SMTL ID : 4dsn.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 2.03 Å

Oligo State

monomer

Ligands

1 x GCP: PHOSPHOMETHYLPHOSPHONIC ACID GUANYLATE ESTER(Non-covalent)

GCP.1: 25 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, 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:D.13, A:D.13, 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:T.36, A:G.61, A:N.117, A:K.118, A:K.118, A:A.147, A:K.148 Water bridges: A:D.13, A:S.18, A:S.18, A:D.34 Salt bridges: A:D.120 pi-Stacking: A:F.29, A:F.29

2 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 3 residues within 4Å: Chain A: S.18, T.36 Ligands: GCP.1 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:S.18, A:T.36, H2O.1, H2O.1 MG.3: 4 residues within 4Å: Chain A: G.11, A.60, G.61, Y.97 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:A.60, A:G.61, A:Y.97, H2O.1, H2O.3

2 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.4: 4 residues within 4Å: Chain A: K.102, D.106, S.107, E.108 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.107 Water bridges: A:R.103 EDO.5: 4 residues within 4Å: Chain A: T.36, I.37, E.38, D.39 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:I.37, A:E.38

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

2012-04-25

Peptides

GTPase KRas, isoform 2B: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

GTPase KRas, isoform 2B

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