5N9T

Crystal structure of USP7 in complex with a potent, selective and reversible small-molecule inhibitor


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.73 Å
  • R-Value Free: 0.224 
  • R-Value Work: 0.161 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Discovery and characterization of highly potent and selective allosteric USP7 inhibitors.

Gavory, G.O'Dowd, C.R.Helm, M.D.Flasz, J.Arkoudis, E.Dossang, A.Hughes, C.Cassidy, E.McClelland, K.Odrzywol, E.Page, N.Barker, O.Miel, H.Harrison, T.

(2018) Nat. Chem. Biol. 14: 118-125

  • DOI: 10.1038/nchembio.2528
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Given the importance of ubiquitin-specific protease 7 (USP7) in oncogenic pathways, identification of USP7 inhibitors has attracted considerable interest. Despite substantial efforts, however, the development of validated deubiquitinase (DUB) inhibit ...

    Given the importance of ubiquitin-specific protease 7 (USP7) in oncogenic pathways, identification of USP7 inhibitors has attracted considerable interest. Despite substantial efforts, however, the development of validated deubiquitinase (DUB) inhibitors that exhibit drug-like properties and a well-defined mechanism of action has proven particularly challenging. In this article, we describe the identification, optimization and detailed characterization of highly potent (IC50 < 10 nM), selective USP7 inhibitors together with their less active, enantiomeric counterparts. We also disclose, for the first time, co-crystal structures of a human DUB enzyme complexed with small-molecule inhibitors, which reveal a previously undisclosed allosteric binding site. Finally, we report the identification of cancer cell lines hypersensitive to USP7 inhibition (EC50 < 30 nM) and demonstrate equal or superior activity in these cell models compared to clinically relevant MDM2 antagonists. Overall, these findings demonstrate the tractability and druggability of DUBs, and provide important tools for additional target validation studies.


    Organizational Affiliation

    Almac Discovery Ltd, Centre for Precision Therapeutics, Belfast, Northern Ireland, UK.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Ubiquitin carboxyl-terminal hydrolase 7
A, B
357Homo sapiensMutation(s): 0 
Gene Names: USP7 (HAUSP)
EC: 3.4.19.12
Find proteins for Q93009 (Homo sapiens)
Go to Gene View: USP7
Go to UniProtKB:  Q93009
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

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Download CCD File 
A, B
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
8QQ
Query on 8QQ

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Download CCD File 
A, B
3-[4-(aminomethyl)phenyl]-2-methyl-6-[[4-oxidanyl-1-[(3~{R})-4,4,4-tris(fluoranyl)-3-phenyl-butanoyl]piperidin-4-yl]methyl]pyrazolo[4,3-d]pyrimidin-7-one
C29 H31 F3 N6 O3
RLPQYKGBXQQARM-JOCHJYFZSA-N
 Ligand Interaction
GOL
Query on GOL

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Download CCD File 
A
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.73 Å
  • R-Value Free: 0.224 
  • R-Value Work: 0.161 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 75.507α = 90.00
b = 67.623β = 105.90
c = 81.046γ = 90.00
Software Package:
Software NamePurpose
PDB_EXTRACTdata extraction
SCALAdata scaling
MOSFLMdata reduction
REFMACrefinement
PHASERphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2017-12-06
    Type: Initial release
  • Version 1.1: 2017-12-13
    Type: Database references
  • Version 1.2: 2018-01-24
    Type: Database references