SMTL ID : 9bl0.2 (1 other biounit)

KRAS G12D Mutant KRAS 1-169 at 298 K bound to MRTX-1133

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.66 Å

Oligo State

monomer

Ligands

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

GDP.1: 20 residues within 4Å: Chain A: A.11, D.12, G.13, V.14, G.15, K.16, S.17, A.18, F.28, D.30, E.31, Y.32, N.116, K.117, D.119, L.120, S.145, A.146, K.147 Ligands: MG.2 21 PLIP interactions: 21 interactions with chain A Hydrogen bonds: A:A.11, A:G.13, A:V.14, A:G.15, A:K.16, A:S.17, A:A.18, A:E.31, A:E.31, A:N.116, A:K.117, A:K.117, A:A.146, A:K.147 Water bridges: A:D.12, A:S.17, 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 6IC: 4-(4-[(1R,5S)-3,8-diazabicyclo[3.2.1]octan-3-yl]-8-fluoro-2-{[(2R,4R,7aS)-2-fluorotetrahydro-1H-pyrrolizin-7a(5H)-yl]methoxy}pyrido[4,3-d]pyrimidin-7-yl)-5-ethynyl-6-fluoronaphthalen-2-ol(Non-covalent)

6IC.3: 19 residues within 4Å: Chain A: V.9, G.10, D.12, A.59, G.60, Q.61, E.62, E.63, Y.64, R.68, 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:Y.64, A:R.68, A:M.72, A:Y.96, A:Y.96, A:Q.99, A:I.100, A:V.103 Hydrogen bonds: A:G.60, A:Y.64, A:R.68, A:D.69, A:R.102 Water bridges: A:D.12, A:G.60, A:Y.96 Salt bridges: A:E.62

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Xu, M. et al., Room Temperature Structures of Oncogenic KRAS-G12D bound to MRTX-1133. To Be Published

Release Date

2025-05-07

Peptides

Isoform 2B of GTPase KRas: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

Isoform 2B of GTPase KRas

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