SMTL ID : 6f5h.1

Crystal structure of USP7 in complex with a 4-hydroxypiperidine based inhibitor

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.16 Å

Oligo State

homo-dimer

Ligands

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

SO4.1: 6 residues within 4Å: Chain A: Q.13, R.56, G.69, T.70, K.71, K.72 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:Q.13, A:T.70, A:K.71, A:K.72 Water bridges: A:R.56 Salt bridges: A:K.11, A:R.56 SO4.4: 4 residues within 4Å: Chain B: G.69, T.70, K.71, K.72 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:G.69, B:K.71, B:K.72 Water bridges: B:T.70, B:T.70, B:L.73 Salt bridges: B:K.72 SO4.5: 4 residues within 4Å: Chain B: G.269, T.283, K.284, E.285 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:K.284

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.2: 7 residues within 4Å: Chain A: S.124, Y.125, I.126, S.135, D.136, R.137, K.185 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:S.135

2 x CQ5: 3-[[4-oxidanyl-1-[(3~{R})-3-phenylbutanoyl]piperidin-4-yl]methyl]-6-(2-pyrrolidin-1-ylethylamino)pyrimidin-4-one(Non-covalent)

CQ5.3: 15 residues within 4Å: Chain A: Y.18, D.89, V.90, Q.91, L.200, M.201, R.202, F.203, K.214, H.250, D.253, N.254, H.255, Y.259, Y.308 15 PLIP interactions: 15 interactions with chain A Hydrophobic interactions: A:M.201, A:R.202, A:F.203, A:F.203, A:K.214, A:H.250, A:Y.308, A:Y.308 Hydrogen bonds: A:V.90, A:Q.91, A:R.202, A:F.203 Water bridges: A:D.89 Salt bridges: A:D.89 pi-Cation interactions: A:K.214 CQ5.6: 15 residues within 4Å: Chain B: Y.18, D.89, V.90, Q.91, L.200, M.201, R.202, F.203, K.214, H.250, D.253, N.254, H.255, Y.259, Y.308 18 PLIP interactions: 18 interactions with chain B Hydrophobic interactions: B:V.90, B:M.201, B:R.202, B:F.203, B:F.203, B:K.214, B:H.250, B:Y.308, B:Y.308 Hydrogen bonds: B:D.89, B:V.90, B:Q.91, B:R.202, B:F.203, B:Y.259 Water bridges: B:D.89 Salt bridges: B:D.89 pi-Cation interactions: B:K.214

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

O'Dowd, C.R. et al., Identification and Structure-Guided Development of Pyrimidinone Based USP7 Inhibitors. ACS Med Chem Lett (2018)

Release Date

2018-04-11

Peptides

Ubiquitin carboxyl-terminal hydrolase 7: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Ubiquitin carboxyl-terminal hydrolase 7

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