SMTL ID : 7t47.1

KRAS G12D (GppCp) with MRTX-1133

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.27 Å

Oligo State

monomer

Ligands

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.1: 20 residues within 4Å: Chain A: V.28, G.29, D.31, A.78, G.79, Q.80, E.81, E.82, Y.83, S.84, R.87, D.88, M.91, D.111, H.114, Y.115, Q.118, I.119, R.121, V.122 18 PLIP interactions: 18 interactions with chain A Hydrophobic interactions: A:V.28, A:E.81, A:Y.83, A:R.87, A:M.91, A:Y.115, A:Y.115, A:Q.118, A:I.119, A:V.122 Hydrogen bonds: A:G.79, A:Y.83, A:R.87, A:D.88, A:R.121 Water bridges: A:G.79, A:Y.115 Salt bridges: A:E.81

1 x GCP: PHOSPHOMETHYLPHOSPHONIC ACID GUANYLATE ESTER(Non-covalent)

GCP.2: 23 residues within 4Å: Chain A: A.30, D.31, G.32, V.33, G.34, K.35, S.36, A.37, F.47, V.48, D.49, Y.51, P.53, A.78, N.135, K.136, D.138, L.139, S.164, A.165, K.166 Ligands: GDP.3, MG.6 24 PLIP interactions: 24 interactions with chain A Hydrogen bonds: A:G.32, A:V.33, A:G.34, A:K.35, A:K.35, A:S.36, A:A.37, A:P.53, A:N.135, A:K.136, A:K.136, A:A.165, A:K.166 Water bridges: A:S.36, A:S.36, A:S.36, A:S.36, A:Y.51, A:G.79, A:K.166 Salt bridges: A:D.138 pi-Stacking: A:F.47, A:F.47 pi-Cation interactions: A:K.136

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

GDP.3: 20 residues within 4Å: Chain A: A.30, G.32, V.33, G.34, K.35, S.36, A.37, F.47, V.48, D.49, Y.51, N.135, K.136, D.138, L.139, S.164, A.165, K.166 Ligands: GCP.2, MG.6 21 PLIP interactions: 21 interactions with chain A Hydrogen bonds: A:G.32, A:V.33, A:G.34, A:K.35, A:S.36, A:A.37, A:N.135, A:K.136, A:K.136, A:A.165, A:K.166 Water bridges: A:K.35, A:S.36, A:S.36, A:S.36, A:Y.51, A:K.166 Salt bridges: A:K.35, A:D.138 pi-Stacking: A:F.47, A:F.47

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.4: 6 residues within 4Å: Chain A: F.109, E.110, I.112, H.113, L.152, Y.156 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:H.113

1 x ACT: ACETATE ION(Non-functional Binders)

ACT.5: 7 residues within 4Å: Chain A: S.36, I.40, Y.51, D.52, I.55, Y.59, D.76 1 PLIP interactions: 1 interactions with chain A Water bridges: A:D.76

1 x MG: MAGNESIUM ION(Non-covalent)

MG.6: 3 residues within 4Å: Chain A: S.36 Ligands: GCP.2, GDP.3 5 PLIP interactions: 1 interactions with chain A, 4 Ligand-Water interactions Metal complexes: A:S.36, H2O.1, H2O.2, H2O.2, H2O.4

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Christensen, J. et al., A Non-covalent KRASG12D Allele Specific Inhibitor Demonstrates Potent Inhibition of KRAS-dependent Signaling and Regression of KRASG12D-mutant Tumors. Nature (2022)

Release Date

2022-03-16

Peptides

GTPase KRas: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

GTPase KRas