The distribution of ligand-binding pockets around protein-protein interfaces suggests a general mechanism for pocket formation.

ABSTRACT: Protein-protein and protein-ligand interactions are ubiquitous in a biological cell. Here, we report a comprehensive study of the distribution of protein-ligand interaction sites, namely ligand-binding pockets, around protein-protein interfaces where protein-protein interactions occur. We inspected a representative set of 1,611 representative protein-protein complexes and identified pockets with a potential for binding small molecule ligands. The majority of these pockets are within a 6 Å distance from protein interfaces. Accordingly, in about half of ligand-bound protein-protein complexes, amino acids from both sides of a protein interface are involved in direct contacts with at least one ligand. Statistically, ligands are closer to a protein-protein interface than a random surface patch

SUBMITTER: Gao M 

PROVIDER: S-EPMC3309739 | biostudies-literature | 2012 Mar

REPOSITORIES: biostudies-literature