8UMG | pdb_00008umg

Chromodomains of human CHD1 complexed with UNC10142


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.10 Å
  • R-Value Free: 
    0.320 (Depositor), 0.309 (DCC) 
  • R-Value Work: 
    0.238 (Depositor), 0.226 (DCC) 
  • R-Value Observed: 
    0.246 (Depositor) 

Starting Model: experimental
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This is version 1.1 of the entry. See complete history


Literature

Discovery of CHD1 Antagonists for PTEN-Deficient Prostate Cancer.

Johnson, R.L.Graboski, A.L.Li, F.Norris-Drouin, J.L.Walton, W.G.Arrowsmith, C.H.Redinbo, M.R.Frye, S.V.James, L.I.

(2024) J Med Chem 67: 20056-20075

  • DOI: https://doi.org/10.1021/acs.jmedchem.4c01172
  • Primary Citation of Related Structures:  
    8UMG

  • PubMed Abstract: 

    CHD1 is a chromodomain-helicase DNA-binding protein that preferentially recognizes di- and trimethylated lysine 4 on histone H3 (H3K4me2/3). Genetic studies have established CHD1 as a synthetic lethal target in phosphatase and tensin homologue (PTEN)-deficient cancers. Despite this attractive therapeutic link, no inhibitors or antagonists of CHD1 have been reported to date. Herein, we report the discovery of UNC10142, a first-in-class small molecule antagonist of the tandem chromodomains of CHD1 that binds with an IC 50 of 1.7 ± 0.2 μM. A cocrystal structure revealed a unique binding mode and competition pull-down experiments in cell lysates confirmed endogenous target engagement. Treatment of PTEN-deficient prostate cancer cells with UNC10142 led to a dose-dependent reduction in viability while PTEN-intact prostate cancer cells were unaffected, phenocopying genetic loss of CHD1. Overall, this study demonstrates the ligandability of the CHD1 chromodomains and suggests more potent and selective antagonists could translate to compounds of therapeutic value in PTEN-deficient cancers.


  • Organizational Affiliation
    • Center for Integrative Chemical Biology and Drug Discovery, Division of Chemical Biology and Medicinal Chemistry, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Chromodomain-helicase-DNA-binding protein 1
A, B, C
187Homo sapiensMutation(s): 2 
Gene Names: CHD1
EC: 3.6.4
UniProt & NIH Common Fund Data Resources
Find proteins for O14646 (Homo sapiens)
Explore O14646 
Go to UniProtKB:  O14646
PHAROS:  O14646
GTEx:  ENSG00000153922 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO14646
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.10 Å
  • R-Value Free:  0.320 (Depositor), 0.309 (DCC) 
  • R-Value Work:  0.238 (Depositor), 0.226 (DCC) 
  • R-Value Observed: 0.246 (Depositor) 
Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 112.531α = 90
b = 55.193β = 112.779
c = 101.095γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
Cootmodel building
XDSdata reduction
XDSdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute on Drug Abuse (NIH/NIDA)United States5R33DA047023-05
National Institutes of Health/National Cancer Institute (NIH/NCI)United States5R33DA047023-05

Revision History  (Full details and data files)

  • Version 1.0: 2024-10-23
    Type: Initial release
  • Version 1.1: 2025-11-05
    Changes: Database references