SMTL ID : 6bvl.1

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

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.75 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 27 PLIP interactions: 27 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.31, 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.3

1 x EBY: N-{1-[(5-chloro-1H-indol-3-yl)methyl]piperidin-4-yl}-5-methyl-L-tryptophanamide(Non-covalent)

EBY.3: 8 residues within 4Å: Chain B: M.314, N.315, Y.320, D.323, F.326, K.334, E.338, H.341 10 PLIP interactions: 10 interactions with chain B Hydrophobic interactions: B:M.314, B:F.326, B:F.326, B:K.334, B:K.334, B:K.334, B:E.338 Hydrogen bonds: B:M.314, B:F.326 Halogen bonds: B:E.338

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

FMT.4: 5 residues within 4Å: Chain B: Q.2, M.3, H.52, M.53, R.112 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:M.3 FMT.5: 2 residues within 4Å: Chain B: R.203, P.204 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:R.203 FMT.6: 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, B:R.124 Water bridges: A:M.68, A:Q.71 FMT.7: 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.8: 3 residues within 4Å: Chain B: K.466, Y.467, S.468 1 PLIP interactions: 1 interactions with chain B Water bridges: B:S.468 FMT.11: 7 residues within 4Å: Chain B: L.374 Chain C: G.14, G.16, K.17, S.18, A.60, E.63 7 PLIP interactions: 7 interactions with chain C Hydrogen bonds: C:G.14, C:G.16, C:K.17, C:S.18, C:E.63 Water bridges: C:V.15, C:G.61

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.9: 6 residues within 4Å: Chain B: L.226, S.229, D.230, R.233, P.414, Y.415 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:S.229, B:S.229, B:Y.415 Water bridges: B:D.230, B:D.230, B:D.230 GOL.10: 7 residues within 4Å: Chain B: R.222, V.297, E.300, L.301, L.417, V.476, P.478 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:R.222, B:E.300, B:R.477

1 x NA: SODIUM ION(Non-functional Binders)

NA.12: 4 residues within 4Å: Chain C: N.86, N.87, T.88, T.125 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:T.88, C:T.88 Water bridges: C:T.88

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Abbott, J.R. et al., Discovery of Aminopiperidine Indoles That Activate the Guanine Nucleotide Exchange Factor SOS1 and Modulate RAS Signaling. J. Med. Chem. (2018)

Release Date

2018-10-24

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

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