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 find some definitions, and a detailed reference of the sources used for each field.
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 defined 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. This does not mean the drug is currently approved or available, just that it has been approved and marketed at some point, somewhere. Different jurisdictions also have a different concept for "approval". For example drugs that are available over-the-counter in the U.S. may not be technically approved, whereas over-the-counter drugs in Canada are considered approved.
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 confirmed or unconfirmed health benefits)
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Withdrawn
A previously approved drug that has been withdrawn from the market in at least one jurisdiction, at some point in time. Note that because a drug can be approved in one jurisdiction, and withdrawn in another, it's possible for a drug to be in both groups. If a drug has been approved at some point in time, and then withdrawn, it would also be in both drug groups.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 specific proteins in mammals, bacteria, viruses, fungi, or parasites. This includes compounds that are Pre-Investigational New Drug Applications (Pre-IND, or Discovery Phase compounds).
Drug Binding
Each drug can have one or more targets, enzymes, transporters, and carriers associated with it. Here are the definitions 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.
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).
Pharmacological Action
A target is marked with pharmacological action "yes" if the target is directly related to it's clinical mechanism of action. Targets that have a pharmacological action of "no" are considered off-targets, and may be related to side effects or drug interactions. "Unknown" indicates there is not enough evidence, or it has not yet been reviewed.
Guidelines for Cytochrome P-450 Interactions
CYP Substrate Sensitivity:
- >5 fold change in AUC with index strong inhibitor = sensitive
- 2 - 5 fold = moderate sensitivity
- <2 fold = not sensitive
CYP Inhibitor Strength:
- >5 fold change in AUC for index sensitive substrate = strong
- 2 - 5 fold = moderate
- 1.25 - 2 = weak
- <1.25 = no significant inhibition
CYP Inducer Strength:
- >80% reduction in AUC for index sensitive substrate = strong
- 50-80% reduction = moderate
- 20-50% reduction = weak
- <20% = no significant inducement
Drug Field Documentation and Sources
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 |
| yes | yes |
| Creation Date | Date/time the entry was created |
| yes | yes |
| Update Date | Date/time the entry was last updated |
| 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. |
| 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). |
| yes | yes |
| Name | Standard name of drug as provided by drug manufacturer | yes | yes | |
| Type | Can be one of Small molecule or Biotech (see definition list in introduction). |
| yes | yes |
| Groups | Can be one or more of: Approved, Vet approved, Nutraceutical, Illicit, Withdrawn, Investigational, and Experimental. (see definition list in introduction) |
| yes | yes |
| Description | Description of the drug describing general facts, composition and/or preparation. | yes | yes | |
| Kingdom | Organic or Inorganic |
| yes | yes |
| Classes | Drug classes form the major component of the classification system. Drugs with the same class are considered structurally similar. |
| 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. |
| 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 | Drug patents for the given drug | yes | yes | |
| Chemical IUPAC Name | IUPAC or standard chemical name for the drug |
| yes | no |
| Chemical Formula | Chemical formula describing atomic or elemental composition |
| yes | yes |
| Average Molecular Weight | Molecular weight in g/mol, determined from molecular formula or sequence |
| 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. |
| 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 |
| yes | no |
| InChI | Standard InChI identifier |
| yes | no |
| InChI Key | Standard InChI key |
| 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 | 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 |
| yes | no |
| Predicted LogS | Predicted LogS (water solubility) |
| 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, etc.) | 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 |
|
| Molecular Weight (Daltons) | Molecular weight given in Daltons or g/mol |
|
| Theoretical pI | Theoretical isoelectric point |
|
| 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 |
|
| 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 | |
| References | Pubmed references |
|
| Drug References | Specific references for the given drug association |
|