DrugBank

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DrugBank
DrugBank logo.png
Content
Description Drug database
Data types
captured		 Chemical structures, small molecule drugs, biotech drugs, drug targets, drug transporters, drug target sequences, drug target SNPs, drug metabolites, drug descriptions, disease associations, dosage data, food and drug interactions, adverse drug reactions, pharmacology, mechanisms of action, drug metabolism, chemical synthesis, patent and pricing data, chemical properties, nomenclature, synonyms, chemical taxonomy, drug NMR spectra, drug GC-MS spectra, drug LC-MS spectra
Contact
Research center University of Alberta and The Metabolomics Innovation Centre
Laboratory Dr. David Wishart
Primary citation DrugBank: a comprehensive resource for in silico drug discovery and exploration.[1]
Access
Website www.drugbank.ca
Download URL www.drugbank.ca/downloads
Miscellaneous
Data release
frequency		 Every 2 years with monthly corrections and updates
Curation policy Manually curated

The DrugBank database is a comprehensive, freely accessible, online database containing information on drugs and drug targets.[1] As both a bioinformatics and a cheminformatics resource, DrugBank combines detailed drug (i.e. chemical, pharmacological and pharmaceutical) data with comprehensive drug target (i.e. sequence, structure, and pathway) information.[1][2] Because of its broad scope, comprehensive referencing and unusually detailed data descriptions, DrugBank is more akin to a drug encyclopedia than a drug database. As a result, links to DrugBank are maintained for nearly all drugs listed in Wikipedia. DrugBank is widely used by the drug industry, medicinal chemists, pharmacists, physicians, students and the general public. Its extensive drug and drug-target data has enabled the discovery and repurposing of a number of existing drugs to treat rare and newly identified illnesses.

The latest release of the database (version 5.0) contains 8227 drug entries including 2003 FDA-approved small molecule drugs, 221 FDA-approved biotech (protein/peptide) drugs, 93 nutraceuticals and over 6000 experimental drugs.[3] Additionally, 4270 non-redundant protein (i.e. drug target/enzyme/transporter/carrier) sequences are linked to these drug entries.

Fig. 1. DrugBank DrugCard

Each DrugCard (Fig. 1) entry contains more than 200 data fields with half of the information being devoted to drug/chemical data and the other half devoted to drug target or protein data.[3]

Four additional databases, HMDB,[4] T3DB,[5] SMPDB [6] and FooDB are also part of a general suite of metabolomic/cheminformatic databases. HMDB contains equivalent information on more than 40,000 human metabolites, T3DB contains information on 3100 common toxins and environmental pollutants, SMPDB contains pathway diagrams for nearly 700 human metabolic pathways and disease pathways, while FooDB contains equivalent information on ~28,000 food components and food additives.

Version history[edit]

The first version of DrugBank was released in 2006.[1] This early release contained relatively modest information about 841 FDA-approved small molecule drugs and 113 biotech drugs. It also included information on 2133 drug targets. The second version of DrugBank was released in 2009.[2] This greatly expanded and improved version of the database included 1344 approved small molecule drugs and 123 biotech drugs as well as 3037 unique drug targets. Version 2.0 also included, for the first time, withdrawn drugs and illicit drugs, extensive food-drug and drug-drug interactions as well as ADMET (absorption, distribution, metabolism, excretion and toxicity) parameters. Version 3.0 was released in 2011.[7] This version contained 1424 approved small molecule drugs and 132 biotech drugs as well as >4000 unique drug targets. Version 3.0 also included drug transporter data, drug pathway data, drug pricing, patent and manufacturing data as well as data on >5000 experimental drugs. Version 4.0 was released in 2014.[3] This version included 1558 FDA-approved small molecule drugs, 155 biotech drugs and 4200 unique drug targets. Version 4.0 also incorporated extensive information on drug metabolites (structures and reactions), drug taxonomy, drug spectra, drug binding constants and drug synthesis information. Table 1 provides a more complete statistical summary of the history of DrugBank’s development.

Table 1. Comparison between the coverage in DrugBank 1.0, 2.0, 3.0 and DrugBank 4.0.
Category 1.0 2.0 3.0 4.0
No. of data fields per DrugCard 88 108 148 208
No. of search types 8 12 16 18
No. of illustrated drug-action pathways 0 0 168 232
No. of drugs with metabolizing enzyme data 0 0 762 1,037
No. of drug metabolites with structures 0 0 0 1,239
No. of drug-metabolism reactions 0 0 0 1,308
No. of illustrated drug metabolism pathways 0 0 0 53
No. of drugs with drug transporter data 0 0 516 623
No. of drugs with taxonomic classification information 0 0 0 6,713
No. of SNP-associated drug effects 0 0 113 201
No. of drugs with patent/pricing/manufacturer data 0 0 1,208 1,450
'No. of food–drug interactions 0 714 1,039 1,180
No. of drug–drug interactions 0 13,242 13,795 14,150
No. of ADMET parameters (Caco-2, LogS) 0 276 890 6,667
No. of QSAR parameters per drug 5 6 14 23
No. of drugs with drug-target binding constant data 0 0 0 791
No. of drugs with NMR spectra 0 0 0 306
No. of drugs with MS spectra 0 0 0 384
No. of drugs with chemical synthesis information 0 38 38 1,285
No. of FDA-approved small molecule drugs 841 1,344 1,424 1,558
No. of biotech drugs 113 123 132 155
No. of nutraceutical drugs 61 69 82 87
No. of withdrawn drugs 0 57 68 78
No. of illicit drugs 0 188 189 190
No. of experimental drugs 2,894 3,116 5,210 6,009
Total No. of experimental and FDA small molecule drugs 3,796 4,774 6,684 7,561
Total No. of experimental and FDA drugs (all types) 3,909 4,897 6,816 7,713
No. of all drug targets (unique) 2,133 3,037 4,326 4,115
No. of approved-drug enzymes/carriers (unique) 0 0 164 245
No. of all drug enzymes/carriers (unique) 0 0 169 253
No. of external database links 12 18 31 33

Scope and access[edit]

All data in DrugBank is non-proprietary or is derived from a non-proprietary source. It is freely accessible and available to anyone. In addition, nearly every data item is fully traceable and explicitly referenced to the original source. DrugBank data is available through a public web interface and downloads.

Users may query DrugBank in a number of ways:

  • Fig. 2. DrugBank browse
    Simple text queries of the entire textual component of the database are supported. Clicking on the Browse button generates a tabular synopsis of DrugBank's content. This view allows users to casually scroll through the database or re-sort its contents (Fig. 2).
  • Clicking on a given DrugCard button brings up the full data content for the corresponding drug. A complete explanation of all the DrugCard fields and sources is given there.
  • The PharmaBrowse button allows users to browse through drugs as grouped by their indication. This is particularly useful for pharmacists and physicians, but also for pharmaceutical researchers looking for potential drug leads.
  • Fig. 3. DrugBank ChemQuery
    The ChemQuery button allows users to draw (using ChemAxon applets) or write (as a SMILES string) a chemical compound and to search DrugBank for chemicals similar or identical to the query compound (Fig. 3).
  • The TextQuery button supports a more sophisticated text search (partial word matches, case sensitive, misspellings, etc.) of the text portion of DrugBank.
  • The SeqSearch button allows users to conduct BLAST (protein) sequence searches of the 18,000 sequences contained in DrugBank. Both single and multiple sequence (i.e. whole proteome) BLAST queries are supported.
  • The Data Extractor button opens an easy-to-use relational query search tool that allows users to select or search over various combinations of subfields. The Data Extractor is the most sophisticated search tool for DrugBank.

Users may download selected text components and sequence data from DrugBank and track the latest news about DrugBank through regular news feeds through its website as well as through Twitter and Facebook.

See also[edit]

References[edit]

  1. ^ a b c d Wishart, DS; Knox C; Guo AC; et al. (Jan 2006). "DrugBank: a comprehensive resource for in silico drug discovery and exploration". Nucleic Acids Research. 34 (Database issue): D668-D672. doi:10.1093/nar/gkj067. PMC 1347430Freely accessible. PMID 16381955. 
  2. ^ a b Wishart, DS; Knox C; Guo AC; et al. (Jan 2008). "DrugBank: a knowledgebase for drugs, drug actions and drug targets". Nucleic Acids Research. 36 (Database issue): D901–906. doi:10.1093/nar/gkm958. PMC 2238889Freely accessible. PMID 18048412. 
  3. ^ a b c Law, V; Knox, C; Djoumbou, Y; Jewison, T; Guo, AC; Liu, Y; Maciejewski, A; Arndt, D; Wilson, M; Neveu, V; Tang, A; Gabriel, G; Ly, C; Adamjee, S; Dame, ZT; Han, B; Zhou, Y; Wishart, DS (Jan 2014). "DrugBank 5.0: shedding new light on drug metabolism". Nucleic Acids Research. 42 (Database issue): D1091-7. doi:10.1093/nar/gkt1068. PMC 3965102Freely accessible. PMID 24203711. 
  4. ^ Wishart, DS; Guo, AC; Eisner, R; Young, N; Gautam, B; Hau, DD; Psychogios, N; Dong, E; Bouatra, S; Mandal, R; Sinelnikov, I; Xia, J; Jia, L; Cruz, JA; Lim, E; Sobsey, CA; Shrivastava, S; Huang, P; Liu, P; Fang, L; Peng, J; Fradette, R; Cheng, D; Tzur, D; Clements, M; Lewis, A; De Souza, A; Zuniga, A; Dawe, M; Xiong, Y; Clive, D; Greiner, R; Nazyrova, A; Shaykhutdinov, R; Li, L; Vogel, HJ; Forsythe, I (Jan 2009). "HMDB: a knowledgebase for the human metabolome". Nucleic Acids Research. 37 (Database issue): D603-10. doi:10.1093/nar/gkn810. PMC 2686599Freely accessible. PMID 18953024. 
  5. ^ Lim, E; Pon A; Djoumbou Y; Knox C; Shrivastava S; Guo AC; Neveu V; Wishart DS. (Jan 2010). "T3DB: a comprehensively annotated database of common toxins and their targets.". Nucleic Acids Research. 38 (Database issue): D781-6. doi:10.1093/nar/gkp934. PMC 2808899Freely accessible. PMID 19897546. 
  6. ^ Jewison, T; Su Y; Disfany FM; et al. (Jan 2014). "Small Molecule Pathway Database.". Nucleic Acids Research. 42 (Database issue): D478-84. doi:10.1093/nar/gkt1067. PMC 3965088Freely accessible. PMID 24203708. 
  7. ^ Knox, C; Law, V; Jewison, T; Liu, P; Ly, S; Frolkis, A; Pon, A; Banco, K; Mak, C; Neveu, V; Djoumbou, Y; Eisner, R; Guo, AC; Wishart, DS. (Jan 2011). "DrugBank 3.0: a comprehensive resource for 'omics' research on drugs.". Nucleic Acids Research. 39 (Database issue): D1035–41. doi:10.1093/nar/gkq1126. PMC 3013709Freely accessible. PMID 21059682. 
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