SMTL ID : 6d5g.1

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

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.92 Å

Oligo State

hetero-1-1-1-mer

Ligands

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

GNP.1: 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.2 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:A.19, A:V.30, 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:S.18, A:D.34, A:Q.62, A:Q.62, A:K.148 Salt bridges: 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: GNP.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

6 x FMT: FORMIC ACID(Non-functional Binders)

FMT.3: 3 residues within 4Å: Chain A: E.99, Q.100, R.103 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.103 FMT.6: 4 residues within 4Å: Chain B: Q.2, M.3, H.52, M.53 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:M.3 FMT.7: 2 residues within 4Å: Chain B: R.203, P.204 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:R.203 FMT.8: 6 residues within 4Å: Chain A: I.37, E.38, M.68, Q.71 Chain B: A.55, R.124 4 PLIP interactions: 3 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:E.38, A:M.68, B:R.124 Water bridges: A:Q.71 FMT.9: 6 residues within 4Å: Chain B: E.47, Y.51, H.52, R.83, Y.117, V.121 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:E.47, B:E.47, B:H.52, B:R.83, B:R.83 FMT.10: 3 residues within 4Å: Chain B: K.466, Y.467, S.468 3 PLIP interactions: 3 interactions with chain B Water bridges: B:K.465, B:K.466, B:S.468

3 x CL: CHLORIDE ION(Non-functional Binders)

CL.4: 3 residues within 4Å: Chain A: Y.41, R.42 Chain B: N.412 Ligand excluded by PLIP CL.14: 4 residues within 4Å: Chain C: V.46, I.47, D.48, R.162 Ligand excluded by PLIP CL.15: 4 residues within 4Å: Chain C: N.86, N.87, T.88, T.125 Ligand excluded by PLIP

1 x FVD: 6-chloro-1-[(4-fluoro-3,5-dimethylphenyl)methyl]-2-(piperazin-1-yl)-4-(1,2,3,6-tetrahydropyridin-4-yl)-1H-benzimidazole(Non-covalent)

FVD.5: 15 residues within 4Å: Chain B: V.288, V.311, M.314, N.315, V.319, Y.320, L.322, D.323, F.326, I.329, L.337, E.338, H.341, E.345 Ligands: GOL.13 7 PLIP interactions: 7 interactions with chain B Hydrophobic interactions: B:V.319, B:L.322, B:F.326, B:L.337 Hydrogen bonds: B:D.323, B:E.338 Halogen bonds: B:V.311

3 x GOL: GLYCEROL(Non-functional Binders)

GOL.11: 8 residues within 4Å: Chain B: R.222, V.297, E.300, L.301, L.417, V.476, R.477, P.478 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:R.222, B:E.300, B:R.477 GOL.12: 5 residues within 4Å: Chain B: S.229, D.230, R.233, P.414, Y.415 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:S.229, B:S.229, B:Y.415 GOL.13: 4 residues within 4Å: Chain B: F.326, K.334, E.338 Ligands: FVD.5 No protein-ligand interaction detected (PLIP)

1 x BME: BETA-MERCAPTOETHANOL(Non-functional Binders)

BME.16: 10 residues within 4Å: Chain B: T.246, L.374 Chain C: G.13, G.14, G.16, K.17, S.18, A.60, G.61, E.63 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:G.14, C:G.61, C:E.63 Water bridges: C:E.63

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
Son of sevenless homolog 1: B
GTPase HRas: C

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

GTPase HRas

Son of sevenless homolog 1

GTPase HRas

Related Entries With Identical Sequence