Hi,

I couldn't understand what exactly you want - ligands or binding pockets in proteins?

If you want to determine ligands for your proteins, you can use RCSB PDB where you can simply put in your query protein and find out the small ligands which are compatible with your protein.

or,

If you want to find out the binding pockets in your protein where your ligand can bind, you please use the following tools:-

i) 3DLigandSite

ii) COACH

iii) COFACTOR

I hope my answer was helpful.

Best regards,

If I understand you correctly, you have a ligand and you are looking for a database where you can find a library of small molecules with similar structures?

If that is the case, try Zinc database.

http://zinc.docking.org/

Input the smiles code of the ligand or the chemical/generic name. Do a similarity search using the vast search tools available on that website.

Hi

you can search in this site the section of databases (https://www.click2drug.org/) or specifically here (https://www.click2drug.org/directory_SmallMoleculesDatabase.html)

Here you can find several of the most used databases.

Best wishes

You can use PDB (Protein Data Bank).

you can find detailed information from here : http://autodock.scripps.edu/faqs-help/how-to/how-to-prepare-a-ligand-file-for-autodock4

use this servers:

pubchem, zinc15, sigma, chemspider, enhanced nci, ch ebi