How to obtain all PDB IDs containing similar binding sites with a specific ligand

Question

[antoniaa]

Hi. I need to obtain all PDB IDs containing similar binding residues/sites for a specific ligand. Do you recommend any program/server/software to do that? Thank you!

Answer 1

[Jiyao Wang]

Here are some thoughts to share. First, you need to find all structures containing the ligand. You can either search in PDB web site, or use NCBI elink with PubChem CID for this ligand (E.g., https://www.ncbi.nlm.nih.gov/structure?linkname=pccompound_structure&from_uid=439454 for NAG). Then you can use iCn3D Node.js script such as "ligand.js" (https://github.com/ncbi/icn3d/blob/master/icn3dnode/ligand.js) to get the interacting residues for all structures to do further analysis.

[antoniaa]

Thank you for your answer Dr. Jiyao. Indeed, I got all structures that are bounded my ligand of interest. Here my problem is I have more than 2000 proteins. Therefore, I am really struggling to classify them based on their binding site similarity. Here, I need to reliable tool which can serve all PDB IDs having similar binding sites when I give a reference ligand bound protein. I prefer a tool that classifies the proteins based on their RMSDs.