PDBsum entry 4g2f

Transferase/transferase inhibitor

PDB id: 4g2f

Contents

Protein chain

275 a.a.

Ligands

C07

Waters ×225

References listed in PDB file

Key reference

• Title: Discovery of a novel chemotype of tyrosine kinase inhibitors by fragment-Based docking and molecular dynamics.
• Authors: H.Zhao, J.Dong, K.Lafleur, C.Nevado, A.Caflisch.
• Ref.: Acs Med Chem Lett, 2012, 3, 834-838. [DOI no: 10.1021/ml3001984]
• PubMed id: 24900387

Abstract

We have discovered a novel chemical class of inhibitors of the EphB4 tyrosine kinase by fragment-based high-throughput docking followed by explicit solvent molecular dynamics simulations for assessment of the binding mode. The synthesis of a single derivative (compound 7) of the hit identified in silico has resulted in an improvement of the inhibitory potency in an enzymatic assay from 8.4 μM to 160 nM and a ligand efficiency of 0.39 kcal/mol per non-hydrogen atom. Such remarkable improvement in affinity is due to an additional hydroxyl group involved in two favorable (buried) hydrogen bonds as predicted by molecular dynamics and validated by the crystal structure of the complex with EphA3 solved at 1.7 Å resolution.