SMTL ID : 8dni.1

Crystal structure of human KRAS G12C covalently bound with Araxes WO2020/028706A1 compound I-1

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.50 Å

Oligo State

monomer

Ligands

1 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 2 residues within 4Å: Chain A: S.31 Ligands: GDP.2 5 PLIP interactions: 1 interactions with chain A, 4 Ligand-Water interactions Metal complexes: A:S.31, H2O.1, H2O.1, H2O.1, H2O.2

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

GDP.2: 19 residues within 4Å: Chain A: A.25, C.26, G.27, V.28, G.29, K.30, S.31, A.32, F.42, D.44, N.130, K.131, D.133, L.134, S.159, A.160, K.161 Ligands: MG.1, U4L.3 19 PLIP interactions: 19 interactions with chain A Hydrogen bonds: A:A.25, A:G.27, A:V.28, A:G.29, A:K.30, A:S.31, A:A.32, A:D.44, A:Y.46, A:N.130, A:K.131, A:K.131, A:A.160, A:K.161 Water bridges: A:S.31 Salt bridges: A:K.30, A:D.133 pi-Stacking: A:F.42, A:F.42

1 x U4L: (4P)-4-(5-methyl-1H-indazol-4-yl)-6-(2-propanoyl-2,6-diazaspiro[3.4]octan-6-yl)-2-(pyrrolidin-1-yl)pyrimidine-5-carbonitrile(Covalent)

U4L.3: 20 residues within 4Å: Chain A: G.24, C.26, K.30, P.48, T.72, A.73, G.74, Q.75, E.76, E.77, Y.78, S.79, R.82, D.83, M.86, H.109, Y.110, Q.113, R.116 Ligands: GDP.2 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:P.48, A:H.109, A:Y.110, A:Q.113 Hydrogen bonds: A:K.30, A:S.79, A:R.82, A:D.83, A:Y.110, A:R.116

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

GTPase KRas: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

GTPase KRas

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