9FIP

Structure-guided discovery of selective USP7 inhibitors with in vivo activity


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.06 Å
  • R-Value Free: 0.264 
  • R-Value Work: 0.169 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


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Literature

Structure-Guided Discovery of Selective USP7 Inhibitors with In Vivo Activity.

Vasas, A.Ivanschitz, L.Molnar, B.Kiss, A.Baker, L.Fiumana, A.Macias, A.Murray, J.B.Sanders, E.Whitehead, N.Hubbard, R.E.Saunier, C.Monceau, E.Girard, A.M.Rousseau, M.Chanrion, M.Demarles, D.Geneste, O.Weber, C.Lewkowicz, E.Kotschy, A.

(2024) J Med Chem 

  • DOI: https://doi.org/10.1021/acs.jmedchem.4c01472
  • Primary Citation of Related Structures:  
    9FIO, 9FIP, 9FIQ, 9FIR, 9FIS, 9FIT, 9FIU, 9FIV

  • PubMed Abstract: 

    Inhibition of ubiquitin-specific protease 7, USP7, has been proposed as a mechanism to affect many disease processes, primarily those implicated in oncology. The bound crystal structure of a published high-throughput screening hit with low-micromolar affinity for USP7 identified three regions of the compound for structure-guided optimization. Replacing one side of the compound with different aromatic moieties gave little improvement in affinity, and the central piperidine could not be improved. However, the binding site for the other side of the compound was poorly defined in the crystal structure, which suggested a wide variety of synthetically accessible options for optimization. These were assessed by screening reaction mixtures that introduced different substituents to this other side. Subsequent optimization led to a compound with low-nanomolar affinity for USP7, which showed target engagement in tumors, was tolerated in mice, and showed efficacy in xenograft models.


  • Organizational Affiliation

    Servier Research Institute of Medicinal Chemistry, Záhony u. 7., Budapest H-1031, Hungary.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Ubiquitin carboxyl-terminal hydrolase 7
A, B
355Homo sapiensMutation(s): 0 
Gene Names: USP7HAUSP
EC: 3.4.19.12
UniProt & NIH Common Fund Data Resources
Find proteins for Q93009 (Homo sapiens)
Explore Q93009 
Go to UniProtKB:  Q93009
PHAROS:  Q93009
GTEx:  ENSG00000187555 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ93009
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
A1ICU (Subject of Investigation/LOI)
Query on A1ICU

Download Ideal Coordinates CCD File 
C [auth A],
D [auth B]
3-[[4-oxidanyl-1-[(1~{R},2~{R})-2-phenylcyclohexyl]carbonyl-piperidin-4-yl]methyl]quinazolin-4-one
C27 H31 N3 O3
FPRPKRNRTCFBRF-FCHUYYIVSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.06 Å
  • R-Value Free: 0.264 
  • R-Value Work: 0.169 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 75.05α = 90
b = 68.28β = 92
c = 77.66γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
AMoREphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Not funded--

Revision History  (Full details and data files)

  • Version 1.0: 2024-11-06
    Type: Initial release