7MS7 | pdb_00007ms7

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

• PDB DOI: https://doi.org/10.2210/pdb7MS7/pdb

• Classification: HYDROLASE/INHIBITOR
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2021-05-10 Released: 2021-06-09 
• Deposition Author(s): Mann, M.K., Zepeda-Velazquez, C.A., Alvarez, H.G., Dong, A., Kiyota, T., Aman, A., Arrowsmith, C.H., Al-Awar, R., Harding, R.J., Schapira, M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.45 Å
• R-Value Free: 
  0.181 (Depositor), 0.201 (DCC) 
• R-Value Work: 
  0.169 (Depositor) 
• R-Value Observed: 
  0.170 (Depositor) 

Starting Model: experimental

Literature

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

• PubMed: 34648286 
• DOI: https://doi.org/10.1021/acs.jmedchem.1c00889
• Primary Citation 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.

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Organizational Affiliation: 
• Structural Genomics Consortium, University of Toronto, 101 College Street, MaRS South Tower, Suite 700, Toronto, Ontario M5G 1L7, Canada.
Department of Pharmacology and Toxicology, University of Toronto, 1 King's College Circle, Toronto, Ontario M5S 1A8, Canada.
Ontario Institute for Cancer Research, 661 University Avenue, Toronto, Ontario M5G 0A3, Canada.
Leslie Dan Faculty of Pharmacy, University of Toronto, 144 College Street, Toronto, Ontario M5S 3M2, Canada.
Princess Margaret Cancer Centre, 661 University Avenue, Toronto, Ontario M5G 2C4, Canada.
Department of Medical Biophysics, University of Toronto, 101 College Street, Toronto, Ontario M5G 1L7, Canada.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: light scattering

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 27.76 kDa 
• Atom Count: 2,218 
• Modeled Residue Count: 227 
• Deposited Residue Count: 242 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Ubiquitin carboxyl-terminal hydrolase 5	A, B	121	Homo sapiens	Mutation(s): 0  Gene Names: USP5, ISOT 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 GTEx:  ENSG00000111667

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ZQ1 (Subject of Investigation/LOI)	D [auth A]	N-{5-[4-(4-chlorophenyl)piperidine-1-sulfonyl]pyridine-2-carbonyl}glycine C19 H20 Cl N3 O5 S HIWYRXWPCQHOSO-UHFFFAOYSA-N
ZN	C [auth A], G [auth B]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
EDO	E [auth A]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N
ACT	F [auth A]	ACETATE ION C2 H3 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-M

Binding Affinity Annotations
ID	Source	Binding Affinity
ZQ1	BindingDB:  7MS7	Kd: min: 2800, max: 8000 (nM) from 2 assay(s)
		IC50: min: 800, max: 4.60e+4 (nM) from 4 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.45 Å
• R-Value Free:  0.181 (Depositor), 0.201 (DCC) 
• R-Value Work:  0.169 (Depositor) 
• R-Value Observed: 0.170 (Depositor) 

Diffraction Data: https://doi.org/10.18430/m37ms7

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 61.556	α = 90
b = 84.87	β = 98.86
c = 59.542	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
Aimless	data scaling
PDB_EXTRACT	data extraction
xia2	data reduction

Structure Validation

Entry History 

Deposition Data

• Released Date: 2021-06-09 
Deposition Author(s): Mann, M.K., Zepeda-Velazquez, C.A., Alvarez, H.G., Dong, A., Kiyota, T., Aman, A., Arrowsmith, C.H., Al-Awar, R., Harding, R.J., Schapira, M.

Revision History  

• 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
• Version 1.4: 2024-11-06
  Changes: Structure summary