SMTL ID : 7yce.1

KRas G12C in complex with Compound 7b

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.80 Å

Oligo State

monomer

Ligands

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

GDP.1: 21 residues within 4Å: Chain A: A.12, C.13, G.14, V.15, G.16, K.17, S.18, A.19, F.29, V.30, D.31, Y.33, N.117, K.118, D.120, L.121, S.146, A.147, K.148 Ligands: MG.2, IQN.4 21 PLIP interactions: 21 interactions with chain A Hydrogen bonds: A:G.14, A:V.15, A:G.16, A:K.17, A:S.18, A:A.19, A:V.30, 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, A:S.18, A:D.58 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.2, H2O.2

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

SO4.3: 2 residues within 4Å: Chain A: K.89 Ligands: IQN.4 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:K.89

1 x IQN: 1-[7-[6-chloranyl-2-(1-ethylpiperidin-4-yl)oxy-8-fluoranyl-7-(5-methyl-1~{H}-indazol-4-yl)quinazolin-4-yl]-2,7-diazaspiro[3.5]nonan-2-yl]propan-1-one(Covalent)

IQN.4: 22 residues within 4Å: Chain A: G.11, C.13, K.17, P.35, T.59, A.60, G.61, Q.62, E.63, S.66, R.69, D.70, M.73, D.93, H.96, Y.97, Q.100, I.101, R.103, V.104 Ligands: GDP.1, SO4.3 15 PLIP interactions: 15 interactions with chain A Hydrophobic interactions: A:R.69, A:M.73, A:Y.97, A:Q.100, A:I.101, A:V.104 Hydrogen bonds: A:K.17, A:S.66, A:D.70, A:R.103 Water bridges: A:S.18 Salt bridges: A:D.93 pi-Stacking: A:Y.97, A:Y.97 pi-Cation interactions: A:H.96

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Imaizumi, T. et al., Discovery and biological evaluation of 1-{2,7-diazaspiro[3.5]nonan-2-yl}prop-2-en-1-one derivatives as covalent inhibitors of KRAS G12C with favorable metabolic stability and anti-tumor activity. Bioorg.Med.Chem. (2022)

Release Date

2022-08-10

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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