SMTL ID : 8afd.2 (3 other biounits)

CRYSTAL STRUCTURE OF BIT-BLOCKED KRAS-G12V-S39C IN COMPLEX WITH COMPOUND 20a

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.63 Å

Oligo State

monomer

Ligands

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

GDP.1: 22 residues within 4Å: Chain A: A.12, V.13, G.14, V.15, G.16, K.17, S.18, A.19, F.29, V.30, 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 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:D.31, 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:P.35 Salt bridges: A:K.17, A:D.120 pi-Stacking: A:F.29, 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 4 PLIP interactions: 1 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:S.18, H2O.1, H2O.1, H2O.1

1 x 2XO: 1H-benzimidazol-2-ylmethanethiol(Non-covalent)

2XO.3: 11 residues within 4Å: Chain A: K.6, L.7, V.8, C.40, D.55, I.56, L.57, Y.72, M.73, T.75, G.76 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:K.6, A:V.8, A:L.57 Hydrogen bonds: A:K.6, A:D.55 pi-Cation interactions: A:K.6

1 x LXU: (4~{S})-4-[3-(4-aminophenyl)-1,2,4-oxadiazol-5-yl]-2-azanyl-4-methyl-6,7-dihydro-5~{H}-1-benzothiophene-3-carbonitrile(Non-covalent)

LXU.4: 20 residues within 4Å: Chain A: V.8, V.10, V.13, T.59, G.61, Q.62, E.63, E.64, Y.65, S.66, R.69, D.70, M.73, F.79, H.96, Y.97, Q.100, I.101, R.103, V.104 14 PLIP interactions: 14 interactions with chain A Hydrophobic interactions: A:V.10, A:E.63, A:E.63, A:M.73, A:Y.97, A:Q.100, A:I.101 Hydrogen bonds: A:G.61, A:E.63, A:E.64, A:D.70, A:H.96, A:R.103 Water bridges: A:R.69

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Broker, J. et al., Fragment Optimization of Reversible Binding to the Switch II Pocket on KRAS Leads to a Potent, In Vivo Active KRAS G12C Inhibitor. J.Med.Chem. (2022)

Release Date

2022-11-09

Peptides

GTPase KRas: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

GTPase KRas

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