SMPDB (The Small Molecule Pathway Database) is an interactive, visual database containing more than 30 000 small molecule pathways found in humans only. The majority of these pathways are not found in any other pathway database. SMPDB is designed specifically to support pathway elucidation and pathway discovery in metabolomics, transcriptomics, proteomics and systems biology. It is able to do so, in part, by providing exquisitely detailed, fully searchable, hyperlinked diagrams of human metabolic pathways, metabolic disease pathways, metabolite signaling pathways and drug-action pathways. All SMPDB pathways include information on the relevant organs, subcellular compartments, protein_complex cofactors, protein_complex locations, metabolite locations, chemical structures and protein_complex quaternary structures. Each small molecule is hyperlinked to detailed descriptions contained in the HMDB or DrugBank and each protein_complex or enzyme complex is hyperlinked to UniProt. All SMPDB pathways are accompanied with detailed descriptions and references, providing an overview of the pathway, condition or processes depicted in each diagram. The database is easily browsed and supports full text, sequence and chemical structure searching. Users may query SMPDB with lists of metabolite names, drug names, genes/protein_complex names, SwissProt IDs, GenBank IDs, Affymetrix IDs or Agilent microarray IDs. These queries will produce lists of matching pathways and highlight the matching molecules on each of the pathway diagrams. Gene, metabolite and protein_complex concentration data can also be visualized through SMPDB's mapping interface. All of SMPDB's images, image maps, descriptions and tables are downloadable.
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Vitamin B6 Metabolism: Vitamin B6 is a water-soluble vitamin and is part of the vitamin B complex group ...
Pentose Phosphate Pathway: The pentose phosphate pathway (also called phosphogluconate pathway, or hexose monophosphate shunt or the pentose phosphate shunt) is a process that serves to generate NADPH and the synthesis of pentose (5-carbon) sugars ...
Methionine Metabolism: Methionine metabolism in mammals consists of 2 pathways, the methionine cycle and the transsulfuration sequence ...
Glycolysis: Glycolysis, (Embden-Meyerhof pathway) is a near universal metabolic pathway that converts glucose into pyruvate ...
Gluconeogenesis: Gluconeogenesis, which is essentially the reverse of glycolysis, results in the generation of glucose from non-carbohydrate carbon substrates such as lactate, glycerol, and glucogenic amino acids ...
Canavan Disease: Canavan Disease (Canavan-Van Bogaert-Bertrand Disease; Aminoacylase 2 Deficiency; Spongy Degeneration of the Central Nervous System; Aspartoacylase Deficiency; ASP Deficiency; ACY2 Deficiency; ASPA) is a rare autosomal recessive disease caused by a defect in the ASPA gene which codes for aspartoacylase ...
Lactose Synthesis: Lactose synthesis occurs only in the mammary glands, producing lactose (4-O-B-D-galactosylpyranosyl-a-D-glucopyranoside), the major sugar in milk ...
Dopamine Beta-hydroxylase Deficiency: Dopamine beta-hydroxylase deficiency (or norepinephrine deficiency) is caused by mutation in the gene encoding dopamine beta-hydroxylase. ...
SMPDB is supported by David Wishart, Departments of Computing Science & Biological Sciences, University of Alberta. Use and re-distribution of the data, in whole or in part, for commercial purposes requires explicit permission of the authors and explicit acknowledgment of the source material (SMPDB) and the original publication (see below). We ask that users who download significant portions of the database cite the SMPDB paper in any resulting publications.
- Wishart DS, Frolkis A, Knox C, et al. SMPDB: The Small Molecule Pathway Database. Nucleic Acids Res. 2010 Jan;38(Database issue):D480-7.
- Jewison T, Su Y, Disfany FM, et al. SMPDB 2.0: Big Improvements to the Small Molecule Pathway Database Nucleic Acids Res. 2014 Jan;42(Database issue):D478-84.