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Documentation and Sources

Introduction to DrugBank

DrugBank is a detailed database on small molecule and biotech drugs. Each drug entry ("DrugCard") extensive information on properties, structure, and biology (what the drug does in the body). Each drug can have 1 or more targets, enzymes, transporters, and carriers associated. Below is a quick definition list to get you started.

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Cytochrome P450 enzymes
Small Molecule Drug
A drug from largely synthetic origins, typically under 1000 MW, however there are some exceptions (for example, Ivermectin)
Biotech Drug
Drugs which are peptide, protein or nucleic acid drugs
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.
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 specifically target transporters, and in this case a transporter can also be the target (for example: Procaine targeting the Sodium-dependent dopamine transporter).

Drug Field Documentation and Sources

Hint Data sources indicate the source of the information present in each field. Data sources do not indicate that all sources were used for a particular field and drug. Individual drug reference information can be found in the "General References" section of each drug.

Field Description Sources Small 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
DrugBank ID (Primary Accession Number) Unique DrugBank accession number consisting of a 2 letter prefix (DB) and a 5 number suffix. 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.
  • Automatic
 yes yes
Secondary Accession Number DrugBank release 1.0 accession number consisting of the 4 letter prefix and a 5 number suffix. Each Accession number is unique to the drug's generic name. The 4 letter suffix (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).
  • Automatic
 yes yes
Name Standard name of drug as provided by drug manufacturer yes yes
Type Small molecule or Biotech. Small molecule drugs are drugs which are not from biological origin and are synthesized. Biotech drugs consist of peptide, protein or nucleic acid drugs.
  • Manual Search
 yes yes
Groups Can be one or more of:
  • Approved — Drug has been approved in at least one country
  • Experimental — Drug has been shown experimentally to bind specific proteins in mammals, bacteria, viruses, fungi, or parasites. An experimental drug is not necessarily being formally investigated
  • Nutraceutical — Drug is a food product which has experimentally confirmed health benefits
  • Illicit — Drug is a scheduled drug in at least one country
  • Withdrawn — Drug has been removed from the market by a manufacturer in at least one country
A drug can be approved and withdrawn at the same time if it is still available commercially in one country while pulled in another country. Typically the Description field will contain further details.
  • Manual Search
 yes yes
Description Description of the drug describing general facts, composition and/or preparation. yes yes
Kingdom Organic or Inorganic
  • Calculated from <a href="#drug_structure">structure</a>
 yes yes
Classes Drug classes form the major component of the classification system. Drugs with the same class are considered structurally similar.
  • Calculated from <a href="#drug_structure">structure</a>
 yes yes
Substructures and Functional Groups All substructures and functional groups calculated from the structure for the drug. This is a superset of the Classes.
  • Calculated from <a href="#drug_structure">structure</a>
 yes yes
Synonyms Alternate names of the drug yes yes
Brand Names Brand names from different manufacturers yes yes
Brand Mixtures Brand names and composition of mixtures that include the given drug yes yes
Manufacturers Companies known to manufacturer the given drug yes yes
Packaging Companies Companies which package and sell the given drug yes yes
Prices Unit cost drug prices in U.S. dollars yes yes
Patents The first and last drug patent, including approval and expiry dates yes yes
Chemical IUPAC Name IUPAC or standard chemical name for the drug
  • Calculated from <a href="#drug_structure">structure</a>
 yes no
Chemical Formula Chemical formula describing atomic or elemental composition
  • Calculated from <a href="#drug_structure">structure</a>
 yes yes
Average Molecular Weight Molecular weight in g/mol, determined from molecular formula or sequence
  • Calculated from <a href="#drug_structure">structure</a>
 yes yes
Monoisotopic Molecular Weight The sum of the masses of the atoms in a molecule using the unbound, ground-state, rest mass of the principle (most abundant) isotope for each element instead of the isotopic average mass.
  • Calculated from <a href="#drug_structure">structure</a>
 yes no
Structure For small molecule drugs, the 2D chemical 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 in the structure viewer. 		yes yes
SMILES Isomeric SMILES string corresponding to drug structure
  • Calculated from <a href="#drug_structure">structure</a>
 yes no
InChI Standard InChI identifier
  • Calculated from <a href="#drug_structure">structure</a>
 yes no
InChI Key Standard InChI key
  • Calculated from <a href="#drug_structure">structure</a>
 yes no
CAS Registry Number Chemical Abstract Service identification number yes yes
KEGG Drug ID Kyoto Encyclopedia of Genes and Genomes drug identification number (if molecule is in KEGG) yes yes
KEGG Compound ID Kyoto Encyclopedia of Genes and Genomes compound identification number (if molecule is in KEGG) yes yes
PubChem Compound ID NCBI's PubChem database compound identification number yes yes
PubChem Substance ID NCBI's PubChem database subtance identification number
  • PubChem
  • Calculated from <a href="#drug_structure">structure</a>
 yes no
ChemSpider ID ChemSpider identification number yes no
BindingDB ID BindingDB identification number yes yes
ChEBI ID EBI's Chemicals of Biological Interest identification number (if drug is in ChEBI) yes no
ChEMBL ID ChEMBL identification number yes no
Stitch ID Stitch identification number yes yes
Therapeutic Targets Database (TTD) ID Therapeutic Targets Database identification number yes yes
PharmGKB ID Pharmacogenomics Knowledge Base identification number (if molecule is in PharmGKB) yes yes
HET ID PDB identificatin number (if molecule is in PDB, ChemPDB or Ligand Depot) yes no
UniProt ID/Name UniProt database ID number no yes
GenBank ID GenBank database ID number no yes
Drug Product ID Drug Product Database Drug Identification Number yes yes
RxList Link Link to RxList entry for the given drug (if it exists) yes yes
Drugs.com Link Link to Drugs.com for the given drug (if it exists) yes yes
PDRhealth Link Link to PDRhealth entry for the given drug (if it exists) yes yes
Wikipedia Link Link to Wikipedia entry for the given drug (if it exists) yes yes
FDA Label Food and Drug Administration approval label (if it exists) yes yes
Material Safety Data Sheet Material Safety Data Sheet (MSDS) (if it exists) yes yes
Synthesis Reference Reference or patent number to description of drug's synthesis yes yes
State Physical state (solid, liquid, gas) yes yes
Melting Point Melting point in degrees Celsius yes yes
Boiling Point Boiling point in degrees Celsius yes yes
Experimental Water Solubility Water solubility in mg/mL or g/L yes yes
Predicted Water Solubility Predicted water solubility in mg/mL yes no
Experimental LogP/Hydrophobicity Water/octanol partition coefficient (if small molecule) or hydrophobicity score (Gravy score) if protein/peptide yes yes
Predicted LogP/Hydrophobicity Predicted water/octanol partition coefficient
  • Calculated from <a href="#drug_structure">structure</a>
 yes no
Predicted LogS Predicted LogS (water solubility)
  • Calculated from <a href="#drug_structure">structure</a>
 yes no
Experimental LogS Experimental LogS (water solubility) yes yes
Experimental Caco2 Permeability Caco-2 permeability coefficients yes yes
pKa/Isoelectric Point Dissociation constant (pKa) if small molecule, pH at which protein has no charge (if protein drug) yes yes
Mass Spectrum Image of EI Mass Spectrum of drug (if it exists) yes no
Experimental PDB Entries PDB identification number if structure of drug exists in PDB yes yes
Category Therapeutic category or general category of drug (anti-convulsant, antibacterial, etc.) yes yes
ATC Codes WHO drug classification system (ATC) identifiers yes yes
AHFS Codes AHFS Drug Information identifiers yes yes
Indication Description or common names of diseases that the drug is used to treat yes yes
Pharmacodynamics Description of how the drug works at a clinical or physiological level yes yes
Mechanism of Action Description of how the drug works or what it binds to at a molecular level yes yes
Absorption Description of how much of the drug or how readily the drug is taken up by the body yes yes
Toxicity Lethal dose (LD50) values from test animals, description of side effects and toxic effects seen in humans yes yes
Protein Binding Percentage of the drug that is bound in plasma proteins yes yes
Metabolism Mechanism by which or organ location where the drug is neutralized yes yes
Half Life Half life of drug in body, measured in hours or days yes yes
Route of Elimination Route by which the drug is eliminated. Drugs are cleared primarily by the liver and kidneys. yes yes
Volume of Distribution The apparent volume of distribution is the theoretical volume of fluid into which the total drug administered would have to be diluted to produce the concentration in plasma yes yes
Clearance Clearance is a descriptive term used to evaluate efficiency of drug removal from the body yes yes
Dosage Forms How the drug is dispensed (tablets, capsules, solutions) yes yes
Patient Information Information on how the drug should and shouldn't be used yes yes
Contraindications Cautions or conditions indicating why or when the drug should not be taken yes yes
Drug Interactions Drugs that are known to interact, interfere or cause adverse reactions when taken with this drug yes yes
Food Interactions Foods that are known to interact, interfere or cause adverse reactions when taken with this drug yes yes
Pathways Drug pathways in which the given drug is involved yes yes
Organisms Affected Names of organisms for which the drug is most effective yes yes
General References General on-line reference to other details about the drug yes yes

Target/Enzyme/Transporter/Carrier Field Documentation

Field Description Sources
Name Name of the protein or macromolecule (or other small molecule)
Gene Name Gene name
Synonyms Alternate names (protein names, abbreviations, etc.)
Protein Sequence Amino acid sequence
Number of Residues Number of amino acids in the protein sequence
  • Automatic
Molecular Weight (Daltons) Molecular weight given in Daltons or g/mol
  • Automatic
Theoretical pI Theoretical isoelectric point
  • Automatic
GO Classification Gene ontology classification including function, cellular process and location
General Function Short 3-4 word summary of the primary functions
Specific Function Detailed 30-40 word summary of the specific functions
Pathways Key pathways or processes (from SMPD) that the given molecule is involved in
Reaction Reaction(s) that the given molecule participates in
Pfam Domain Function Names and ID numbers of PFAM domains
Signals Location of signal peptide or other localization signals in the sequence
Transmembrane Regions Number and location of the transmembrane helices
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)
UniProt ID/Name UniProt ID (if it exists)
PDB ID PDB ID (if it exists)
Cellular Location Location of the given protein or macromolecule inside or around the cell (cytoplasm, nucleus, membrane, etc.)
Gene Sequence DNA sequence (from cDNA) of the given molecule
GenBank ID Gene GenBank database gene identifier and link
GeneCards ID GeneCards database identifier and link
GenAtlas ID GenAtlas database identifier and link
HGNC ID HGNC database identifier and link
Chromosome Location Location of the molecule on any of the 23 human chromosomes (no location is given if the molecule is bacterial)
Locus More detailed location of the chromosomal position of the gene
SNPs Link to SNPJam, an in-house tool used to profile SNPs for the given molecule gene
References Pubmed references
  • PubMed
  • Automatic
  • Manual Search
Drug References Specific references for the given drug association
  • PubMed
  • Automatic
  • Manual Search