SMTL ID : 9l6a.1

Crystal structure of KRas G12D (GDP) in complex with compound 1

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.36 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, V.30, D.31, Y.33, N.117, K.118, D.120, L.121, S.146, A.147, K.148 Ligands: MG.2 25 PLIP interactions: 25 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:V.30, A:Y.33, A:N.117, A:K.118, A:K.118, A:A.147, A:K.148 Water bridges: A:D.13, A:K.17, A:K.17, A:K.17, A:S.18, A:S.18, A:Y.33, A:Y.33 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.1, H2O.2, H2O.2

1 x 01: 6-cyclopropyl-4-[(1~{S},4~{S})-2,5-diazabicyclo[2.2.1]heptan-2-yl]-7-(6-fluoranyl-5-methyl-1~{H}-indazol-4-yl)-2-(oxan-4-yloxy)-8-phenylmethoxy-quinazoline

01.3: 21 residues within 4Å: Chain A: V.10, G.11, A.12, D.13, T.59, A.60, G.61, Q.62, E.63, E.64, Y.65, S.66, R.69, D.70, M.73, H.96, Y.97, Q.100, I.101, R.103, V.104 16 PLIP interactions: 16 interactions with chain A Hydrophobic interactions: A:V.10, A:T.59, A:Y.65, A:Y.65, A:Y.97, A:Q.100, A:V.104 Hydrogen bonds: A:D.13, A:S.66, A:D.70, A:Y.97 Water 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
A

Isoform 2B of GTPase KRas

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