SMTL ID : 9dmm.1

Crystal structure of human KRAS G12C covalently bound to Divarasib (GDC6036)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.90 Å

Oligo State

monomer

Ligands

1 x 01: 1-{(3S)-4-[(7M)-7-[6-amino-4-methyl-3-(trifluoromethyl)pyridin-2-yl]-6-chloro-8-fluoro-2-{[(2S)-1-methylpyrrolidin-2-yl]methoxy}quinazolin-4-yl]-3-methylpiperazin-1-yl}propan-1-one

01.1: 27 residues within 4Å: Chain A: V.10, G.11, A.12, C.13, G.14, K.17, P.35, T.59, A.60, G.61, Q.62, E.63, E.64, Y.65, R.69, D.70, M.73, F.79, K.89, D.93, H.96, Y.97, Q.100, I.101, R.103, V.104 Ligands: GDP.3 14 PLIP interactions: 14 interactions with chain A Hydrophobic interactions: A:P.35, A:M.73, A:Y.97, A:Q.100, A:V.104, A:V.104 Hydrogen bonds: A:K.17, A:D.70, A:H.96, A:R.103 Water bridges: A:R.69, A:Y.97 Salt bridges: A:E.63 Halogen bonds: A:Y.97

1 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 5 residues within 4Å: Chain A: S.18, Y.33, P.35, A.60 Ligands: GDP.3 5 PLIP interactions: 1 interactions with chain A, 4 Ligand-Water interactions Metal complexes: A:S.18, H2O.1, H2O.2, H2O.2, H2O.3

1 x GDP: GUANOSINE-5'-DIPHOSPHATE(Non-covalent)

GDP.3: 21 residues within 4Å: Chain A: A.12, C.13, G.14, V.15, G.16, K.17, S.18, A.19, F.29, D.31, E.32, Y.33, N.117, K.118, D.120, L.121, S.146, A.147, K.148 Ligands: 01.1, MG.2 21 PLIP interactions: 21 interactions with chain A Hydrogen bonds: A:G.14, A:V.15, A:G.16, A:K.17, A:S.18, A:A.19, A:D.31, A:Y.33, A:N.117, A:K.118, A:K.118, A:S.146, A:A.147, A:K.148 Water bridges: A:Y.33, A:Y.33, A:Y.33 Salt bridges: A:K.17, A:D.120 pi-Stacking: A:F.29, A:F.29

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Fernando, M.C. et al., The structure of KRAS G12C bound to divarasib highlights features of potent switch-II pocket engagement. Small Gtpases (2024)

Release Date

2025-05-21

Peptides

Isoform 2B of GTPase KRas: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Isoform 2B of GTPase KRas