Pocketome: an encyclopedia of small-molecule binding sites in 4D

Abstract

The importance of binding site plasticity in protein-ligand interactions is well-recognized, and so are the difficulties in predicting the nature and the degree of this plasticity by computational means. To assist in understanding the flexible protein-ligand interactions, we constructed the Pocketome, an encyclopedia of about one thousand experimentally solved conformational ensembles of druggable binding sites in proteins, grouped by location and consistent chain/cofactor composition. The multiplicity of pockets within the ensembles adds an extra, fourth dimension to the Pocketome entry data. Within each ensemble, the pockets were carefully classified by the degree of their pairwise similarity and compatibility with different ligands. The core of the Pocketome is derived regularly and automatically from the current releases of the Protein Data Bank and the Uniprot Knowledgebase; this core is complemented by entries built from manually provided seed ligand locations. The Pocketome website (www.pocketome.org) allows searching for the sites of interest, analysis of conformational clusters, important residues, binding compatibility matrices and interactive visualization of the ensembles using the ActiveICM web browser plugin. The Pocketome collection can be used to build multi-conformational docking and 3D activity models as well as to design cross-docking and virtual ligand screening benchmarks.

Figure 1.

Pocketome data flow. The central part of the pipeline is the siteFinder algorithm. The input for it is generated automatically (by joining several major external databases) or manually. The output of the siteFinder utility in the form of tagged 3D ensembles forms the core of the Pocketome encyclopedia.

Figure 2.

Summary of a single Pocketome page content exemplified by the entry for adenosine A_2A receptor. The snapshots were made in August 2011, when four structures of this protein with various modulators were available in PDB (29–31). (A) Summary information: binding site composition (a single polypeptide chain, A1, representing the Uniprot entry AA2AR_HUMAN), list of binding site residues, full PDB list with links. (B) Pocket contact map allows quick identification of conserved (e.g. F168) or ligand-specific (e.g. C185 for NECA, PDB 2ydv) residue contacts; site contact map highlights in red the residues that require significant rearrangement to accommodate at least one of the ligands. (C) Pairwise pocket comparison: the conformation from a co-crystal with agonist UK-432097 (PDB 3eml) is significantly different from the other three, giving rise to two sterically distinct clusters. (D) A snapshot of the ActiveICM ensemble visualization window: NECA-bound conformation appears sterically incompatible with UK-432097 because of multiple rearrangements in the extracellular part of the protein; clashing residues highlighted in the site contact map in panel (B) are shown as transparent red spheres.