SMTL ID : 5f2e.1

Crystal Structure of small molecule ARS-853 covalently bound to K-Ras G12C

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.40 Å

Oligo State

monomer

Ligands

1 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 2 residues within 4Å: Chain A: S.18 Ligands: GDP.6 5 PLIP interactions: 1 interactions with chain A, 4 Ligand-Water interactions Metal complexes: A:S.18, H2O.2, H2O.2, H2O.2, H2O.4

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.2: 6 residues within 4Å: Chain A: F.91, E.92, I.94, H.95, Q.130, L.134 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:I.94, A:H.95, A:Q.130 GOL.3: 4 residues within 4Å: Chain A: R.98, E.108, S.137, Y.138 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.98, A:K.102, A:E.108, A:S.137

1 x 5UT: 1-[3-[4-[2-[[4-chloranyl-5-(1-methylcyclopropyl)-2-oxidanyl-phenyl]amino]ethanoyl]piperazin-1-yl]azetidin-1-yl]prop-2-en-1-one(Covalent)

5UT.4: 21 residues within 4Å: Chain A: V.10, G.11, C.13, K.17, P.35, T.59, A.60, G.61, Q.62, E.63, E.64, Y.65, S.66, R.69, D.70, M.73, Y.97, Q.100, I.101, V.104 Ligands: GDP.6 15 PLIP interactions: 15 interactions with chain A Hydrophobic interactions: A:V.10, A:P.35, A:Y.65, A:Y.65, A:Y.97, A:Q.100, A:I.101 Hydrogen bonds: A:K.17, A:E.64, A:S.66, A:R.69, A:D.70, A:D.70 Water bridges: A:E.64 Salt bridges: A:E.63

1 x GLY: GLYCINE(Non-covalent)

GLY.5: 4 residues within 4Å: Chain A: T.3, Y.5, E.50, R.165 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:T.3, A:Y.5, A:Y.5, A:E.50

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

GDP.6: 21 residues within 4Å: Chain A: A.12, C.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, 5UT.4 25 PLIP interactions: 25 interactions with chain A Hydrogen bonds: 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:S.18, A:S.18, A:S.18, A:D.31, A:E.32, A:D.120, A:K.148 Salt bridges: A:K.17, A:D.120 pi-Stacking: A:F.29, A:F.29 pi-Cation interactions: A:K.118

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Patricelli, M.P. et al., Selective Inhibition of Oncogenic KRAS Output with Small Molecules Targeting the Inactive State. Cancer Discov (2016)

Release Date

2016-01-13

Peptides

GTPase KRas: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

GTPase KRas

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