SMTL ID : 5v6s.1

Crystal structure of small molecule acrylamide 1 covalently bound to K-Ras G12C

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.70 Å

Oligo State

monomer

Ligands

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

GDP.1: 22 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, E.32, Y.33, N.117, K.118, D.120, L.121, S.146, A.147, K.148 Ligands: MG.2, 8YD.3 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:S.18, A:A.19, A:V.30, A:N.117, A:K.118, A:K.118, A:S.146, A:S.146, A:A.147, 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

1 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 5 residues within 4Å: Chain A: 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.1, H2O.2, H2O.2

1 x 8YD: 1-{4-[6-chloro-8-fluoro-7-(5-methyl-1H-indazol-4-yl)quinazolin-4-yl]piperazin-1-yl}propan-1-one(Covalent)

8YD.3: 24 residues within 4Å: Chain A: V.10, G.11, A.12, C.13, G.14, K.17, P.35, T.59, A.60, G.61, Q.62, E.63, E.64, Y.65, R.69, D.70, M.73, H.96, Y.97, Q.100, I.101, R.103, V.104 Ligands: GDP.1 11 PLIP interactions: 11 interactions with chain A Hydrophobic interactions: A:Y.65, A:M.73, A:Y.97, A:Y.97, A:Q.100, A:V.104 Hydrogen bonds: A:K.17, A:D.70, A:D.70, A:R.103 Water bridges: A:Y.97

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

McGregor, L.M. et al., Expanding the Scope of Electrophiles Capable of Targeting K-Ras Oncogenes. Biochemistry (2017)

Release Date

2017-06-28

Peptides

GTPase KRas: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

GTPase KRas

Related Entries With Identical Sequence