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.
As far as I know you can download information about FDA approved drugs from the FDA site (see link below) but all information are in PDF.
However at the second link you could find FDA approved drugs and structures can be downloaded in SDF format.
Kind regards
http://www.accessdata.fda.gov/scripts/cder/daf/
https://pubchem.ncbi.nlm.nih.gov/
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
Dear william, thanks for putting some efforts for creating that add file. It will be definitely useful for me
William Bains, Thats really great to have the approved drugs ibrary . Thanks a lot for it.
But how to know their names and categories??@William Bains
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 so much for your immediate reply. you have really saved my time...
Thanks William for sharing that! Exactly what I was looking for.
If people come to this question in 2021 or later, they can maybe find a more updated version here:
https://www.selleckchem.com/screening/fda-approved-drug-library.html
Or go to selleckchem.com and click until you find their fda approved screening library.
https://chemoinfo.ipmc.cnrs.fr/MOLDB/index.php
see Article Data Sets Representative of the Structures and Experimental ...
https://tripod.nih.gov/npc/
Currently having more than 7000 FDA approved compounds.
It is free and updated daily.
Install it and select criteria according to your need and export file as .tsv(can be opened in excel)
The exported file will have drug name, SMILES and other required information.
SMILES can be converted to SDF or mol or mol2 according to your need using OpenBabel tool.
As Shradheya Raj Rajeshwar Gupta suggested, NCGC Pharm Collection NPC Browser is a pretty useful tool!
Thank you very much Shradheya Gupta for this information. I will try it
https://academic.oup.com/nar/article/46/D1/D1137/4616872
http://cheminfo.charite.de/superdrug2/
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 a lot!
Adarsh Singh Yes, you will find Compounds.tsv file in the zipped folder. For details you can refer ReadMe file.
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.
Direct link to download the 2D structures and basic info of 3035 FDA-approved drugs in sdf format
https://file.selleckchem.com/downloads/library/20220301-L1300-FDA-approved-Drug-Library.SDF
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