SMTL ID : 6d5v.1

Ras:SOS:Ras in complex with a small molecule activator

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.04 Å

Oligo State

hetero-1-1-1-mer

Ligands

1 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 3 residues within 4Å: Chain A: S.18, T.36 Ligands: GNP.2 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:S.18, A:T.36, H2O.2, H2O.2

1 x GNP: PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER(Non-covalent)

GNP.2: 25 residues within 4Å: Chain A: A.12, G.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, G.61, Q.62, N.117, K.118, D.120, L.121, S.146, A.147, K.148 Ligands: MG.1 26 PLIP interactions: 26 interactions with chain A Hydrogen bonds: A:G.14, A:V.15, A:G.16, A:K.17, A:K.17, A:K.17, A:S.18, A:S.18, A:A.19, A:V.30, A:T.36, A:T.36, A:G.61, A:Q.62, A:N.117, A:K.118, A:K.118, A:A.147, A:K.148 Water bridges: A:S.18, A:D.34, A:Q.62, A:Q.62 Salt bridges: A:D.120 pi-Stacking: A:F.29, A:F.29

1 x FVY: 1-[(3-chloro-4-fluorophenyl)methyl]-5,6-dimethyl-1H-benzimidazol-2-amine(Non-covalent)

FVY.3: 12 residues within 4Å: Chain C: V.288, M.314, N.315, V.319, Y.320, L.322, T.325, F.326, I.329, L.337, E.338, H.341 8 PLIP interactions: 8 interactions with chain C Hydrophobic interactions: C:Y.320, C:L.322, C:F.326, C:F.326, C:L.337, C:L.337 Hydrogen bonds: C:Y.320 pi-Cation interactions: C:F.326

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Hodges, T.R. et al., Discovery and Structure-Based Optimization of Benzimidazole-Derived Activators of SOS1-Mediated Nucleotide Exchange on RAS. J. Med. Chem. (2018)

Release Date

2018-09-19

Peptides

GTPase HRas: A
GTPase HRas: B
Son of sevenless homolog 1: C

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
Q

B
R

C
S

GTPase HRas

GTPase HRas

Son of sevenless homolog 1

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