SMTL ID : 9kpm.1

Crystal structure of KRAS-G12C in complex with compound 16 (JAB-16)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.41 Å

Oligo State

monomer

Ligands

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

GDP.1: 21 residues within 4Å: Chain A: A.26, C.27, G.28, V.29, G.30, K.31, S.32, A.33, F.43, V.44, D.45, Y.47, N.131, K.132, D.134, L.135, S.160, A.161, K.162 Ligands: 01.2, MG.3 20 PLIP interactions: 20 interactions with chain A Hydrogen bonds: A:A.26, A:G.28, A:V.29, A:G.30, A:K.31, A:S.32, A:A.33, A:V.44, A:N.131, A:K.132, A:K.132, A:A.161, A:K.162 Water bridges: A:D.45, A:E.46 Salt bridges: A:K.31, A:D.134 pi-Stacking: A:F.43, A:F.43 pi-Cation interactions: A:K.132

1 x 01: 7-[2-azanyl-3,5-bis(chloranyl)-6-fluoranyl-phenyl]-6-chloranyl-1-(4-methyl-2-propan-2-yl-pyridin-3-yl)-2-oxidanylidene-4-(4-prop-2-enoylpiperazin-1-yl)-1,8-naphthyridine-3-carbonitrile

01.2: 15 residues within 4Å: Chain A: V.24, G.25, C.27, K.31, P.49, T.73, A.74, G.75, M.87, F.93, H.110, Y.111, Q.114, I.115 Ligands: GDP.1 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:P.49, A:Y.111, A:Q.114 Hydrogen bonds: A:K.31, A:Q.114 pi-Stacking: A:Y.111, A:Y.111

1 x MG: MAGNESIUM ION(Non-covalent)

MG.3: 2 residues within 4Å: Chain A: S.32 Ligands: GDP.1 5 PLIP interactions: 1 interactions with chain A, 4 Ligand-Water interactions Metal complexes: A:S.32, H2O.2, H2O.2, H2O.3, H2O.3

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Li, A. et al., Design, Structure Optimization, and Preclinical Characterization of JAB-21822, a Covalent Inhibitor of KRAS G12C. J.Med.Chem. (2025)

Release Date

2025-03-12

Peptides

Isoform 2B of GTPase KRas: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Isoform 2B of GTPase KRas

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