SMTL ID : 6zl5.1

CRYSTAL STRUCTURE OF KRAS-G12D(C118S) IN COMPLEX WITH BI-2852 AND GDP

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.64 Å

Oligo State

monomer

Ligands

1 x MG: MAGNESIUM ION(Non-covalent)

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

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

GDP.2: 18 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, N.117, K.118, D.120, L.121, S.146, A.147, K.148 Ligands: MG.1 21 PLIP interactions: 21 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:N.117, A:K.118, A:K.118, A:A.147, A:K.148 Water bridges: A:K.17, A:S.18, A:V.30, A:D.31, A:D.31 Salt bridges: A:K.17, A:D.120 pi-Stacking: A:F.29, A:F.29

1 x F0K: (3~{S})-3-[2-[[[1-[(1-methylimidazol-4-yl)methyl]indol-6-yl]methylamino]methyl]-1~{H}-indol-3-yl]-5-oxidanyl-2,3-dihydroisoindol-1-one(Non-covalent)

F0K.3: 11 residues within 4Å: Chain A: K.6, L.7, V.8, D.39, S.40, D.55, L.57, M.68, Y.72, T.75, G.76 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:K.6, A:K.6, A:V.8, A:L.57, A:Y.72, A:T.75 Hydrogen bonds: A:D.55 Water bridges: A:D.55 pi-Cation interactions: A:K.6

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

SO4.4: 2 residues within 4Å: Chain A: I.47, D.48 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:D.48 Water bridges: A:V.46, A:D.48, A:G.49

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kessler, D. et al., Drugging all RAS isoforms with one pocket. Future Med Chem (2020)

Release Date

2020-08-19

Peptides

GTPase KRas: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

GTPase KRas

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