SMTL ID : 5trf.6 (7 other biounits)

MDM2 in complex with SAR405838

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.10 Å

Oligo State

homo-dimer

Ligands

2 x 7HC: (2'S,3R,4'S,5'R)-6-chloro-4'-(3-chloro-2-fluorophenyl)-2'-(2,2-dimethylpropyl)-N-(trans-4-hydroxycyclohexyl)-2-oxo-1,2-dihydrospiro[indole-3,3'-pyrrolidine]-5'-carboxamide(Non-covalent)

7HC.1: 19 residues within 4Å: Chain A: V.5, T.7, L.45, L.48, G.49, I.52, M.53, Y.58, H.64, F.77, F.82, V.84, K.85, H.87, I.90, Y.91 Chain B: T.1, Q.50, M.53 20 PLIP interactions: 18 interactions with chain A, 2 interactions with chain B Hydrophobic interactions: A:V.5, A:V.5, A:T.7, A:L.45, A:L.45, A:L.48, A:I.52, A:I.52, A:Y.58, A:F.82, A:V.84, A:V.84, A:I.90, B:T.1, B:Q.50 Hydrogen bonds: A:L.45, A:H.64, A:K.85 pi-Stacking: A:H.87 Halogen bonds: A:H.87 7HC.6: 19 residues within 4Å: Chain A: T.1, Q.50, M.53 Chain B: V.5, T.7, L.45, L.48, G.49, I.52, M.53, Y.58, H.64, F.77, F.82, V.84, K.85, H.87, I.90, Y.91 21 PLIP interactions: 18 interactions with chain B, 3 interactions with chain A Hydrophobic interactions: B:V.5, B:V.5, B:T.7, B:L.45, B:L.45, B:L.48, B:I.52, B:I.52, B:Y.58, B:F.82, B:V.84, B:V.84, B:I.90, A:T.1, A:Q.50 Hydrogen bonds: B:L.45, B:H.64, B:K.85 pi-Stacking: B:H.87 Halogen bonds: B:H.87 Water bridges: A:T.54

2 x SO4: SULFATE ION(Non-functional Binders)

SO4.2: 3 residues within 4Å: Chain A: K.36, D.37, T.38 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:D.37, A:T.38, A:T.38 SO4.7: 3 residues within 4Å: Chain B: K.36, D.37, T.38 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:D.37, B:T.38

6 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 2 residues within 4Å: Chain A: Y.95, V.100 No protein-ligand interaction detected (PLIP) GOL.4: 1 residues within 4Å: Chain A: R.96 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.96 GOL.5: 3 residues within 4Å: Chain A: D.75, L.76, R.96 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:D.75, A:R.96 Water bridges: A:N.97 GOL.8: 2 residues within 4Å: Chain B: Y.95, V.100 No protein-ligand interaction detected (PLIP) GOL.9: 1 residues within 4Å: Chain B: R.96 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:R.96 GOL.10: 3 residues within 4Å: Chain B: D.75, L.76, R.96 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:D.75, B:R.96 Water bridges: B:N.97

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Wang, S. et al., SAR405838: an optimized inhibitor of MDM2-p53 interaction that induces complete and durable tumor regression. Cancer Res. (2014)

Release Date

2016-11-09

Peptides

E3 ubiquitin-protein ligase Mdm2: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

E3 ubiquitin-protein ligase Mdm2

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