SMTL ID : 7a1w.1

KRASG12C GDP form in complex with Cpd3

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.76 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, V.30, D.31, Y.33, N.117, K.118, D.120, L.121, S.146, A.147, K.148 Ligands: MG.2 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:N.117, A:K.118, A:K.118, A:A.147, A:K.148 Water bridges: A:G.11, A:K.17, A:S.18, A:S.18, A:D.31 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.1, H2O.2

1 x PO4: PHOSPHATE ION(Non-functional Binders)

PO4.3: 8 residues within 4Å: Chain A: A.12, C.13, A.60, G.61, Q.62, E.63, Y.97 Ligands: QWK.4 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:C.13, A:Q.62, A:Y.97 Water bridges: A:G.11, A:Y.97

2 x QWK: ~{N}-[6-(phenylmethyl)-7,8-dihydro-5~{H}-pyrido[4,3-d]pyrimidin-2-yl]propanamide(Covalent)

QWK.4: 9 residues within 4Å: Chain A: C.13, P.35, T.36, A.60, E.63, E.64, Y.65, M.68 Ligands: PO4.3 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:A.60, A:E.63, A:E.64 Hydrogen bonds: A:A.60 pi-Stacking: A:Y.65 QWK.5: 3 residues within 4Å: Chain A: C.119, D.120, Q.151 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Q.151

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Mathieu, M. et al., KRAS G12C fragment screening renders new binding pockets. Small Gtpases (2022)

Release Date

2021-10-13

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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