6P9G

Structure of USP5 zinc-finger ubiquitin binding domain co-crystallized with 2-(4-oxoquinazolin-3(4H)-yl)propanoic acid


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.248 
  • R-Value Work: 0.224 
  • R-Value Observed: 0.225 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


Literature

Discovery of Small Molecule Antagonists of the USP5 Zinc Finger Ubiquitin-Binding Domain.

Mann, M.K.Franzoni, I.de Freitas, R.F.Tempel, W.Houliston, S.Smith, L.Vedadi, M.Arrowsmith, C.H.Harding, R.J.Schapira, M.

(2019) J Med Chem 62: 10144-10155

  • DOI: 10.1021/acs.jmedchem.9b00988
  • Primary Citation of Related Structures:  
    6DXH, 6DXT, 6NFT, 6P9G

  • PubMed Abstract: 
  • USP5 disassembles unanchored polyubiquitin chains to recycle free monoubiquitin, and is one of the 12 ubiquitin specific proteases featuring a zinc finger ubiquitin-binding domain (ZnF-UBD). This distinct structural module has been associated with substrate positioning or allosteric modulation of catalytic activity, but its cellular function remains unclear ...

    USP5 disassembles unanchored polyubiquitin chains to recycle free monoubiquitin, and is one of the 12 ubiquitin specific proteases featuring a zinc finger ubiquitin-binding domain (ZnF-UBD). This distinct structural module has been associated with substrate positioning or allosteric modulation of catalytic activity, but its cellular function remains unclear. We screened a chemical library focused on the ZnF-UBD of USP5, crystallized hits in complex with the protein, and generated a preliminary structure-activity relationship, which enables the development of more potent and selective compounds. This work serves as a framework for the discovery of a chemical probe to delineate the function of USP5 ZnF-UBD in proteasomal degradation and other ubiquitin signaling pathways in health and disease.


    Organizational Affiliation

    Department of Pharmacology and Toxicology , University of Toronto , 1 King's College Circle , Toronto , Ontario M5S 1A8 , Canada.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Ubiquitin carboxyl-terminal hydrolase 5A121Homo sapiensMutation(s): 0 
Gene Names: USP5ISOT
EC: 3.4.19.12
UniProt & NIH Common Fund Data Resources
Find proteins for P45974 (Homo sapiens)
Explore P45974 
Go to UniProtKB:  P45974
PHAROS:  P45974
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP45974
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
O4Y (Subject of Investigation/LOI)
Query on O4Y

Download Ideal Coordinates CCD File 
C [auth A](2R)-2-(4-oxoquinazolin-3(4H)-yl)propanoic acid
C11 H10 N2 O3
AOIOGRLXASIYJK-SSDOTTSWSA-N
 Ligand Interaction
ZN
Query on ZN

Download Ideal Coordinates CCD File 
B [auth A]ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
UNX
Query on UNX

Download Ideal Coordinates CCD File 
D [auth A],
E [auth A],
F [auth A],
G [auth A],
H [auth A],
D [auth A],
E [auth A],
F [auth A],
G [auth A],
H [auth A],
I [auth A],
J [auth A],
K [auth A],
L [auth A],
M [auth A],
N [auth A],
O [auth A],
P [auth A]
UNKNOWN ATOM OR ION
X
 Ligand Interaction
Experimental Data & Validation

Experimental Data

Unit Cell:
Length ( Å )Angle ( ˚ )
a = 47.846α = 90
b = 82.405β = 90
c = 99.819γ = 90
Software Package:
Software NamePurpose
Aimlessdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
REFMACphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Revision History  (Full details and data files)

  • Version 1.0: 2019-09-18
    Type: Initial release
  • Version 1.1: 2021-06-09
    Changes: Database references