
1676
486
10
regular
78
78
31997
7491
2
false
1249
1241
8
subunit
regular
150
70
31998
7343
8
false
659
1184
8
subunit
regular
140
85
31999
7255
2
false
709
1239
8
subunit
regular
150
70
32112
7211
2
false
1527
867
8
subunit
regular
150
70
32113
7336
2
false
890
382
8
subunit
regular
150
70
32115
7374
2
false
1526
381
8
subunit
regular
150
70
26932
3979
1779
31679
31997
26933
3956
1779
31680
31998
26934
3980
1779
31681
31999
27025
3978
1779
31794
32112
27026
3976
1779
31795
32113
27028
3977
1779
31797
32115
98865
M1374 700 C1374 730 1375 900 1375 930
5
false
18
98866
M1314 745 C1351 747 1374.5 778 1374.5 808
5
false
18
98867
M1375 930 C1375 900 1374 730 1374 700
5
false
18
true
M 25.946855044164835 604.8681550852657 L 11 603.6065987889697 L 17.380887721185843 617.181733112048
false
98868
M1313 905 C1357 894 1375.5 862 1374.5 804
5
false
18
true
M 25.946855044164835 604.8681550852657 L 11 603.6065987889697 L 17.380887721185843 617.181733112048
false
98877
M1554 1277 C1493 1276 1443 1276 1399 1276
5
false
18
98878
M1479 1239 C1480 1269 1462 1279 1399 1276
5
false
18
98879
M1489 1324 C1488 1294 1483 1276 1399 1276
5
false
18
98880
M1104 1273 C1166 1274 1191 1274 1249 1276
5
false
18
true
M 500.43633822536316 1083.8471278914076 L 485.4894831811983 1082.5855715951116 L 491.87037090238414 1096.16070591819
false
98881
M1179 1333 C1180 1280 1194 1275 1249 1276
5
false
18
true
M 500.43633822536316 1083.8471278914076 L 485.4894831811983 1082.5855715951116 L 491.87037090238414 1096.16070591819
false
98882
M1004 1273 C913 1274 919 1274 859 1274
5
false
18
98883
M944 1220 C940 1259 923 1274 859 1274
5
false
18
98884
M939 1315 C939 1278 901 1273 859 1274
5
false
18
98885
M414 1274 C527 1275 639 1273 709 1274
5
false
18
true
M 584.5204212258144 1106.3696501236714 L 569.5735661816495 1105.1080938273753 L 575.9544539028353 1118.6832281504537
false
98886
M559 1229 C559 1277 645 1275 709 1274
5
false
18
true
M 584.5204212258144 1106.3696501236714 L 569.5735661816495 1105.1080938273753 L 575.9544539028353 1118.6832281504537
false
98887
M709 1274 C583 1275 549.1441422864877 1283.1831679349211 550.1441422864877 1351.1831679349211
5
false
18
true
M 1776.2085432694744 1487.794686029028 L 1791.1441422864877 1489.1831679349211 L 1784.8788033811795 1475.5543188125032
false
99305
M1601 715 C1601 745 1602 836 1602 867
5
false
18
99306
M1666 790 C1627 791 1602 812 1602 867
5
false
18
99307
M1604 1222 C1603 1191 1602 1006 1602 937
5
false
18
true
M 54.49039802654137 729.4927781037917 L 39.543542982376536 728.2312218074957 L 45.92443070356238 741.806356130574
false
99308
M1669 1012 C1625 1014 1603 994 1602 937
5
false
18
true
M 54.49039802654137 729.4927781037917 L 39.543542982376536 728.2312218074957 L 45.92443070356238 741.806356130574
false
99309
M741 417 C788 417 842 417 890 417
5
false
18
99310
M821 382 C819 401 838 417 890 417
5
false
18
99311
M800 463 C800 422 862 418 890 417
5
false
18
99312
M1186 417 C1138 417 1072 417 1040 417
5
false
18
true
M 54.49039802654137 106.36966301116192 L 39.543542982376536 105.10810671486588 L 45.92443070356238 118.68324103794423
false
99313
M1116 477 C1116 447 1114 417 1040 417
5
false
18
true
M 54.49039802654137 106.36966301116192 L 39.543542982376536 105.10810671486588 L 45.92443070356238 118.68324103794423
false
99314
M1125 376 C1124 416 1109 416 1040 417
5
false
18
true
M 54.49039802654137 106.36966301116192 L 39.543542982376536 105.10810671486588 L 45.92443070356238 118.68324103794423
false
99320
M1286 417 C1331 417 1486 416 1526 416
5
false
18
99321
M1457 376 C1457 406 1464 416 1526 416
5
false
18
99322
M1601 615 C1601 585 1601 481 1601 451
5
false
18
true
M 25.946855044164835 616.880166942473 L 11 615.618610646177 L 17.380887721185843 629.1937449692554
false
99323
M1374 600 C1375 536 1375 501 1376 450 C1455 451 1530 451 1601 451
5
false
18
true
M 25.946855044164835 616.880166942473 L 11 615.618610646177 L 17.380887721185843 629.1937449692554
false
99324
M1676 525 C1646 529 1600 527 1601 451
5
false
18
true
M 25.946855044164835 616.880166942473 L 11 615.618610646177 L 17.380887721185843 629.1937449692554
false
3659970
M641 417 C611 417 586 416 556 416
5
false
18
20253
1779
5907
78656
69487
98865
Left
78657
69489
98866
Left
78658
69490
98867
Right
78659
69491
98868
Right
20256
1779
5909
78668
69496
98877
Left
78669
69498
98878
Left
78670
69499
98879
Left
78671
69500
98880
Right
78672
69501
98881
Right
20432
5871
26932
20257
1779
5910
78673
69500
98882
Left
78674
69502
98883
Left
78675
69503
98884
Left
78676
69504
98885
Right
78677
69505
98886
Right
20433
5872
26933
20434
5873
26934
20335
1779
5908
79013
69852
99305
Left
79014
69854
99306
Left
79015
69496
99307
Right
79016
69855
99308
Right
20512
5870
27025
20336
1779
5905
79017
69856
99309
Left
79018
69857
99310
Left
79019
69858
99311
Left
79020
69859
99312
Right
79021
69860
99313
Right
79022
69861
99314
Right
20513
5868
27026
20338
1779
5906
79028
69859
99320
Left
79029
69865
99321
Left
79030
69852
99322
Right
79031
69487
99323
Right
79032
69866
99324
Right
20515
5869
27028
109471
109799
1779
14
false
406
381
16
regular
106167
69856
3659970
Right
1978
98887
186422
398
535
1.3
1.3
0
2
92
479
481
3475
M127 224 C127 174 177 124 227 124 C712 124 1341 124 1826 124 C1876 124 1926 174 1926 224 C1926 604 1926 1097 1926 1477 C1926 1527 1876 1577 1826 1577 C1341 1577 712 1577 227 1577 C177 1577 127 1527 127 1477 C127 1097 127 604 127 224
1
true
6
1799.0
1453.0
3476
M226 325 C226 275 276 225 326 225 C751 225 1302 225 1727 225 C1777 225 1827 275 1827 325 C1827 644 1827 1059 1827 1378 C1827 1428 1777 1478 1727 1478 C1302 1478 751 1478 326 1478 C276 1478 226 1428 226 1378 C226 1059 226 644 226 325
1
true
6
1601.0
1253.0
1603
15
Excretion
462
1326
20
1.0
1.0
160
15