SMTL ID : 5hmh.3 (2 other biounits)

HDM2 in complex with a 3,3-Disubstituted Piperidine

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.79 Å

Oligo State

homo-dimer

Ligands

2 x 62R: 4-[2-(4-{[(2R,3S)-2-propyl-1-{[4-(trifluoromethyl)pyridin-3-yl]carbonyl}-3-{[5-(trifluoromethyl)thiophen-3-yl]oxy}piperidin-3-yl]carbonyl}piperazin-1-yl)phenoxy]butanoic acid(Non-covalent)

62R.1: 19 residues within 4Å: Chain A: Q.6, L.36, L.39, G.40, I.43, M.44, Y.49, Q.54, V.57, F.73, V.75, H.78, I.81, Y.82 Chain B: K.33, E.34, L.36, Y.37 Ligands: 62R.3 12 PLIP interactions: 9 interactions with chain A, 3 interactions with chain B Hydrophobic interactions: A:L.36, A:L.36, A:V.75, A:H.78, A:I.81, A:Y.82, B:L.36, B:Y.37, B:Y.37 Hydrogen bonds: A:Q.6 pi-Stacking: A:Y.49, A:H.78 62R.3: 20 residues within 4Å: Chain A: K.33, L.36, Y.37 Chain B: Q.6, K.33, L.36, L.39, G.40, I.43, M.44, Y.49, Q.54, H.55, V.57, F.73, V.75, H.78, I.81, Y.82 Ligands: 62R.1 15 PLIP interactions: 11 interactions with chain B, 4 interactions with chain A Hydrophobic interactions: B:L.36, B:L.36, B:V.75, B:H.78, B:I.81, B:Y.82, A:K.33, A:L.36 Hydrogen bonds: B:Q.6 Water bridges: B:Q.54 Salt bridges: B:K.33, A:K.76 pi-Stacking: B:Y.49, B:H.78 pi-Cation interactions: A:K.33

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

SO4.2: 4 residues within 4Å: Chain A: K.76, E.77, H.78, R.79 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:H.78, A:R.79 Water bridges: A:K.80 Salt bridges: A:R.79

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Bogen, S.L. et al., Discovery of Novel 3,3-Disubstituted Piperidines as Orally Bioavailable, Potent, and Efficacious HDM2-p53 Inhibitors. Acs Med.Chem.Lett. (2016)

Release Date

2016-04-06

Peptides

E3 ubiquitin-protein ligase Mdm2: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

E3 ubiquitin-protein ligase Mdm2

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