Can anyone please tell me from where I can download all FDA approved drugs in SDF format or in smileys format? I have used drug bank and found majority of the approved drugs are not included in their list.
Target Molecule Inc have a list. I do not know how complete it is, I have not checked it against the FDA's own web site. I have converted this to an SDF file (attached). Does this help? William
As mentioned, the list was generated from a company (Target Molecule Inc) list of compounds, so that is all there is. Selek also have a list of FDA approved drugs which you can download here https://file.selleckchem.com/downloads/library/20200113-L1300-FDA-approved-Drug-Library.sdf . This includes the molecular target, but not the drug class or therapeutic category. Sorry.
Thank you Shradheya Raj Rajeshwar Gupta for your database, it actually seems very helpful. One question, did you put together any csv/tsv/xls file having the name of drugs in those SDF file. I can extract names for SDF file itself, but it contains only Pubchem names, not general names. For ex: I need Velptasvir, methyl N-[(1R)-2-[(2S,4S)-2-[5-[6-[(2S,5S)-1-[(2S)-2-(methoxycarbonylamino)-3-methylbutanoyl]-5-methylpyrrolidin-2-yl]-21-oxa-5,7-diazapentacyclo[11.8.0.03,11.04,8.014,19]henicosa-1(13),2,4(8),5,9,11,14(19),15,17-nonaen-17-yl]-1H-imidazol-2-yl]-4-(methoxymethyl)pyrrolidin-1-yl]-2-oxo-1-phenylethyl]carbamate (Pubchem IUPAC name).
Or any other suggestions to achieve what I intend to?
Thanks for your quick response, Shradheya Raj Rajeshwar Gupta
In Compound.tsv file, I couldn't any such column, I could see these columns only:
1 - BABEL_SMILES
2 - PUBCHEM_CID
3 - PUBCHEM_IUPAC_CAS_NAME
4 - PUBCHEM_IUPAC_TRADITIONAL_NAME
5 - PUBCHEM_OPENEYE_CAN_SMILES
6 - PUBCHEM_OPENEYE_ISO_SMILES
7 - PUBCHEM_IUPAC_INCHI
8 - PUBCHEM_IUPAC_INCHIKEY
I think what I am asking is if there is any way to get common names corresponding to IUPAC names? One more thing, the number of entries in the CSV file (16748) does not match with the number of SDF (14552) files. Can you clarify this?
Also, is this database dereplicated? that is, are all 14k approved drugs unique?
Adarsh Singh Within the current available sets common names are not provided.
Yes, there are some replicated entries in TSV file, in the coming version I will try to remove them. SDF's are unique. If you find more scope of improvement do comment, I will work on it.