SMTL ID : 5vbm.1

Crystal Structure of Small Molecule Disulfide 2C07 Bound to K-Ras Cys Light M72C GDP

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.49 Å

Oligo State

monomer

Ligands

1 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 4 residues within 4Å: Chain A: S.18, Y.33, P.35 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.2

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

GDP.2: 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.1 20 PLIP interactions: 20 interactions with chain A Hydrogen bonds: 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:Y.33, A:N.117, A:K.118, A:K.118, A:S.146, A:A.147, A:K.148 Water bridges: A:T.59 Salt bridges: A:K.17, A:D.120 pi-Stacking: A:F.29, A:F.29

1 x 92V: 1-(4-methoxyphenyl)-N-(3-sulfanylpropyl)-5-(trifluoromethyl)-1H-pyrazole-4-carboxamide(Non-covalent)

92V.3: 12 residues within 4Å: Chain A: V.8, V.10, T.59, R.69, C.73, F.79, K.89, D.93, H.96, Y.97, Q.100, I.101 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:H.96, A:Y.97 Hydrogen bonds: A:R.69

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Gentile, D.R. et al., Ras Binder Induces a Modified Switch-II Pocket in GTP and GDP States. Cell Chem Biol (2017)

Release Date

2017-10-25

Peptides

GTPase KRas: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

GTPase KRas