SMTL ID : 8jhl.1

GDP-bound KRAS G12D in complex with YK-8S

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.10 Å

Oligo State

monomer

Ligands

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

GDP.1: 21 residues within 4Å: Chain A: A.11, D.12, G.13, V.14, G.15, K.16, S.17, A.18, F.28, V.29, D.30, E.31, Y.32, N.116, K.117, D.119, L.120, S.145, A.146, K.147 Ligands: MG.2 19 PLIP interactions: 19 interactions with chain A Hydrogen bonds: A:G.13, A:V.14, A:G.15, A:K.16, A:S.17, A:A.18, A:V.29, A:E.31, A:N.116, A:K.117, A:K.117, A:S.145, A:A.146, A:K.147 Water bridges: A:Y.32 Salt bridges: A:K.16, A:D.119 pi-Stacking: A:F.28, A:F.28

1 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 2 residues within 4Å: Chain A: S.17 Ligands: GDP.1 4 PLIP interactions: 1 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:S.17, H2O.1, H2O.1, H2O.2

1 x DNU: 1-[4-[7-(8-ethynyl-7-fluoranyl-naphthalen-1-yl)-8-fluoranyl-2-[[(2~{R},8~{S})-2-fluoranyl-1,2,3,5,6,7-hexahydropyrrolizin-8-yl]methoxy]pyrido[4,3-d]pyrimidin-4-yl]piperazin-1-yl]-3-oxidanyl-propan-1-one(Covalent)

DNU.3: 17 residues within 4Å: Chain A: V.9, D.12, P.34, A.59, G.60, E.62, E.63, Y.64, D.69, M.72, D.92, H.95, Y.96, Q.99, I.100, R.102, V.103 17 PLIP interactions: 17 interactions with chain A Hydrophobic interactions: A:V.9, A:D.12, A:E.62, A:Y.64, A:Y.64, A:M.72, A:Y.96, A:Y.96, A:Q.99, A:I.100, A:V.103, A:V.103 Hydrogen bonds: A:G.60 Water bridges: A:Y.64, A:R.68, A:Y.96 Salt bridges: A:E.62

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Yu, Z. et al., Simultaneous Covalent Modification of K-Ras(G12D) and K-Ras(G12C) with Tunable Oxirane Electrophiles. J.Am.Chem.Soc. (2023)

Release Date

2024-01-31

Peptides

GTPase KRas, N-terminally processed: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

GTPase KRas, N-terminally processed