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The Small Molecule Pathway Database (SMPDB) is a comprehensive, high-quality, freely accessible, online database containing more than 600
small molecule Within the fields of molecular biology and pharmacology, a small molecule or micromolecule is a low molecular weight (≤ 1000 daltons) organic compound that may regulate a biological process, with a size on the order of 1 nm. Many drugs ...
(i.e. metabolic) pathways found in humans. SMPDB is designed specifically to support pathway elucidation and pathway discovery in
metabolomics Metabolomics is the scientific study of chemical processes involving metabolites, the small molecule substrates, intermediates, and products of cell metabolism. Specifically, metabolomics is the "systematic study of the unique chemical fingerprin ...
,
transcriptomics Transcriptomics technologies are the techniques used to study an organism's transcriptome, the sum of all of its RNA transcripts. The information content of an organism is recorded in the DNA of its genome and expressed through transcription. H ...
, 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 pathway In biochemistry, a metabolic pathway is a linked series of chemical reactions occurring within a cell. The reactants, products, and intermediates of an enzymatic reaction are known as metabolites, which are modified by a sequence of chemical reac ...
s; 2) human metabolic disease pathways; 3) human metabolite signaling pathways; 4) drug-action pathways and 5)
drug metabolism Drug metabolism is the metabolic breakdown of drugs by living organisms, usually through specialized enzymatic systems. More generally, xenobiotic metabolism (from the Greek xenos "stranger" and biotic "related to living beings") is the set o ...
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 In biology, an organ is a collection of tissues joined in a structural unit to serve a common function. In the hierarchy of life, an organ lies between tissue and an organ system. Tissues are formed from same type cells to act together in a f ...
, subcellular compartments,
protein Proteins are large biomolecules and macromolecules that comprise one or more long chains of amino acid residues. Proteins perform a vast array of functions within organisms, including catalysing metabolic reactions, DNA replication, res ...
cofactors, protein locations, metabolite locations,
chemical structure A chemical structure determination includes a chemist's specifying the molecular geometry and, when feasible and necessary, the electronic structure of the target molecule or other solid. Molecular geometry refers to the spatial arrangement of ...
s and protein quaternary structures (Fig. 1). Each
small molecule Within the fields of molecular biology and pharmacology, a small molecule or micromolecule is a low molecular weight (≤ 1000 daltons) organic compound that may regulate a biological process, with a size on the order of 1 nm. Many drugs ...
in SMPDB is hyperlinked to detailed descriptions contained in the HMDB or DrugBank and each
protein Proteins are large biomolecules and macromolecules that comprise one or more long chains of amino acid residues. Proteins perform a vast array of functions within organisms, including catalysing metabolic reactions, DNA replication, res ...
or
enzyme Enzymes () are proteins that act as biological catalysts by accelerating chemical reactions. The molecules upon which enzymes may act are called substrates, and the enzyme converts the substrates into different molecules known as products ...
complex is hyperlinked to UniProt. 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 A chemical structure determination includes a chemist's specifying the molecular geometry and, when feasible and necessary, the electronic structure of the target molecule or other solid. Molecular geometry refers to the spatial arrangement of ...
searching. More powerful queries are also possible including searching with lists of gene or protein names, drug names, metabolite names,
GenBank The GenBank sequence database is an open access, annotated collection of all publicly available nucleotide sequences and their protein translations. It is produced and maintained by the National Center for Biotechnology Information (NCBI; a part ...
IDs, Swiss-Prot IDs,
Agilent Agilent Technologies, Inc. is an American life sciences company that provides instruments, software, services, and consumables for the entire laboratory workflow. Its global headquarters is located in Santa Clara, California. Agilent was establi ...
or Affymetrix microarray IDs. These queries will produce lists of matching pathways and highlight the matching molecules on each of the pathway diagrams.
Gene In biology, the word gene (from , ; "... Wilhelm Johannsen coined the word gene to describe the Mendelian units of heredity..." meaning ''generation'' or ''birth'' or ''gender'') can have several different meanings. The Mendelian gene is a b ...
, metabolite and
protein Proteins are large biomolecules and macromolecules that comprise one or more long chains of amino acid residues. Proteins perform a vast array of functions within organisms, including catalysing metabolic reactions, DNA replication, res ...
concentration data can also be visualized through SMPDB's mapping interface. SMPDB is part of a suite of
metabolomics Metabolomics is the scientific study of chemical processes involving metabolites, the small molecule substrates, intermediates, and products of cell metabolism. Specifically, metabolomics is the "systematic study of the unique chemical fingerprin ...
databases that also includes Human Metabolome Database,
DrugBank The DrugBank database is a comprehensive, freely accessible, online database containing information on drugs and drug targets created and maintained by the University of Alberta and The Metabolomics Innovation Centre located in Alberta, Canada. ...
, and the Toxin and Toxin-Target Database (T3DB). While
DrugBank The DrugBank database is a comprehensive, freely accessible, online database containing information on drugs and drug targets created and maintained by the University of Alberta and The Metabolomics Innovation Centre located in Alberta, Canada. ...
includes information on 7000 drugs and >4200 non-redundant drug targets, enzymes, transporters, and carriers, HMDB houses over 40,000
small molecule Within the fields of molecular biology and pharmacology, a small molecule or micromolecule is a low molecular weight (≤ 1000 daltons) organic compound that may regulate a biological process, with a size on the order of 1 nm. Many drugs ...
metabolites In biochemistry, a metabolite is an intermediate or end product of metabolism. The term is usually used for small molecules. Metabolites have various functions, including fuel, structure, signaling, stimulatory and inhibitory effects on enzymes, ...
found in the human body. The suite is complemented by T3DB with its over 3100 common toxic substances and over 1300 corresponding toxin targets.


Version History

The first version of SMPDB was released on January 1, 2010. This release contained more than 350 image-mapped pathways for small molecule pathways. The viewer interface was limited to scroll-bar image navigation with 3-step (small, medium, large) zooming. The pathways in this first version were limited to 1) human
metabolic pathway In biochemistry, a metabolic pathway is a linked series of chemical reactions occurring within a cell. The reactants, products, and intermediates of an enzymatic reaction are known as metabolites, which are modified by a sequence of chemical reac ...
s; 2) human metabolic disease pathways; and 3) human metabolite signaling pathways. The second version of SMPDB was released in 2014. This version contained more than 620 small molecule pathways. The viewer interface was enhanced to include a Google-Map-like interface with click-n-drag image navigation and unlimited, interactive zooming. The pathways in this second version were expanded to include: 1) general human metabolic pathways; 2) human metabolic disease pathways; 3) human metabolite signaling pathways; 4)
drug action The action of drugs on the human body (or any other organism's body) is called pharmacodynamics, and the body's response to drugs is called pharmacokinetics. The drugs that enter an individual tend to stimulate certain receptors, ion channels, ac ...
pathways and 5)
drug metabolism Drug metabolism is the metabolic breakdown of drugs by living organisms, usually through specialized enzymatic systems. More generally, xenobiotic metabolism (from the Greek xenos "stranger" and biotic "related to living beings") is the set o ...
pathways.


See also

*
KEGG KEGG (Kyoto Encyclopedia of Genes and Genomes) is a collection of databases dealing with genomes, biological pathways, diseases, drugs, and chemical substances. KEGG is utilized for bioinformatics research and education, including data analysis i ...
* HMDB *
DrugBank The DrugBank database is a comprehensive, freely accessible, online database containing information on drugs and drug targets created and maintained by the University of Alberta and The Metabolomics Innovation Centre located in Alberta, Canada. ...
*
Reactome Reactome is a free online database of biological pathways. There are several Reactomes that concentrate on specific organisms, the largest of these is focused on human biology, the following description concentrates on the human Reactome. It is aut ...
* MetaCyc * List of biological databases


References

{{reflist Metabolomic databases Medical databases Biological databases