SMTL ID : 4dso.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 1.85 Å

Oligo State

monomer

Ligands

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

GSP.1: 26 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, P.35, T.36, T.59, A.60, G.61, N.117, K.118, D.120, L.121, S.146, A.147, K.148 Ligands: MG.2 24 PLIP interactions: 24 interactions with chain A Hydrogen bonds: A:G.14, A:V.15, A:G.16, A:K.17, A:K.17, A:S.18, A:A.19, A:E.32, A:Y.33, A:T.36, A:G.61, A:N.117, A:K.118, A:K.118, A:A.147, A:K.148 Water bridges: A:S.18, A:T.36, A:T.36, A:Q.62 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: 3 residues within 4Å: Chain A: S.18, T.36 Ligands: GSP.1 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:S.18, A:T.36, H2O.1, H2O.3

1 x BEN: BENZAMIDINE(Non-functional Binders)

BEN.3: 8 residues within 4Å: Chain A: L.7, V.8, S.40, R.42, D.55, I.56, L.57, T.75 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:V.8, A:L.57, A:T.75 Hydrogen bonds: A:S.40, A:D.55

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.4: 6 residues within 4Å: Chain A: E.63, R.69, D.93, H.96, Y.97, Q.100 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:D.93, A:Q.100 Water bridges: A:K.89, A:Q.100

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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