5VBM

Crystal Structure of Small Molecule Disulfide 2C07 Bound to K-Ras Cys Light M72C GDP

Summary for 5VBM

• Entry DOI: 10.2210/pdb5vbm/pdb
• Related: 5VBE
• Descriptor: GTPase KRas, MAGNESIUM ION, GUANOSINE-5'-DIPHOSPHATE, ... (5 entities in total)
• Functional Keywords: gtpase, inhibitor, gdp, hydrolase
• Biological source: Homo sapiens (Human)
• Total number of polymer chains: 1
• Total formula weight: 20105.52

Authors

Gentile, D.R.,Jenkins, M.L.,Moss, S.M.,Burke, J.E.,Shokat, K.M. (deposition date: 2017-03-29, release date: 2017-10-25, Last modification date: 2023-10-04)

Primary citation

Gentile, D.R.,Rathinaswamy, M.K.,Jenkins, M.L.,Moss, S.M.,Siempelkamp, B.D.,Renslo, A.R.,Burke, J.E.,Shokat, K.M.
Ras Binder Induces a Modified Switch-II Pocket in GTP and GDP States.
Cell Chem Biol, 24:1455-1466.e14, 2017

PubMed Abstract: Covalent inhibitors of K-Ras(G12C) have been reported that exclusively recognize the GDP state. Here, we utilize disulfide tethering of a non-natural cysteine (K-Ras(M72C)) to identify a new switch-II pocket (S-IIP) binding ligand (2C07) that engages the active GTP state. Co-crystal structures of 2C07 bound to H-Ras(M72C) reveal binding in a cryptic groove we term S-IIG. In the GppNHp state, 2C07 binding to a modified S-IIP pushes switch I away from the nucleotide, breaking the network of polar contacts essential for adopting the canonical GTP state. Biochemical studies show that 2C07 alters nucleotide preference and inhibits SOS binding and catalyzed nucleotide exchange. 2C07 was converted to irreversible covalent analogs, which target both nucleotide states, inhibit PI3K activation in vitro, and function as occupancy probes to detect reversible engagement in competition assays. Targeting both nucleotide states opens the possibility of inhibiting oncogenic mutants of Ras, which exist predominantly in the GTP state in cells.

PubMed: 29033317
DOI: 10.1016/j.chembiol.2017.08.025

Experimental method

X-RAY DIFFRACTION (1.49 Å)