Documentation and Sources

2017-6-27 Documentation and Sources - DrugBank
Documentation and Sources
Introduction to DrugBank
DrugBank is a detailed database on small molecule and biotech drugs. Each drug entry ("DrugCard") includes extensive information on properties, structure, and
biology (what the drug does in the body). Below you can nd some de nitions, and a detailed reference of the sources used for each eld.
Drug Type
Drugs are categorized by type, which determines their origin. Here is the list of possible types:
Small Molecule Low molecular weight drugs (900 daltons) which are produced by chemical synthesis. These drugs have well de ned structures and
chemical properties. In DrugBank, some drugs larger than 900 daltons are considered small molecule drugs (such as monomers: ribo-
or deoxyribonucleotides, amino acids, and monosaccharides), as long as they are chemically synthesized.
Biotech Drugs with a biological origin (manufactured in, extracted from, or semisynthesized from biological sources). These include vaccines,
blood, blood components, allergenics, somatic cells, gene therapies, tissues, recombinant therapeutic protein, and living cells used in
cell therapy. Biotech drugs are also known as biopharmaceuticals or biologics.
Drug Group(s)
Drugs are categorized by group, which determines their drug development status. Here is the list of possible groups:
Approved A drug that has been approved in at least one jurisdiction, at some point in time.
Vet Approved A drug that has been approved in at least one jurisdiction, at some point in time for the treatment of animals.
Nutraceutical A drug that is a pharmaceutical-grade and standardized nutrient (with con rmed or uncon rmed health bene ts)
Illicit A drug that is scheduled in at least one jurisdiction, at some point in time.
Withdrawn A previously approved drug that has been withdrawn from the market in at least one jurisdiction, at some point in time. Note that
because a drug can be approved in one jurisdiction, and withdrawn in another, it's possible for a drug to be in both groups.
Investigational A drug that is in some phase of the drug approval process in at least one jurisdiction.
Experimental A compound that has been shown experimentally to bind speci c proteins in mammals, bacteria, viruses, fungi, or parasites. This
includes compounds that are Pre-Investigational New Drug Applications (Pre-IND).
Drug Binding
Each drug can have one or more targets, enzymes, transporters, and carriers associated with it. Here are the de nitions for these different relationships:
Target A protein, macromolecule, nucleic acid, or small molecule to which a given drug binds, resulting in an alteration of the normal function
of the bound molecule and a desirable therapeutic effect. Drug targets are most commonly proteins such as enzymes, ion channels,
and receptors.
Enzyme A protein which catalyzes chemical reactions involving the a given drug (substrate). Most drugs are metabolized by the Cytochrome
P450 enzymes (http://en.wikipedia.org/wiki/Cytochrome_P450).
Transporter A membrane bound protein which shuttles ions, small molecules or macromolecules across membranes, into cells or out of cells.
Carrier A secreted protein which binds to drugs, carrying them to cell transporters, where they are moved into the cell. Drug carriers may be
used in drug design to increase the effectiveness of drug delivery to the target sites of pharmacological actions.
Targets, Enzymes, Carriers, And Transporters may switch roles depending on the drug to which they bind. Some drugs speci cally target transporters, and in this
case a transporter can also be the target (for example: Procaine (/drugs/DB00721) targeting the Sodium-dependent dopamine transporter
(/biodb/bio_entities/BE0000647)).
Drug Field Documentation and Sources
Data sources indicate the source of the information present in each eld. Data sources do not indicate that all sources were used for a particular eld and
drug. Individual drug reference information can be found in the "General References" section of each drug.
Small
Field Description Sources Molecule? Biotech?
Version Entry version Automatic yes yes
Creation Date Date/time the entry was created Automatic yes yes
Update Date Date/time the entry was last updated Automatic yes yes
https://www.drugbank.ca/documentation 1/10
Small
DrugBank ID Unique DrugBank accession number Automatic yes yes

(Primary Accession consisting of a 2 letter pre x (DB) and a 5
Number) number suf x. This ID is used to access the
drug entry via the URL. If an entry is deleted,
it's DrugBank ID will not be reused.
Secondary Accession DrugBank release 1.0 accession number Automatic yes yes
Number consisting of the 4 letter pre x and a 5
number suf x. Each Accession number is
unique to the drug's generic name. The 4
letter suf x (APRD, EXPT, BIOD, NUTR)
indicates the type of drug (APRD=approved
small molecule drug, EXPT=experimental
drug, BIOD=biotech drug,
NUTR=nutraceutical or natural product).
Name Standard name of drug as provided by drug Manual Search yes yes
manufacturer
PubChem (http://pubchem.ncbi.nlm.nih.gov)
KEGG (http://www.genome.jp/kegg/)
PubMed (http://www.ncbi.nlm.nih.gov/pubmed/)
Merck Manual
(http://www.merckandcoinc.net/mmpe/index.html)
ChEBI (http://www.ebi.ac.uk/chebi)
SciFinder (http://www.cas.org/products/sci ndr/)
MetaCyc (http://metacyc.org)
OMMBID (http://www.ommbid.com/)
Type Can be one of Small molecule or Biotech (see Manual Search yes yes
de nition list in introduction).
Groups Can be one or more of: Approved, Vet Manual Search yes yes
approved, Nutraceutical, Illicit, Withdrawn,
Investigational, and Experimental. (see
de nition list in introduction)
Description Description of the drug describing general Manual Search yes yes
facts, composition and/or preparation.
Wikipedia (http://en.wikipedia.org)
Merck Manual
STAT!Ref (AHFS) (http://online.statref.com)
e-Therapeutics (http://www.e-therapeutics.ca)
Kingdom Organic or Inorganic Calculated from structure yes yes
Classes Drug classes form the major component of Calculated from structure yes yes
the classi cation system. Drugs with the
same class are considered structurally similar.
Substructures and All substructures and functional groups Calculated from structure yes yes
Functional Groups calculated from the structure for the drug.
This is a superset of the Classes.
Small
Synonyms Alternate names of the drug Manual Search yes yes
Merck Manual
Medicines Complete
(http://www.medicinescomplete.com/mc/)
Brand Names Brand names from different manufacturers Manual Search yes yes
Merck Manual
Medicines Complete
Brand Mixtures Brand names and composition of mixtures Manual Search yes yes
that include the given drug
Merck Manual
Medicines Complete
Manufacturers Companies known to manufacturer the given Drug Product Database (http://webprod.hc-sc.gc.ca/dpd- yes yes
drug bdpp/index-eng.jsp)
FDA (http://www.fda.gov)
Packaging Companies which package and sell the given drugstore (http://www.drugstore.com) yes yes
Companies drug
Prices Unit cost drug prices in U.S. dollars drugstore (http://www.drugstore.com) yes yes
Patents The rst and last drug patent, including FDA (http://www.fda.gov) yes yes
approval and expiry dates
Drug Product Database (http://webprod.hc-sc.gc.ca/dpd-
bdpp/index-eng.jsp)
Chemical IUPAC IUPAC or standard chemical name for the Calculated from structure yes no
Name drug
Chemical Formula Chemical formula describing atomic or Calculated from structure yes yes
elemental composition
Small
Average Molecular Molecular weight in g/mol, determined from Calculated from structure yes yes
Weight molecular formula or sequence
Monoisotopic The sum of the masses of the atoms in a Calculated from structure yes no
Molecular Weight molecule using the unbound, ground-state,
rest mass of the principle (most abundant)
isotope for each element instead of the
isotopic average mass.
Structure For small molecule drugs, the 2D chemical Manual Search yes yes
structure including links to download and
view the structure in various formats.
For biotech drugs, an image of the 3D
structure and links to view the 3D structure Merck Manual
in the structure viewer. (http://www.merckandcoinc.net/mmpe/index.html)
ChemSpider (http://www.chemspider.com)
SMILES Isomeric SMILES string corresponding to Calculated from structure yes no

drug structure
InChI Standard InChI identi er Calculated from structure yes no
InChI Key Standard InChI key Calculated from structure yes no
CAS Registry Chemical Abstract Service identi cation SciFinder (http://www.cas.org/products/sci ndr/) yes yes
Number number
KEGG Drug ID Kyoto Encyclopedia of Genes and Genomes KEGG (http://www.genome.jp/kegg/) yes yes
drug identi cation number (if molecule is in
KEGG)
KEGG Compound ID Kyoto Encyclopedia of Genes and Genomes KEGG (http://www.genome.jp/kegg/) yes yes
compound identi cation number (if molecule
is in KEGG)
PubChem Compound NCBI's PubChem database compound PubChem (http://pubchem.ncbi.nlm.nih.gov) yes yes
ID identi cation number
PubChem Substance NCBI's PubChem database subtance PubChem (http://pubchem.ncbi.nlm.nih.gov) yes no

ID identi cation number
Calculated from structure
ChemSpider ID ChemSpider identi cation number ChemSpider (http://www.chemspider.com) yes no
BindingDB ID BindingDB identi cation number ChEBI (http://www.ebi.ac.uk/chebi) yes yes
ChEBI ID EBI's Chemicals of Biological Interest ChEBI (http://www.ebi.ac.uk/chebi) yes no

identi cation number (if drug is in ChEBI)
ChEMBL ID ChEMBL identi cation number ChEBI (http://www.ebi.ac.uk/chebi) yes no
Stitch ID Stitch identi cation number PubChem (http://pubchem.ncbi.nlm.nih.gov) yes yes
Therapeutic Targets Therapeutic Targets Database identi cation TTD: Therapeutic Target Database yes yes
Database (TTD) ID number (http://xin.cz3.nus.edu.sg/group/cjttd/ttd.asp)
PharmGKB ID Pharmacogenomics Knowledge Base PharmGKB (http://www.pharmgkb.org) yes yes

identi cation number (if molecule is in
PharmGKB)
HET ID PDB identi catin number (if molecule is in PDBeChem (http://pdbe.org/pdbechem) yes no
PDB, ChemPDB or Ligand Depot)
PDB (http://www.rcsb.org)
Small
UniProt ID/Name UniProt database ID number UniProt (http://www.uniprot.org) no yes
GenBank ID GenBank database ID number GenBank (http://www.ncbi.nlm.nih.gov/genbank) no yes
Drug Product ID Drug Product Database Drug Identi cation Drug Product Database (http://webprod.hc-sc.gc.ca/dpd- yes yes
Number bdpp/index-eng.jsp)
RxList Link Link to RxList entry for the given drug (if it RxList (http://www.rxlist.com) yes yes
exists)
Drugs.com Link Link to Drugs.com for the given drug (if it Drugs.com (http://www.drugs.com) yes yes
exists)
PDRhealth Link Link to PDRhealth entry for the given drug (if PDRhealth (http://www.pdrhealth.com) yes yes
it exists)
Wikipedia Link Link to Wikipedia entry for the given drug (if Wikipedia (http://en.wikipedia.org) yes yes
it exists)
FDA Label Food and Drug Administration approval label FDA (http://www.fda.gov) yes yes
(if it exists)
Material Safety Data Material Safety Data Sheet (MSDS) (if it Manual Search yes yes
Sheet exists)
Sigma-Aldrich (http://www.sigmaaldrich.com)
ScienceLab.com (http://www.sciencelab.com)
Synthesis Reference Reference or patent number to description of Manual Search yes yes
drug's synthesis
Merck Manual
State Physical state (solid, liquid, gas) MSDS yes yes
Melting Point Melting point in degrees Celsius FDA (http://www.fda.gov) yes yes
MSDS
PhysProp (http://www.syrres.com/what-we-
do/databaseforms.aspx?id=386)
Boiling Point Boiling point in degrees Celsius FDA (http://www.fda.gov) yes yes
MSDS
Experimental Water Water solubility in mg/mL or g/L MSDS yes yes

Solubility
Predicted Water Predicted water solubility in mg/mL ALOGPS (http://www.vcclab.org/lab/alogps/) yes no

Solubility
Experimental Water/octanol partition coef cient (if small MSDS yes yes
LogP/Hydrophobicity molecule) or hydrophobicity score (Gravy
score) if protein/peptide
Small
Predicted Predicted water/octanol partition coef cient Calculated from structure yes no
LogP/Hydrophobicity
Predicted LogS Predicted LogS (water solubility) Calculated from structure yes no
Experimental LogS Experimental LogS (water solubility) BiGG (http://bigg1.ucsd.edu/) yes yes
Experimental Caco2 Caco-2 permeability coef cients BiGG (http://bigg1.ucsd.edu/) yes yes
Permeability
pKa/Isoelectric Point Dissociation constant (pKa) if small molecule, Manual Search yes yes
pH at which protein has no charge (if protein
drug)
ProtParam (http://www.expasy.ch/tools/protparam.html)
Mass Spectrum Image of EI Mass Spectrum of drug (if it SDBS (http://sdbs.db.aist.go.jp/sdbs/cgi-bin/cre_index.cgi? yes no
exists) lang=eng)
NIST Chemistry WebBook

(http://webbook.nist.gov/chemistry/)
Experimental PDB PDB identi cation number if structure of PDB (http://www.rcsb.org) yes yes
Entries drug exists in PDB
Category Therapeutic category or general category of Manual Search yes yes

drug (anti-convulsant, antibacterial, etc.)
ATC Codes WHO drug classi cation system (ATC) WHO ATC Index (http://www.whocc.no/atc_ddd_index/) yes yes
identi ers
AHFS Codes AHFS Drug Information identi ers Drug Product Database (http://webprod.hc-sc.gc.ca/dpd- yes yes
bdpp/index-eng.jsp)
Indication Description or common names of diseases Manual Search yes yes

that the drug is used to treat
Merck Manual
TTD: Therapeutic Target Database

(http://xin.cz3.nus.edu.sg/group/cjttd/ttd.asp)
Pharmacodynamics Description of how the drug works at a Manual Search yes yes
clinical or physiological level
Merck Manual
Small
Mechanism of Action Description of how the drug works or what it Manual Search yes yes
binds to at a molecular level
Merck Manual
Absorption Description of how much of the drug or how Manual Search yes yes
readily the drug is taken up by the body
PharmGKB (http://www.pharmgkb.org)
Toxicity Lethal dose (LD50) values from test animals, Manual Search yes yes
description of side effects and toxic effects
ToxNet (http://toxnet.nlm.nih.gov/)
seen in humans
BC Cancer Agency Drug Manual
(http://www.bccancer.bc.ca/HPI/DrugDatabase/default.htm)
Protein Binding Percentage of the drug that is bound in Manual Search yes yes
plasma proteins
Metabolism Mechanism by which or organ location where Manual Search yes yes
the drug is neutralized
Half Life Half life of drug in body, measured in hours or Manual Search yes yes
days
Route of Elimination Route by which the drug is eliminated. Drugs Manual Search yes yes
are cleared primarily by the liver and kidneys.
DailyMed (http://dailymed.nlm.nih.gov/)
Volume of The apparent volume of distribution is the Manual Search yes yes
Distribution theoretical volume of uid into which the
total drug administered would have to be
diluted to produce the concentration in DailyMed (http://dailymed.nlm.nih.gov/)
plasma
Small
Clearance Clearance is a descriptive term used to Manual Search yes yes

evaluate ef ciency of drug removal from the
body
DailyMed (http://dailymed.nlm.nih.gov/)
Dosage Forms How the drug is dispensed (tablets, capsules, FDA (http://www.fda.gov) yes yes
solutions, etc.)
Drug Product Database (http://webprod.hc-sc.gc.ca/dpd-
bdpp/index-eng.jsp)
Drug Interactions Drugs that are known to interact, interfere or Physician's Desk Reference (http://www.pdr.net) yes yes
cause adverse reactions when taken with this
drug
Medicines Complete
Epocrates RX (http://www.epocrates.com/products/rx/)
Drugs.com (http://www.drugs.com)
Food Interactions Foods that are known to interact, interfere or Manual Search yes yes
cause adverse reactions when taken with this
drug
Physician's Desk Reference (http://www.pdr.net)
Harvard Food-Drug Database
Epocrates RX (http://www.epocrates.com/products/rx/)
DynaMed (http://www.ebscohost.com/dynamed/)
Pathways Drug pathways in which the given drug is SMPDB (http://www.smpdb.ca) yes yes
involved
Organisms Affected Names of organisms for which the drug is Manual Search yes yes
most effective
General References General on-line reference to other details Manual Search yes yes
about the drug
Target/Enzyme/Transporter/Carrier Field Documentation

Field Description Sources
Name Name of the protein or macromolecule (or other small molecule) Manual Search
PubMed
(http://www.ncbi.nlm.nih.gov/pubmed/)
UniProt (http://www.uniprot.org)
Gene Name Gene name UniProt (http://www.uniprot.org)
Synonyms Alternate names (protein names, abbreviations, etc.) UniProt (http://www.uniprot.org)
Protein Sequence Amino acid sequence UniProt (http://www.uniprot.org)
GenBank
(http://www.ncbi.nlm.nih.gov/genbank)
Number of Residues Number of amino acids in the protein sequence Automatic
Molecular Weight Molecular weight given in Daltons or g/mol Automatic

(Daltons)
Theoretical pI Theoretical isoelectric point Automatic
GO Classi cation Gene ontology classi cation including function, cellular process and location Gene Ontology
(http://www.geneontology.org/)
Automatic
General Function Short 3-4 word summary of the primary functions UniProt (http://www.uniprot.org)
ProtFun
(http://www.cbs.dtu.dk/services/ProtFun/)
Automatic
Manual Search
Speci c Function Detailed 30-40 word summary of the speci c functions UniProt (http://www.uniprot.org)
Pathways Key pathways or processes (from SMPD) that the given molecule is involved in KEGG (http://www.genome.jp/kegg/)
UniProt (http://www.uniprot.org)
Reaction Reaction(s) that the given molecule participates in UniProt (http://www.uniprot.org)
Pfam Domain Names and ID numbers of PFAM domains UniProt (http://www.uniprot.org)

Function
Signals Location of signal peptide or other localization signals in the sequence UniProt (http://www.uniprot.org)
Automatic
Transmembrane Number and location of the transmembrane helices UniProt (http://www.uniprot.org)

Regions
TMHMM
(http://www.cbs.dtu.dk/services/TMHMM/)
Essentiality Importance or essentialness in terms of the organism's ability to survive without it Manual Search
GenBank ID Protein GenBank protein ID (if it exists) GenBank

GeneCards (http://www.genecards.org/)
UniProt ID/Name UniProt ID (if it exists) UniProt (http://www.uniprot.org)
PDB ID PDB ID (if it exists) PDB (http://www.rcsb.org)
Cellular Location Location of the given protein or macromolecule inside or around the cell (cytoplasm, UniProt (http://www.uniprot.org)
nucleus, membrane, etc.)
Gene Sequence DNA sequence (from cDNA) of the given molecule GeneCards (http://www.genecards.org/)
GenBank ID Gene GenBank database gene identi er and link GenBank

GeneCards (http://www.genecards.org/)
GeneCards ID GeneCards database identi er and link GeneCards (http://www.genecards.org/)
GenAtlas ID GenAtlas database identi er and link GenAtlas (http://genatlas.medecine.univ-

paris5.fr/)
HGNC ID HGNC database identi er and link HGNC (http://www.genenames.org/)
Chromosome Location of the molecule on any of the 23 human chromosomes (no location is given if GeneCards (http://www.genecards.org/)
Location the molecule is bacterial)
Locus More detailed location of the chromosomal position of the gene GeneCards (http://www.genecards.org/)
References Pubmed references PubMed

Automatic
Manual Search
Drug References Speci c references for the given drug association PubMed
Automatic
Manual Search
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2017-6-27 Documentation and Sources - DrugBank

Drug Field Documentation and Sources

Version Entry version Automatic yes yes

DrugBank ID Unique DrugBank accession number Automatic yes yes

SciFinder (http://www.cas.org/products/sci ndr/)

STAT!Ref (AHFS) (http://online.statref.com)

Kingdom Organic or Inorganic Calculated from structure yes yes

Synonyms Alternate names of the drug Manual Search yes yes

SciFinder (http://www.cas.org/products/sci ndr/)

SciFinder (http://www.cas.org/products/sci ndr/)

SciFinder (http://www.cas.org/products/sci ndr/)

SMILES Isomeric SMILES string corresponding to Calculated from structure yes no

InChI Standard InChI identi er Calculated from structure yes no

InChI Key Standard InChI key Calculated from structure yes no

PubChem Substance NCBI's PubChem database subtance PubChem (http://pubchem.ncbi.nlm.nih.gov) yes no

ChemSpider ID ChemSpider identi cation number ChemSpider (http://www.chemspider.com) yes no

BindingDB ID BindingDB identi cation number ChEBI (http://www.ebi.ac.uk/chebi) yes yes

ChEBI ID EBI's Chemicals of Biological Interest ChEBI (http://www.ebi.ac.uk/chebi) yes no

ChEMBL ID ChEMBL identi cation number ChEBI (http://www.ebi.ac.uk/chebi) yes no

Stitch ID Stitch identi cation number PubChem (http://pubchem.ncbi.nlm.nih.gov) yes yes

PharmGKB ID Pharmacogenomics Knowledge Base PharmGKB (http://www.pharmgkb.org) yes yes

UniProt ID/Name UniProt database ID number UniProt (http://www.uniprot.org) no yes

GenBank ID GenBank database ID number GenBank (http://www.ncbi.nlm.nih.gov/genbank) no yes

State Physical state (solid, liquid, gas) MSDS yes yes

Experimental Water Water solubility in mg/mL or g/L MSDS yes yes

Predicted Water Predicted water solubility in mg/mL ALOGPS (http://www.vcclab.org/lab/alogps/) yes no

NIST Chemistry WebBook

Category Therapeutic category or general category of Manual Search yes yes

STAT!Ref (AHFS) (http://online.statref.com)

STAT!Ref (AHFS) (http://online.statref.com)

Indication Description or common names of diseases Manual Search yes yes

SciFinder (http://www.cas.org/products/sci ndr/)

STAT!Ref (AHFS) (http://online.statref.com)

TTD: Therapeutic Target Database

SciFinder (http://www.cas.org/products/sci ndr/)

STAT!Ref (AHFS) (http://online.statref.com)

SciFinder (http://www.cas.org/products/sci ndr/)

STAT!Ref (AHFS) (http://online.statref.com)

STAT!Ref (AHFS) (http://online.statref.com)

STAT!Ref (AHFS) (http://online.statref.com)

STAT!Ref (AHFS) (http://online.statref.com)

STAT!Ref (AHFS) (http://online.statref.com)

STAT!Ref (AHFS) (http://online.statref.com)

Clearance Clearance is a descriptive term used to Manual Search yes yes

Harvard Food-Drug Database

Target/Enzyme/Transporter/Carrier Field Documentation

Gene Name Gene name UniProt (http://www.uniprot.org)

Synonyms Alternate names (protein names, abbreviations, etc.) UniProt (http://www.uniprot.org)

Protein Sequence Amino acid sequence UniProt (http://www.uniprot.org)

Number of Residues Number of amino acids in the protein sequence Automatic

Molecular Weight Molecular weight given in Daltons or g/mol Automatic

Theoretical pI Theoretical isoelectric point Automatic

Field Description Sources

Reaction Reaction(s) that the given molecule participates in UniProt (http://www.uniprot.org)

Pfam Domain Names and ID numbers of PFAM domains UniProt (http://www.uniprot.org)

Transmembrane Number and location of the transmembrane helices UniProt (http://www.uniprot.org)

GenBank ID Protein GenBank protein ID (if it exists) GenBank

UniProt ID/Name UniProt ID (if it exists) UniProt (http://www.uniprot.org)

PDB ID PDB ID (if it exists) PDB (http://www.rcsb.org)

GenBank ID Gene GenBank database gene identi er and link GenBank

GeneCards ID GeneCards database identi er and link GeneCards (http://www.genecards.org/)

GenAtlas ID GenAtlas database identi er and link GenAtlas (http://genatlas.medecine.univ-

HGNC ID HGNC database identi er and link HGNC (http://www.genenames.org/)