Good binding site

There is a whole literature on the druggability of binding sites. Different people mean different things when they say "druggable". Here we discuss what makes a good binding site for docking small molecules, and thus, by extension, in our view, a site for which one can hope to find a low micromolar or better ligand

• site is deeply invaginated. Should hold a napthelene equivalent amount of ligand mass away from solvent

• protein-protein binding sites are a problem - they often are not deeply invaginated enough for tight small molecule docking

• sites with highly flexible loops, termini can be problems

• sites on the interface of two domains, or at a flexible hinge region, can be problematic