SMTL ID : 9l6f.2 (7 other biounits)

Crystal structure of KRas G12D (GDP) in complex with ASP3082

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 3.18 Å

Oligo State

monomer

Ligands

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

GDP.1: 19 residues within 4Å: Chain A: D.13, G.14, G.16, K.17, S.18, A.19, F.29, V.30, D.31, Y.33, P.35, N.117, K.118, D.120, L.121, S.146, A.147, K.148 Ligands: MG.2 16 PLIP interactions: 16 interactions with chain A Hydrogen bonds: A:G.14, A:G.16, A:K.17, A:S.18, A:A.19, A:D.31, A:Y.33, A:N.117, A:K.118, A:S.146, A:A.147, A:K.148 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: 4 residues within 4Å: Chain A: K.17, S.18, D.58 Ligands: GDP.1 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:S.18

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Yoshinari, T. et al., Discovery of KRAS(G12D) selective degrader ASP3082. Commun Chem (2025)

Release Date

2025-09-03

Peptides

Isoform 2B of GTPase KRas: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
D

Isoform 2B of GTPase KRas

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