SMTL ID : 9qq0.1

KRAS-G12D(1-169) - GDP IN covalent COMPLEX WITH compound (3R,4R)-3

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.55 Å

Oligo State

monomer

Ligands

1 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 2 residues within 4Å: Chain A: S.18 Ligands: GDP.4 5 PLIP interactions: 1 interactions with chain A, 4 Ligand-Water interactions Metal complexes: A:S.18, H2O.1, H2O.2, H2O.2, H2O.3

1 x SO4: SULFATE ION(Non-functional Binders)

SO4.2: 2 residues within 4Å: Chain A: R.74, K.105 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:K.105 Salt bridges: A:R.74, A:K.105

1 x 01: (2~{R})-2-ethyl-4-[(1~{R},5~{S})-3-[7-(8-ethynyl-7-fluoranyl-3-oxidanyl-naphthalen-1-yl)-8-fluoranyl-2-[[(2~{R},8~{S})-2-fluoranyl-1,2,3,5,6,7-hexahydropyrrolizin-8-yl]methoxy]pyrido[4,3-d]pyrimidin-4-yl]-3,8-diazabicyclo[3.2.1]octan-8-yl]-2-methyl-4-oxidanylidene-butanoic acid

01.3: 20 residues within 4Å: Chain A: V.10, G.11, D.13, P.35, T.36, A.60, G.61, 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 20 PLIP interactions: 20 interactions with chain A Hydrophobic interactions: A:D.13, A:P.35, A:T.36, A:Y.65, A:R.69, A:M.73, A:Y.97, A:Y.97, A:Q.100, A:I.101, A:V.104 Hydrogen bonds: A:D.13, A:G.61, A:E.64, A:Y.65, A:S.66, A:R.69, A:R.103 Salt bridges: A:E.63, A:E.63

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

GDP.4: 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.1 23 PLIP interactions: 23 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: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:K.17, A:K.17, A:D.31, A:Y.33, A:K.148 Salt bridges: A:K.17, A:D.120 pi-Stacking: A:F.29, A:F.29

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Budai, B. et al., Promise and Challenge of beta-Lactone Electrophiles to Target Aspartate 12 of Mutant KRAS G12D . J.Med.Chem. (2025)

Release Date

2025-07-23

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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