SMTL ID : 4dsu.1

Small-molecule ligands bind to a distinct pocket in Ras and inhibit SOS-mediated nucleotide exchange activity

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.70 Å

Oligo State

monomer

Ligands

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

GDP.1: 21 residues within 4Å: Chain A: A.12, D.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 22 PLIP interactions: 22 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:V.30, A:N.117, A:K.118, A:K.118, A:A.147, A:K.148 Water bridges: A:K.17, A:K.17, A:K.17, A:S.18, A:D.34 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: 2 residues within 4Å: Chain A: S.18 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.1, H2O.2

1 x BZI: BENZIMIDAZOLE(Non-covalent)

BZI.3: 8 residues within 4Å: Chain A: K.6, L.7, V.8, S.40, D.55, L.57, Y.72, T.75 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:K.6, A:V.8, A:L.57, A:L.57, A:T.75 Hydrogen bonds: A:D.55

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Maurer, T. et al., Small-molecule ligands bind to a distinct pocket in Ras and inhibit SOS-mediated nucleotide exchange activity. Proc.Natl.Acad.Sci.USA (2012)

Release Date

2012-04-04

Peptides

GTPase KRas, isoform 2B: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

GTPase KRas, isoform 2B

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