How do small, drug-like molecules interact with my protein?

After building a basic idea of your protein’s druggability, the next step is to explore known, and characterised interactions between small molecules and your protein.

As you have seen in ChEMBL so far, there may be a good amount of data available from bioassays and other binding assays to indicate chemicals that may bind your protein, but delving into this data further can give greater insight into binding affinities, effective doses, and other properties. This can help you decide on particular molecules, or groups of molecules, that might have the best effect.

To support this data, you can explore what information is available about your protein of interest using your protein’s Uniprot entry as a start point, then continue exploring by identifying what structures are available in the PDBe. Rather than simply considering availability of structure data on the protein, here you should be looking for structures where both a ligand/chemical has been co-crystallised with your protein. Using the molecular viewer tools at PDBe you can start to better understand the binding position of different molecules with your protein, possibly connecting this to bioassay data in ChEMBL to rank compounds based on structural position and binding affinity.

Complete this section to learn how you can use UniProt and PDBe to learn more about your protein of interest.