SMTL ID : 9u5t.1

GDP-bound KRAS G12D in complex with MCB-294

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.80 Å

Oligo State

monomer

Ligands

1 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 3 residues within 4Å: Chain A: S.23, D.63 Ligands: GDP.3 5 PLIP interactions: 1 interactions with chain A, 4 Ligand-Water interactions Metal complexes: A:S.23, H2O.2, H2O.3, H2O.3, H2O.3

1 x 01: (3~{R})-1-[2-[[(8~{S})-6-[bis(fluoranyl)methylidene]-2,3,5,7-tetrahydro-1~{H}-pyrrolizin-8-yl]methoxy]-7-(8-ethynyl-7-fluoranyl-3-oxidanyl-naphthalen-1-yl)-8-fluoranyl-pyrido[4,3-d]pyrimidin-4-yl]-3-methyl-piperidin-3-ol

01.2: 22 residues within 4Å: Chain A: V.15, G.16, D.18, T.64, A.65, G.66, Q.67, E.68, E.69, Y.70, S.71, R.74, D.75, M.78, K.94, D.98, H.101, Y.102, Q.105, I.106, R.108, V.109 19 PLIP interactions: 19 interactions with chain A Hydrophobic interactions: A:E.68, A:Y.70, A:R.74, A:M.78, A:H.101, A:Y.102, A:Y.102, A:Q.105, A:I.106, A:V.109 Hydrogen bonds: A:E.69, A:S.71, A:R.74, A:D.75, A:Y.102, A:R.108 Water bridges: A:G.16, A:G.16 Salt bridges: A:E.68

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

GDP.3: 20 residues within 4Å: Chain A: A.17, D.18, G.19, V.20, G.21, K.22, S.23, A.24, F.34, V.35, D.36, Y.38, N.122, K.123, D.125, L.126, S.151, A.152, K.153 Ligands: MG.1 20 PLIP interactions: 20 interactions with chain A Hydrogen bonds: A:A.17, A:G.19, A:V.20, A:G.21, A:K.22, A:S.23, A:A.24, A:V.35, A:N.122, A:K.123, A:K.123, A:A.152, A:K.153 Water bridges: A:D.18, A:D.18, A:D.36 Salt bridges: A:K.22, A:D.125 pi-Stacking: A:F.34, A:F.34

1 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)

PEG.4: 3 residues within 4Å: Chain A: D.159, D.160, Y.163 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:D.159 Water bridges: A:R.155, A:R.155

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Li, K.K. et al., GDP-bound KRAS G12D in complex with MCB-294. To Be Published

Release Date

2025-07-30

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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