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Retrieving details of a drug molecule
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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 browse”. 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 

 

 

 

 

 

 

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