8JIG | pdb_00008jig

A Novel UHRF1-Targeted Compound


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 
    0.244 (Depositor), 0.250 (DCC) 
  • R-Value Work: 
    0.208 (Depositor), 0.210 (DCC) 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


Literature

A Hybrid compound H93 treats prostate cancer by directly binding UHRF1 and promoting protein dimerization.

Fu, Y.Jiang, L.Xie, G.Peng, Y.Fu, Y.Zhu, Q.Liu, Y.Zhao, G.Liu, X.Peng, Y.Chen, Y.Li, X.

(2025) Commun Chem 8: 356-356

  • DOI: https://doi.org/10.1038/s42004-025-01744-3
  • Primary Citation of Related Structures:  
    8JIG

  • PubMed Abstract: 

    UHRF1 is a pivotal epigenetic regulator bridging DNA methylation and histone modifications, frequently overexpressed in prostate cancer (PCa). However, no UHRF1-targeted therapeutics have advanced to clinical trials. Here, we report the development of H93, a hybrid small molecule integrating functional groups derived from NSC232003 and vorinostat, respectively. H93 exhibits potent anticancer activity in vitro, correlating with UHRF1 protein abundance, and co-crystallization studies confirm that H93 directly binding to the SRA domain of UHRF1. Intriguingly, H93 promotes UHRF1 dimerization, generating a defined binding pocket that stabilizes compound engagement and enhances druggability of UHRF1 as a non-kinase target. Dimerized UHRF1 adopts a "closed" conformation that disrupts its interaction with DNMT1, impairs DNA methylation maintenance, and reactivates epigenetically silenced tumor suppressor genes. In vivo, H93 demonstrates significant antitumor efficacy. Overall, this study elucidates the structural and mechanistic basis of H93, establishing it as a promising UHRF1-targeted therapy for PCa.


  • Organizational Affiliation
    • Xiangya Cancer Center, National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, China.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
E3 ubiquitin-protein ligase UHRF1
A, B
212Homo sapiensMutation(s): 0 
Gene Names: UHRF1ICBP90NP95RNF106
EC: 2.3.2.27
UniProt & NIH Common Fund Data Resources
Find proteins for Q96T88 (Homo sapiens)
Explore Q96T88 
Go to UniProtKB:  Q96T88
PHAROS:  Q96T88
GTEx:  ENSG00000276043 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ96T88
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free:  0.244 (Depositor), 0.250 (DCC) 
  • R-Value Work:  0.208 (Depositor), 0.210 (DCC) 
Space Group: P 31
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 65.875α = 90
b = 65.875β = 90
c = 95.634γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling
HKL-3000phasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Natural Science Foundation of China (NSFC)China81572542, 81874096, 81974074, 82172654

Revision History  (Full details and data files)

  • Version 1.0: 2024-05-29
    Type: Initial release
  • Version 1.1: 2025-12-10
    Changes: Database references, Structure summary