SMTL ID : 9gbj.1

KRAS G12D in complex with covalent inhibitor

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.71 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.3 22 PLIP interactions: 22 interactions with chain A Hydrogen bonds: A:A.12, A:G.14, A:V.15, A:G.16, A:K.17, A:S.18, A:S.18, A:A.19, A:Y.33, A:N.117, A:K.118, A:K.118, A:A.147, A:K.148 Water bridges: A:K.17, 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 01: 1-[(3S)-1-[2-[5-[(4S)-2-azanyl-3-cyano-4-methyl-6,7-dihydro-5H-1-benzothiophen-4-yl]-1,2,4-oxadiazol-3-yl]-6-[(1S)-1-[(2S)-1-methylpyrrolidin-2-yl]ethoxy]pyrimidin-4-yl]pyrrolidin-3-yl]-3-[1-(methoxymethyl)cyclopropyl]urea

01.2: 22 residues within 4Å: Chain A: V.8, V.10, D.13, T.59, A.60, G.61, Q.62, E.63, E.64, Y.65, S.66, R.69, D.70, M.73, F.79, D.93, H.96, Y.97, Q.100, I.101, R.103, V.104 21 PLIP interactions: 21 interactions with chain A Hydrophobic interactions: A:V.10, A:E.63, A:Y.65, A:H.96, A:Y.97, A:Q.100, A:I.101 Hydrogen bonds: A:D.13, A:E.64, A:E.64, A:Y.65, A:Y.65, A:R.69, A:D.70, A:H.96, A:Y.97, A:R.103 Water bridges: A:D.13, A:D.13, A:R.69 Salt bridges: A:E.63

1 x MG: MAGNESIUM ION(Non-covalent)

MG.3: 5 residues within 4Å: Chain A: S.18, Y.33, P.35, A.60 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.4

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Sirocchi, L.S. et al., Discovery of Carbodiimide Warheads to Selectively and Covalently Target Aspartic Acid in KRAS G12D . J.Am.Chem.Soc. (2025)

Release Date

2025-04-30

Peptides

GTPase KRas: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

GTPase KRas

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