Are protein-ligand complexes robust structures?

The predominant view in structure-based drug design is that small-molecule ligands, once bound to their target structures, display a well-defined binding mode. While this is convenient from a design perspective, it ignores the fact that structural stability (robustness) is not necessary for thermodynamic stability (binding affinity). In fact, any potential benefit of a rigid binding mode will have to be balanced against the entropic penalty that it entails. Surprisingly, little is known about the causes, consequences and real degree of robustness of protein-ligand complexes. Here we investigate two diverse sets of structures, comprising 79 drug-like and 27 fragment ligands, respectively. We focus on hydrogen bond interactions (469 in total), as they have been described as essential for structural stability. We find that 75% of complexes are anchored by at least one robust hydrogen bond, the remaining 25% either form loose complexes or are constrained by other interactions types. The first type of complexes generally combine a single anchoring point with looser regions, thus balancing order and disorder. Completely constricted protein-ligand complexes are rare and seem to fulfil a functional necessity. Structural stability analysis reveals a hidden layer of complexity in protein-ligand complexes that should be considered in ligand design.