SMTL ID : 8afb.1

CRYSTAL STRUCTURE OF KRAS-G12C IN COMPLEX WITH COMPOUND 23 (BI-0474)

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.12 Å

Oligo State

monomer

Ligands

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

GDP.1: 18 residues within 4Å: Chain A: A.12, C.13, G.14, V.15, G.16, K.17, S.18, A.19, D.31, Y.33, N.117, K.118, D.120, L.121, S.146, A.147, K.148 Ligands: MG.2 20 PLIP interactions: 20 interactions with chain A Hydrogen bonds: A:A.12, 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:A.147, A:K.148 Water bridges: A:S.18, A:S.18 Salt bridges: A:K.17, A:D.120 pi-Stacking: A:F.29, A:F.29

1 x MG: MAGNESIUM ION(Non-covalent)

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

1 x LXD: (4~{S})-2-azanyl-4-[3-[6-[(2~{S})-2,4-dimethylpiperazin-1-yl]-4-(4-prop-2-enoylpiperazin-1-yl)pyridin-2-yl]-1,2,4-oxadiazol-5-yl]-4-methyl-6,7-dihydro-5~{H}-1-benzothiophene-3-carbonitrile(Covalent)

LXD.3: 19 residues within 4Å: Chain A: V.10, C.13, P.35, A.60, G.61, Q.62, E.63, E.64, Y.65, R.69, D.70, M.73, D.93, H.96, Y.97, Q.100, I.101, R.103, V.104 13 PLIP interactions: 13 interactions with chain A Hydrophobic interactions: A:V.10, A:M.73, A:H.96, A:Y.97, A:I.101 Hydrogen bonds: A:E.63, A:E.64, A:E.64, A:Y.65, A:R.103 Water bridges: A:R.69 Salt bridges: A:E.63, A:D.93

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Broker, J. et al., Fragment Optimization of Reversible Binding to the Switch II Pocket on KRAS Leads to a Potent, In Vivo Active KRAS G12C Inhibitor. J.Med.Chem. (2022)

Release Date

2022-11-09

Peptides

GTPase KRas: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

GTPase KRas

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