SMTL ID : 9ib4.1

Structure of 12 in complex with GDP-KRAS

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.06 Å

Oligo State

monomer

Ligands

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

GDP.1: 21 residues within 4Å: Chain A: A.12, G.13, G.14, V.15, G.16, K.17, S.18, A.19, F.29, D.31, E.32, Y.33, P.35, N.117, K.118, D.120, L.121, S.146, A.147, K.148 Ligands: MG.2 24 PLIP interactions: 24 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:D.31, A:D.31, 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, A:D.58 Salt bridges: A:K.17, A:D.120 pi-Stacking: A:F.29

1 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 6 residues within 4Å: Chain A: K.17, 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

2 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.3: 7 residues within 4Å: Chain A: F.91, E.92, D.93, I.94, H.95, L.134, Y.138 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:E.92, A:I.94, A:H.95 Water bridges: A:E.92, A:Q.130 EDO.4: 4 residues within 4Å: Chain A: S.119, D.120, L.121, P.122 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:D.120

1 x 01: (4~{S})-2-azanyl-4-methyl-4-[3-[2-[[(2~{S})-1-methylpyrrolidin-2-yl]methoxy]pyrimidin-4-yl]-1,2,4-oxadiazol-5-yl]-6,7-dihydro-5~{H}-1-benzothiophene-3-carbonitrile

01.5: 20 residues within 4Å: Chain A: V.8, V.10, T.59, G.61, Q.62, E.63, E.64, Y.65, R.69, D.70, M.73, F.79, K.89, D.93, H.96, Y.97, Q.100, I.101, R.103, V.104 18 PLIP interactions: 18 interactions with chain A Hydrophobic interactions: A:V.10, A:E.63, A:M.73, A:H.96, A:Y.97, A:I.101 Hydrogen bonds: 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:E.63, A:R.69 Salt bridges: A:E.63

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Broker, J. et al., Discovery of BI-2493, a Pan-KRAS Inhibitor Showing In Vivo Efficacy. J.Med.Chem. (2025)

Release Date

2025-08-06

Peptides

GTPase KRas: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

GTPase KRas

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