PDBsum entry 4lyh

Signaling protein/inhibitor

PDB id: 4lyh

Contents

Protein chains

163 a.a.

Ligands

SO4 ×2

GDP ×3

21F ×2

Waters ×389

References listed in PDB file

Key reference

• Title: K-Ras(g12c) inhibitors allosterically control gtp affinity and effector interactions.
• Authors: J.M.Ostrem, U.Peters, M.L.Sos, J.A.Wells, K.M.Shokat.
• Ref.: Nature, 2013, 503, 548-551. [DOI no: 10.1038/nature12796]
• PubMed id: 24256730

Abstract

Somatic mutations in the small GTPase K-Ras are the most common activating lesions found in human cancer, and are generally associated with poor response to standard therapies. Efforts to target this oncogene directly have faced difficulties owing to its picomolar affinity for GTP/GDP and the absence of known allosteric regulatory sites. Oncogenic mutations result in functional activation of Ras family proteins by impairing GTP hydrolysis. With diminished regulation by GTPase activity, the nucleotide state of Ras becomes more dependent on relative nucleotide affinity and concentration. This gives GTP an advantage over GDP and increases the proportion of active GTP-bound Ras. Here we report the development of small molecules that irreversibly bind to a common oncogenic mutant, K-Ras(G12C). These compounds rely on the mutant cysteine for binding and therefore do not affect the wild-type protein. Crystallographic studies reveal the formation of a new pocket that is not apparent in previous structures of Ras, beneath the effector binding switch-II region. Binding of these inhibitors to K-Ras(G12C) disrupts both switch-I and switch-II, subverting the native nucleotide preference to favour GDP over GTP and impairing binding to Raf. Our data provide structure-based validation of a new allosteric regulatory site on Ras that is targetable in a mutant-specific manner.