4MN3

Chromodomain antagonists that target the polycomb-group methyllysine reader protein Chromobox homolog 7 (CBX7)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.54 Å
  • R-Value Free: 0.213 
  • R-Value Work: 0.172 
  • R-Value Observed: 0.174 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Chromodomain Antagonists That Target the Polycomb-Group Methyllysine Reader Protein Chromobox Homolog 7 (CBX7).

Simhadri, C.Daze, K.D.Douglas, S.F.Quon, T.T.Dev, A.Gignac, M.C.Peng, F.Heller, M.Boulanger, M.J.Wulff, J.E.Hof, F.

(2014) J Med Chem 57: 2874-2883

  • DOI: https://doi.org/10.1021/jm401487x
  • Primary Citation of Related Structures:  
    4MN3

  • PubMed Abstract: 

    We report here a peptide-driven approach to create first inhibitors of the chromobox homolog 7 (CBX7), a methyllysine reader protein. CBX7 uses its chromodomain to bind histone 3, lysine 27 trimethylated (H3K27me3), and this recognition event is implicated in silencing multiple tumor suppressors. Small trimethyllysine containing peptides were used as the basic scaffold from which potent ligands for disruption of CBX7-H3K27me3 complex were developed. Potency of ligands was determined by fluorescence polarization and/or isothermal titration calorimetry. Binding of one ligand was characterized in detail using 2D NMR and X-ray crystallography, revealing a structural motif unique among human CBX proteins. Inhibitors with a ∼200 nM potency for CBX7 binding and 10-fold/400-fold selectivity over related CBX8/CBX1 proteins were identified. These are the first reported inhibitors of any chromodomain.


  • Organizational Affiliation

    Department of Chemistry, University of Victoria , P.O. Box 3065, Victoria, British Columbia, V8W 3V6, Canada.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Chromobox protein homolog 756Homo sapiensMutation(s): 0 
Gene Names: CBX7
UniProt & NIH Common Fund Data Resources
Find proteins for O95931 (Homo sapiens)
Explore O95931 
Go to UniProtKB:  O95931
PHAROS:  O95931
GTEx:  ENSG00000100307 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO95931
Sequence Annotations
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  • Reference Sequence

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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
peptide7synthetic constructMutation(s): 0 
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.54 Å
  • R-Value Free: 0.213 
  • R-Value Work: 0.172 
  • R-Value Observed: 0.174 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 63.29α = 90
b = 31.86β = 119.02
c = 38.39γ = 90
Software Package:
Software NamePurpose
Blu-Icedata collection
PHASERphasing
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2014-04-02
    Type: Initial release
  • Version 1.1: 2014-06-18
    Changes: Database references
  • Version 1.2: 2014-10-08
    Changes: Structure summary