SMTL ID : 9l6f.8 (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, D.31, Y.33, D.34, P.35, N.117, K.118, D.120, L.121, S.146, A.147, K.148 Ligands: MG.2 17 PLIP interactions: 17 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:D.31, A:Y.33, A:N.117, A:K.118, A:A.147, A:K.148 Salt bridges: A:K.17, A:D.120 pi-Stacking: A:F.29, A:F.29 pi-Cation interactions: A:K.118

1 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 7 residues within 4Å: Chain A: S.18, D.34, P.35, T.36, I.37, D.58 Ligands: GDP.1 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:S.18, A:D.34

1 x 01: ASP3082

01.3: 19 residues within 4Å: Chain A: G.11, A.12, D.13, T.59, A.60, G.61, Q.62, E.63, Y.65, S.66, R.69, D.70, M.73, D.93, H.96, Y.97, E.99, Q.100, R.103 16 PLIP interactions: 16 interactions with chain A Hydrophobic interactions: A:T.59, A:Y.65, A:Y.65, A:Y.97, A:Q.100 Hydrogen bonds: A:G.61, A:S.66, A:D.70, A:E.99, A:E.99, A:Q.100 Salt bridges: A:D.13, A:E.63 pi-Stacking: A:H.96, A:Y.97, A:Y.97

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
P

Isoform 2B of GTPase KRas

Related Entries With Identical Sequence