SMTL ID : 8dnk.1

Crystal structure of human KRAS G12C covalently bound with Taiho WO2020/085493A1 compound 6

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.23 Å

Oligo State

monomer

Ligands

1 x MG: MAGNESIUM ION(Non-covalent)

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

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

GDP.2: 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: MG.1, U50.3 17 PLIP interactions: 17 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 Salt bridges: A:K.31, A:D.134 pi-Stacking: A:F.43 pi-Cation interactions: A:K.132

1 x U50: 2-{[(5-tert-butyl-6-chloro-1H-indazol-3-yl)amino]methyl}-4-chloro-1-methyl-N-(1-propanoylazetidin-3-yl)-1H-imidazole-5-carboxamide(Covalent)

U50.3: 19 residues within 4Å: Chain A: V.24, G.25, C.27, K.31, P.49, E.52, A.74, G.75, Q.76, E.77, E.78, Y.79, S.80, R.83, D.84, M.87, Y.111, I.115 Ligands: GDP.2 11 PLIP interactions: 11 interactions with chain A Hydrophobic interactions: A:P.49, A:Y.79, A:Y.111 Hydrogen bonds: A:K.31, A:Q.76, A:S.80, A:R.83, A:R.83, A:D.84, A:Y.111 Halogen bonds: A:A.74

1 x SO4: SULFATE ION(Non-functional Binders)

SO4.4: 2 residues within 4Å: Chain A: N.41, K.57 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.41 Salt bridges: A:K.57

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Zhu, K. et al., Modeling receptor flexibility in the structure-based design of KRAS G12C inhibitors. J.Comput.Aided Mol.Des. (2022)

Release Date

2022-08-17

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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