SMTL ID : 4nyi.1

Approach for Targeting Ras with Small Molecules that Activate SOS-Mediated Nucleotide Exchange

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.96 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.1, H2O.1

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

GNP.2: 26 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, A.60, 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:A.19, A:V.30, A:D.31, A:Y.33, A:T.36, A:G.61, A:Q.62, A:Q.62, A:N.117, A:K.118, A:K.118, A:A.147, A:K.148 Water bridges: A:T.36, A:T.36 Salt bridges: A:D.120 pi-Stacking: A:F.29, A:F.29 pi-Cation interactions: A:K.118

1 x 2PX: N-{1-[(5-methyl-1H-indol-3-yl)methyl]piperidin-4-yl}-L-tryptophanamide(Non-covalent)

2PX.3: 9 residues within 4Å: Chain C: M.313, N.314, Y.319, D.322, F.325, K.333, L.336, E.337, H.340 11 PLIP interactions: 11 interactions with chain C Hydrophobic interactions: C:M.313, C:F.325, C:F.325, C:K.333, C:K.333, C:K.333, C:L.336, C:L.336, C:H.340 Hydrogen bonds: C:M.313, C:E.337

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Burns, M.C. et al., Approach for targeting Ras with small molecules that activate SOS-mediated nucleotide exchange. Proc.Natl.Acad.Sci.USA (2014)

Release Date

2014-03-12

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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