PDBsum entry 3ukr

Structural protein

PDB id: 3ukr

Contents

Protein chains

401 a.a.

193 a.a.

349 a.a.

282 a.a.

173 a.a.

167 a.a.

136 a.a.

Ligands

CKH

Waters ×221

References listed in PDB file

Key reference

• Title: Structural characterization and computer-Aided optimization of a small-Molecule inhibitor of the arp2/3 complex, A key regulator of the actin cytoskeleton.
• Authors: A.W.Baggett, Z.Cournia, M.S.Han, G.Patargias, A.C.Glass, S.Y.Liu, B.J.Nolen.
• Ref.: Chemmedchem, 2012, 7, 1286-1294.
• PubMed id: 22623398

Abstract

CK-666 (1) is a recently discovered small-molecule inhibitor of the actin-related protein 2/3 (Arp2/3) complex, a key actin cytoskeleton regulator with roles in bacterial pathogenesis and cancer cell motility. Although 1 is commercially available, the crystal structure of Arp2/3 complex with 1 bound has not been reported, making its mechanism of action uncertain. Furthermore, its relatively low potency increases its potential for off-target effects in vivo, complicating interpretation of its influence in cell biological studies and precluding its clinical use. Herein we report the crystal structure of 1 bound to Arp2/3 complex, which reveals that 1 binds between the Arp2 and Arp3 subunits to stabilize the inactive conformation of the complex. Based on the crystal structure, we used computational docking and free-energy perturbation calculations of monosubstituted derivatives of 1 to guide optimization efforts. Biochemical assays of ten newly synthesized compounds led to the identification of compound 2, which exhibits a threefold increase in inhibitory activity in vitro relative to 1. In addition, our computational analyses unveiled a surface groove at the interface of the Arp2 and Arp3 subunits that can be exploited for additional structure-based optimization.