SMTL ID : 8t4v.1 (1 other biounit)

Crystal structure of compound 1 bound to K-Ras(G12D)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.47 Å

Oligo State

monomer

Ligands

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

GDP.1: 19 residues within 4Å: Chain A: A.29, D.30, G.31, V.32, G.33, K.34, S.35, A.36, F.46, D.48, Y.50, N.134, K.135, D.137, L.138, S.163, A.164, K.165 Ligands: MG.2 23 PLIP interactions: 23 interactions with chain A Hydrogen bonds: A:A.29, A:D.30, A:G.31, A:V.32, A:G.33, A:K.34, A:S.35, A:A.36, A:D.48, A:Y.50, A:N.134, A:K.135, A:K.135, A:A.164, A:K.165 Water bridges: A:K.34, A:Y.50, A:Y.50 Salt bridges: A:K.34, A:D.137 pi-Stacking: A:F.46, A:F.46 pi-Cation interactions: A:K.135

1 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 3 residues within 4Å: Chain A: S.35, D.75 Ligands: GDP.1 5 PLIP interactions: 1 interactions with chain A, 4 Ligand-Water interactions Metal complexes: A:S.35, H2O.1, H2O.1, H2O.2, H2O.3

1 x Y63: 4-{(1R,5S)-3-[(7P)-7-(8-ethynylnaphthalen-1-yl)-8-fluoro-2-{[(4s,7as)-tetrahydro-1H-pyrrolizin-7a(5H)-yl]methoxy}pyrido[4,3-d]pyrimidin-4-yl]-3,8-diazabicyclo[3.2.1]octan-8-yl}-4-oxobutanoic acid(Covalent)

Y63.3: 19 residues within 4Å: Chain A: V.27, G.28, D.30, A.77, G.78, Q.79, E.80, E.81, Y.82, R.86, D.87, M.90, D.110, H.113, Y.114, Q.117, I.118, R.120, V.121 15 PLIP interactions: 15 interactions with chain A Hydrophobic interactions: A:V.27, A:D.30, A:E.80, A:Y.82, A:Y.82, A:M.90, A:Y.114, A:Q.117, A:I.118 Hydrogen bonds: A:D.30, A:G.78, A:Y.82, A:R.86, A:Y.114 Salt bridges: A:E.80

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Zheng, Q. et al., Strain-release alkylation of Asp12 enables mutant selective targeting of K-Ras-G12D. Nat.Chem.Biol. (2024)

Release Date

2024-03-13

Peptides

GTPase KRas: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

GTPase KRas

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