Structure of USP5 zinc-finger ubiquitin binding domain co-crystallized with (5-((4-(4-chlorophenyl)piperidin-1-yl)sulfonyl)picolinoyl)glycine

Experimental Data Snapshot

  • Resolution: 1.45 Å
  • R-Value Free: 0.181 
  • R-Value Work: 0.169 
  • R-Value Observed: 0.170 

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This is version 1.3 of the entry. See complete history


Structure-Activity Relationship of USP5 Inhibitors.

Mann, M.K.Zepeda-Velazquez, C.A.Gonzalez-Alvarez, H.Dong, A.Kiyota, T.Aman, A.M.Loppnau, P.Li, Y.Wilson, B.Arrowsmith, C.H.Al-Awar, R.Harding, R.J.Schapira, M.

(2021) J Med Chem 64: 15017-15036

  • DOI: https://doi.org/10.1021/acs.jmedchem.1c00889
  • Primary Citation of Related Structures:  
    7MS5, 7MS6, 7MS7

  • PubMed Abstract: 

    USP5 is a deubiquitinase that has been implicated in a range of diseases, including cancer, but no USP5-targeting chemical probe has been reported to date. Here, we present the progression of a chemical series that occupies the C-terminal ubiquitin-binding site of a poorly characterized zinc-finger ubiquitin binding domain (ZnF-UBD) of USP5 and competitively inhibits the catalytic activity of the enzyme. Exploration of the structure-activity relationship, complemented with crystallographic characterization of the ZnF-UBD bound to multiple ligands, led to the identification of 64 , which binds to the USP5 ZnF-UBD with a K D of 2.8 μM and is selective over nine proteins containing structurally similar ZnF-UBD domains. 64 inhibits the USP5 catalytic cleavage of a di-ubiquitin substrate in an in vitro assay. This study provides a chemical and structural framework for the discovery of a chemical probe to delineate USP5 function in cells.

  • Organizational Affiliation

    Structural Genomics Consortium, University of Toronto, 101 College Street, MaRS South Tower, Suite 700, Toronto, Ontario M5G 1L7, Canada.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Ubiquitin carboxyl-terminal hydrolase 5
A, B
121Homo sapiensMutation(s): 0 
Gene Names: USP5ISOT
UniProt & NIH Common Fund Data Resources
Find proteins for P45974 (Homo sapiens)
Explore P45974 
Go to UniProtKB:  P45974
PHAROS:  P45974
GTEx:  ENSG00000111667 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP45974
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

Unit Cell:
Length ( Å )Angle ( ˚ )
a = 61.556α = 90
b = 84.87β = 98.86
c = 59.542γ = 90
Software Package:
Software NamePurpose
Aimlessdata scaling
PDB_EXTRACTdata extraction
xia2data reduction

Structure Validation

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Ligand Structure Quality Assessment 

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2021-06-09
    Type: Initial release
  • Version 1.1: 2021-10-27
    Changes: Database references
  • Version 1.2: 2021-11-10
    Changes: Database references
  • Version 1.3: 2023-10-18
    Changes: Data collection, Refinement description