Objective:
To retrieve more information about the drug molecules, drug targets,enzymes and pathways related to drugs.
Theory:
Drug is a chemical molecule that can interact and bind to a target and control the function biological receptors to control the disease. Proteins are the important biological receptors which interact with the other biological molecules to maintain various cellular functions. Drugs have a specific activity that goes and binds to the target and can activate/inhibit the reactions in a proper manner. To find more about the drug molecules, their target molecules and the drug enzymatic reactions and the drug involvement in a specific pathway can easily found using different databases like Drugbank.
Drugbank is a freely accessible, web enabled, fully query based database. It contains a data like structure and activity of a drugs and structure/function/sequence of a protein molecule. Drugbank is unique bioinformatics and chemiinformatics database, having the details of drug molecules and their target molecules. It gives well developed concepts search and also comparisons from medicinal chemistry. Database will be updated by semi-annually.
Drugbank database contains 6711 drug entries. It includes 1447 FDA-approved small drugs, 131 FDA-approved protein/peptide drugs, 85 nutraceuticals and 5080 experimental drugs. Additionally, 4227 non-redundant protein sequences are linked to these drug entries.
Each DrugCard entry contains more than 150 data fields with half of the information being devoted to drug/chemical data and the other half devoted to drug target or protein data.
Searching through drug bank can also be supported with the help of logical operators. Keeping the query word in quotes can help to search exact match, in a search by giving “acetic acid†will allow search for only “acetic acid†and not its similar matches. Another type of search can be done by using wild cards is by giving * with the query word, the result would be hits which starts with the query word.
In Drugbank browse option one can get the drug molecules by using “Drug browseâ€ÂÂ. It allows the user to get all the drug molecules which has been stored in the database by alphabetically with an information like Drugbank ID, CAS number, Molecular weight, Structure, Categeories, Therapeutic indication. “Pharma browse “ allows the user to find the drug molecules by categeory wise. Geno browse gives the chemical molecules with Drug name, with which enzyme it is going to bind, SNPs, all the adverse reactions and references belongs to the Drug molecule. “pathway Browse†allows one to search the pathway which is going to affect by the drug molecule. “Class Browse†allows one to search the drug classes by names. “Association browse†allows user to find the name of the drug, Genename , which species it belongs and its specific function.
Drug bank gives the details about the drugs with information like :
Table 1: Information regarding Drugs.
Generic Name |
name |
DrugBank ID |
drugbank_id |
AHFS Code |
ahfs_code |
ATC Code |
atc_code |
Absorption |
absorption |
Affected Organisms |
organism |
Chemical Formula |
formula |
Chemical IUPAC Name |
iupac |
Clearance |
clearance |
DPD ID (DIN) |
dpd_id |
Description |
description |
Dosage Form |
dosage_form |
Dosage Route |
dosage_route |
Drug Group |
group |
Drug Type |
type |
Drug-Food Interaction |
food_interaction |
Genbank ID |
genbank_id |
Guide to Pharmacology ID |
guide_to_pharmacology_id |
H2O Solubility (experimental |
experimental_water_solubility |
HET ID |
het_id |
Brands |
brand |
CAS Number |
cas_number |
Caco2 Permeability (experimental) |
experimental_caco2_permeability |
Category |
category |
ChEBI ID |
chebi_id |
Half Life |
half_life |
ID |
id |
IUPHAR ID |
iuphar_id |
InChI Identifier |
inchi |
InChI Key |
inchikey |
Indication |
indication |
KEGG Compound ID |
kegg_compound_id |
KEGG Drug ID |
kegg_drug_id |
LogP (experimental) |
experimental_logp |
LogP (predicted) |
predicted_logp |
LogS (experimental) |
experimental_logs |
LogS (predicted) |
predicted_logs |
Mechanism of Action |
mechanism_of_action |
Melting Point (°C) |
melting_point |
Metabolism |
metabolism |
Mixture Brand Names |
mixture_name |
Mixture Ingredients |
mixture_ingredient |
Molecular Weight (average) |
average_mass |
PDB ID |
pdb_id |
PDRhealth Link |
pdrhealth_link |
Pathway SMPDB ID |
pathway_smpdb_id |
Pathways |
pathway_name |
PharmGKB ID |
pharmgkb_id |
Pharmacodynamics |
pharmacodynamics |
Protein Binding |
protein_binding |
PubChem Compound ID |
pubchem_compound_id |
Route of Elimination |
route_of_elimination |
RxList Link |
rxlist_link |
SMILES |
smiles |
Secondary Accession Number |
secondary_id |
State |
state |
Synonyms |
synonym |
Target ID |
target_id |
Toxicity |
toxicity |
pKa/Isoelectric Point |
pka_isoelectric_point |
UniProt Name |
uniprot_name |
UniProt ID |
uniprot_id |
Wikipedia Link |
wikipedia_link |