SMTL ID : 6tan.1

X-RAY STRUCTURE OF HUMAN K-RAS G12C IN COMPLEX WITH COVALENT ISOQUINOLINONE INHIBITOR (COMPOUND 17)

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.16 Å

Oligo State

monomer

Ligands

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

GDP.1: 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, Y.33, N.117, K.118, D.120, L.121, S.146, A.147, K.148 Ligands: MG.2, MZN.3 21 PLIP interactions: 21 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:N.117, A:K.118, A:K.118, A:A.147, A:K.148 Water bridges: A:S.18, A:S.18, A:D.31, A:K.148 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.2, H2O.2, H2O.4, H2O.4

1 x MZN: 7-(2-fluoranyl-6-oxidanyl-phenyl)-3-[(3~{R})-1-propanoylpyrrolidin-3-yl]-4~{H}-2,6-naphthyridin-1-one(Covalent)

MZN.3: 18 residues within 4Å: Chain A: V.10, G.11, C.13, G.14, K.17, P.35, T.59, A.60, G.61, Q.62, E.63, R.69, M.73, Y.97, Q.100, I.101, V.104 Ligands: GDP.1 16 PLIP interactions: 16 interactions with chain A Hydrophobic interactions: A:P.35, A:M.73, A:Y.97, A:Y.97, A:Q.100, A:I.101, A:V.104 Hydrogen bonds: A:G.11, A:K.17, A:T.59, A:Y.97 Water bridges: A:R.69, A:R.69, A:R.69, A:D.70, A:Q.100

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Mortier, J. et al., Computationally Empowered Workflow Identifies Novel Covalent Allosteric Binders for KRASG12C. Chemmedchem (2020)

Release Date

2020-04-08

Peptides

GTPase KRas: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

GTPase KRas

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