8HJE

Vismodegib binds to the catalytical domain of human Ubiquitin-Specific Protease 28


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.85 Å
  • R-Value Free: 0.254 
  • R-Value Work: 0.222 
  • R-Value Observed: 0.224 

Starting Model: experimental
View more details

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


Literature

Structure-based discovery of potent USP28 inhibitors derived from Vismodegib.

Zhou, D.Xu, Z.Huang, Y.Wang, H.Zhu, X.Zhang, W.Song, W.Gao, T.Liu, T.Wang, M.Shi, L.Zhang, N.Xiong, B.

(2023) Eur J Med Chem 254: 115369-115369

  • DOI: https://doi.org/10.1016/j.ejmech.2023.115369
  • Primary Citation of Related Structures:  
    8HJE

  • PubMed Abstract: 

    Ubiquitin-specific proteases (USPs) 28 is overexpressed in multiple types of cancers. The development of potent USP28 inhibitors is still in primitive stage. We previously reported our discovery of Vismodegib as a USP28 inhibitor by screening a commercially available drug library. Herein, we report our efforts to solve the cocrystal structure of Vismodegib bound to USP28 for the first time and subsequent structure-based optimization leading to a series of Vismodegib derivatives as potent USP28 inhibitors. Based on the cocrystal structure, elaborative SARs exploration was carried out to afford much more potent USP28 inhibitors than Vismodegib. The representative compounds 9l, 9o and 9p bearing high potency on USP28 showed high selectivity over USP2, USP7, USP8, USP9x, UCHL3 and UCHL5. The detailed cellular assay suggested that compounds 9l, 9o and 9p could cause cytotoxicity in both human colorectal cancer and lung squamous carcinoma cells and significantly enhance the sensitivity of colorectal cancer cells to Regorafenib. Further immunoblotting analysis indicated that compounds 9l, 9o and 9p could dose-dependently down-regulate the cellular level of c-Myc through ubiquitin-proteasome system and anti-cancer effects could mainly be attributed to their inhibition on USP28 but not involving the Hedgehog-Smoothened pathway. Thus, our work provided a series of novel and potent USP28 inhibitors derived from Vismodegib and may contribute to the development of USP28 inhibitors.


  • Organizational Affiliation

    Anhui University of Chinese Medicine, 350 Longzihu Road, Xinzhan District, Hefei, Anhui, 230012, PR China; Yangtze Delta Drug Advnced Research Institute, 100 Dongtinghu Road, Nantong, 226133, PR China.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Ubiquitin carboxyl-terminal hydrolase 28380Homo sapiensMutation(s): 0 
Gene Names: USP28KIAA1515
EC: 3.4.19.12
UniProt & NIH Common Fund Data Resources
Find proteins for Q96RU2 (Homo sapiens)
Explore Q96RU2 
Go to UniProtKB:  Q96RU2
PHAROS:  Q96RU2
GTEx:  ENSG00000048028 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ96RU2
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
VIS (Subject of Investigation/LOI)
Query on VIS

Download Ideal Coordinates CCD File 
B [auth A]2-chloranyl-~{N}-(4-chloranyl-3-pyridin-2-yl-phenyl)-4-methylsulfonyl-benzamide
C19 H14 Cl2 N2 O3 S
BPQMGSKTAYIVFO-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.85 Å
  • R-Value Free: 0.254 
  • R-Value Work: 0.222 
  • R-Value Observed: 0.224 
  • Space Group: H 3 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 105.099α = 90
b = 105.099β = 90
c = 327.422γ = 120
Software Package:
Software NamePurpose
REFMACrefinement
xia2data scaling
xia2data reduction
REFMACphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Natural Science Foundation of China (NSFC)China21977105
National Natural Science Foundation of China (NSFC)China21778061

Revision History  (Full details and data files)

  • Version 1.0: 2023-05-03
    Type: Initial release
  • Version 1.1: 2024-05-29
    Changes: Data collection