Small molecule pathways, metabolic pathways, metabolic disease pathways, metabolite signaling pathways, drug action pathways, drug metabolism pathways
Contact
Research center
University of Alberta and The Metabolomics Innovation Centre
Laboratory
David S. Wishart
Primary citation
SMPDB: The Small Molecule Pathway Database.[1]
Access
Website
http://www.smpdb.ca
Download URL
http://www.smpdb.ca/downloads
Miscellaneous
Data release frequency
Every 2-3 years with periodic corrections and updates
Curation policy
Manually curated
The Small Molecule Pathway Database (SMPDB)[1][2] is a comprehensive, high-quality, freely accessible, online database containing more than 600 small molecule (i.e. metabolic) pathways found in humans. 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 colorful, detailed, fully searchable, hyperlinked diagrams of five types of small molecule pathways: 1) general human metabolic pathways; 2) human metabolic disease pathways; 3) human metabolite signaling pathways; 4) drug-action pathways and 5) drug metabolism pathways. SMPDB pathways may be navigated, viewed and zoomed interactively using a Google Maps-like interface. All SMPDB pathways include information on the relevant organs, subcellular compartments, protein cofactors, protein locations, metabolite locations, chemical structures and protein quaternary structures (Fig. 1). Each small molecule in SMPDB is hyperlinked to detailed descriptions contained in the HMDB[3] or DrugBank[4] and each protein or enzyme complex is hyperlinked to UniProt.[5] Additionally, all SMPDB pathways are accompanied with detailed descriptions and references, providing an overview of the pathway, condition or processes depicted in each diagram. Users can browse the SMPDB (Fig. 2) or search its contents by text searching (Fig. 3), sequence searching, or chemical structure searching. More powerful queries are also possible including searching with lists of gene or protein names, drug names, metabolite names, GenBank IDs, Swiss-Prot IDs, Agilent or Affymetrix 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 concentration data can also be visualized through SMPDB's mapping interface.
SMPDB is part of a suite of metabolomics databases that also includes Human Metabolome Database, DrugBank, and the Toxin and Toxin-Target Database (T3DB). While DrugBank includes information on 7000 drugs and >4200 non-redundant drug targets, enzymes, transporters, and carriers, HMDB houses over 40,000 small molecule metabolites found in the human body. The suite is complemented by T3DB with its over 3100 common toxic substances and over 1300 corresponding toxin targets.
metabolomics databases that also includes Human Metabolome Database (HMDB), DrugBank, Toxin and Toxin-Target Database, and The SmallMoleculePathwayDatabase. The...
The Human Metabolome Database (HMDB) is a comprehensive, high-quality, freely accessible, online database of smallmolecule metabolites found in the human...
present in all bilaterians. The pathway takes its name from its polypeptide ligand, an intracellular signaling molecule called Hedgehog (Hh) found in fruit...
Encyclopedia of Genes and Genomes) is a collection of databases dealing with genomes, biological pathways, diseases, drugs, and chemical substances. KEGG is...
molecule. This yields 2 NADH molecules and 4 ATP molecules, leading to a net gain of 2 NADH molecules and 2 ATP molecules from the glycolytic pathway...
synthesize molecules with the utilization of energy (anabolic pathway), or break down complex molecules and release energy in the process (catabolic pathway)....
containing information on smallmolecule structures and interactions. The databank integrates a number of existing databases to provide a comprehensive...
development. The majority of signal transduction pathways involve the binding of signaling molecules, known as ligands, to receptors that trigger events...
of VAL-083 are registered. Vintafolide is a smallmolecule drug conjugate consisting of a smallmolecule targeting the folate receptor. It is currently...
(/əˈnæbəlɪzəm/) is the set of metabolic pathways that construct macromolecules like DNA or RNA from smaller units. These reactions require energy, known...
molecular interactions. A pathway is most often represented as a relatively small graph with gene, protein, and/or smallmolecule nodes connected by edges...
group) from one molecule (called the donor) to another (called the acceptor). They are involved in hundreds of different biochemical pathways throughout biology...
are intracellular signaling molecules released by the cell in response to exposure to extracellular signaling molecules—the first messengers. (Intercellular...
detailed information about smallmolecule metabolites found in the human body KEGG PATHWAYDatabase (Univ. of Kyoto) MANET database (University of Illinois)...
can denote a metabolic pathway involving a sequence of enzyme-catalyzed reactions of smallmolecules, or a signaling pathway involving a set of protein...
The metabolome refers to the complete set of small-molecule chemicals found within a biological sample. The biological sample can be a cell, a cellular...
reused in different pathways and perform similar functions on different molecules. As well as the evolution of new metabolic pathways, evolution can also...
Wishart, David (6 March 2010). "Glycerol Kinase Deficiency". SmallMoleculePathwayDatabase. Archived from the original on 2 July 2012. Retrieved 21 December...
diacylglycerol and ceramide, respectively. These molecules then participate in signal transduction pathways. It has been reported that the toxin activates...
non-coding RNA molecules, typically 20–24 (normally 21) base pairs in length, similar to miRNA, and operating within the RNA interference (RNAi) pathway. It interferes...
using inorganic molecules other than oxygen as final electron acceptors in the electron transport chain. They share the initial pathway of glycolysis but...
metabolic processes involving or closely related to fatty acids, a family of molecules classified within the lipid macronutrient category. These processes can...
NADH and NAD+. In homolactic fermentation, one molecule of glucose is ultimately converted to two molecules of lactic acid. Heterolactic fermentation, by...
smallmolecules) participating in reactions form a network of biological interactions and are grouped into pathways. Examples of biological pathways in...
also present in small amounts. The uniformity of both specific types of molecules (the biomolecules) and of certain metabolic pathways are invariant features...
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