How do I find a list of PDB structures bound to a peptide inhibitor or peptide-like inhibitor?

Question

I looked up existing databases but ones like iPPI-DB or enter link description here either provide non-peptide inhibitors or only sequences. I need structures of proteins bound to other proteins, the latter of which is an inhibitor of the former, and the complex has a structure deposited in the PDB database. Here's an example: PDB:3U1J

In case there is no existing database in literature, it'd be great even if I can screen for such PDB entries using some code, but I can't come up with an algorithm for it. Thank you!

Welcome to the site @simple_dozer! I'm not sure if there is a code name to know if a protein is an inhibitor, but you can start by subsetting all the structures with at least two genes — llrs, May 28 '18 at 15:00

score 1 · Answer 1 · answered May 28 '18 at 16:26

The quickest way to screen the PDB database is Advanced Search from either RCSB or PDBe.

Since you need entries with 2+ proteins you can set the number of protein chains to at least 2 in the RCSB search. Or you can select "protein/protein complex" in Assembly composition in the PDBe search.

It's less clear how to search for inhibitors. If you'd look for the "inhibitor" word in the molecule names you'd get (together with the previous criterium) 1200+ entries.

How do I find a list of PDB structures bound to a peptide inhibitor or peptide-like inhibitor?

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