SMTL ID : 9kpn.1 (1 other biounit)

Crystal structure of KRAS-G12C in complex with Compound 20 (JAB-20)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.29 Å

Oligo State

monomer

Ligands

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

GDP.1: 22 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, E.46, Y.47, N.131, K.132, D.134, L.135, S.160, A.161, K.162 Ligands: 01.2, MG.3 29 PLIP interactions: 29 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:D.45, A:E.46, A:N.131, A:K.132, A:K.132, A:A.161, A:K.162 Water bridges: A:S.32, A:S.32, A:S.32, A:E.46, A:E.46, A:E.46, A:Y.47, A:Y.47, A:K.162 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-3,4,5,6-tetrakis(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: 20 residues within 4Å: Chain A: V.24, G.25, C.27, K.31, P.49, T.73, A.74, G.75, Q.76, R.83, D.84, M.87, H.110, Y.111, Q.114, I.115, R.117, V.118 Ligands: GDP.1, CL.4 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:P.49, A:Y.111 Hydrogen bonds: A:K.31 Halogen bonds: A:R.117

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.4

1 x CL: CHLORIDE ION(Non-functional Binders)

CL.4: 2 residues within 4Å: Chain A: R.83 Ligands: 01.2 Ligand excluded by PLIP

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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