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The drug and drug target mapping tool shows the top 3 PDB IDs for each drug based on the drug target sequence similarity search and ligand id search. Is there a way to get all the PDB ids of the drug-target PDB files and not only the top 3?

I know you can get this information after clicking the "find" button under the last column of the output table (the column named "All PDB"), but I have a query of several hundreds of drugs and I'm not willing to do it manually for each result.

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Simpler option would be to not use the query interface and directly parse the CSV file found on that page.

I just read @llrs comment and I guess it's very much the same spirit as my own - download the data and query it programmatically. I see now (was on mobile earlier) that the 'FIND' URL links out to a BLAST search. so it might be as easy as retrieving the relevant protein sequence and replicating the URL. Or if you want to go a different route and finding all PDB identifiers with the given ligand, cross-reference the above data with what you'd find here

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