SMTL ID : 6t5b.1

KRasG12C ligand complex

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.37 Å

Oligo State

monomer

Ligands

1 x MG: MAGNESIUM ION(Non-covalent)

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

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

GDP.2: 20 residues within 4Å: Chain A: A.12, C.13, G.14, V.15, G.16, K.17, S.18, A.19, F.29, D.31, E.32, Y.33, N.117, K.118, D.120, L.121, S.146, A.147, K.148 Ligands: MG.1 23 PLIP interactions: 23 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:E.32, A:E.32, A:N.117, A:K.118, A:K.118, A:A.147, A:K.148 Water bridges: A:K.17, A:K.17, A:Y.33, A:Y.33, A:Y.33 Salt bridges: A:K.17, A:D.120 pi-Stacking: A:F.29, A:F.29

1 x O7K: pyrazinoquinolinone(Covalent)

O7K.3: 20 residues within 4Å: Chain A: V.10, G.11, C.13, K.17, P.35, T.59, A.60, G.61, Q.62, E.63, E.64, Y.65, R.69, D.70, M.73, H.96, Y.97, Q.100, I.101, V.104 11 PLIP interactions: 11 interactions with chain A Hydrophobic interactions: A:P.35, A:M.73, A:Q.100, A:I.101, A:V.104, A:V.104 Hydrogen bonds: A:K.17, A:D.70 Water bridges: A:C.13 pi-Stacking: A:Y.97, A:Y.97

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

SO4.4: 0 residues within 4Å: (No contacts) 1 PLIP interactions: 1 interactions with chain A Water bridges: A:K.170

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kettle, J.G. et al., Structure-Based Design and Pharmacokinetic Optimization of Covalent Allosteric Inhibitors of the Mutant GTPase KRASG12C. J.Med.Chem. (2020)

Release Date

2020-02-26

Peptides

GTPase KRas: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

GTPase KRas