SMTL ID : 8txe.2 (1 other biounit)

Crystal structure of KRAS G12D in complex with GDP and compound 5

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.35 Å

Oligo State

monomer

Ligands

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

GDP.1: 20 residues within 4Å: Chain A: A.12, D.13, G.14, V.15, G.16, K.17, S.18, A.19, F.29, D.31, E.32, Y.33, N.117, K.118, D.120, L.121, S.146, A.147, K.148 Ligands: MG.2 22 PLIP interactions: 22 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:E.32, A:N.117, A:K.118, A:K.118, A:A.147, A:K.148 Water bridges: A:D.13, A:S.18, A:S.18, A:Y.33, A:Y.33, A:T.59 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.2, H2O.2, H2O.3

1 x VM9: (6M)-6-(6-chloro-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}quinazolin-7-yl)-4-methyl-5-(trifluoromethyl)pyridin-2-amine(Non-covalent)

VM9.3: 17 residues within 4Å: Chain A: V.10, G.11, A.12, D.13, G.61, E.63, E.64, Y.65, R.69, D.70, M.73, D.93, H.96, Y.97, Q.100, I.101, V.104 12 PLIP interactions: 12 interactions with chain A Hydrophobic interactions: A:M.73, A:Y.97, A:V.104, A:V.104 Hydrogen bonds: A:G.61, A:G.61, A:E.64 Water bridges: A:D.13, A:E.64, A:E.64 Salt bridges: A:E.63 Halogen bonds: A:Y.97

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Cheng, H. et al., Structure-Based Design and Synthesis of Potent and Selective KRAS G12D Inhibitors. Acs Med.Chem.Lett. (2023)

Release Date

2023-11-08

Peptides

GTPase KRas: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

GTPase KRas

Related Entries With Identical Sequence