3MU6

Inhibiting the Binding of Class IIa Histone Deacetylases to Myocyte Enhancer Factor-2 by Small Molecules

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.43 Å
  • R-Value Free: 0.251 
  • R-Value Work: 0.230 
  • R-Value Observed: 0.231 

wwPDB Validation   3D Report Full Report


This is version 1.4 of the entry. See complete history. 


Literature

Inhibition of the function of class IIa HDACs by blocking their interaction with MEF2.

Jayathilaka, N., Han, A., Gaffney, K.J., Dey, R., Jarusiewicz, J.A., Noridomi, K., Philips, M.A., Lei, X., He, J., Ye, J., Gao, T., Petasis, N.A., Chen, L.

(2012) Nucleic Acids Res 40: 5378-5388

  • DOI: 10.1093/nar/gks189
  • Primary Citation of Related Structures:  
    3MU6

  • PubMed Abstract: 

    • Enzymes that modify the epigenetic status of cells provide attractive targets for therapy in various diseases. The therapeutic development of epigenetic modulators, however, has been largely limited to direct targeting of catalytic active site conserved across multiple members of an enzyme family, which complicates mechanistic studies and drug development ...

    Enzymes that modify the epigenetic status of cells provide attractive targets for therapy in various diseases. The therapeutic development of epigenetic modulators, however, has been largely limited to direct targeting of catalytic active site conserved across multiple members of an enzyme family, which complicates mechanistic studies and drug development. Class IIa histone deacetylases (HDACs) are a group of epigenetic enzymes that depends on interaction with Myocyte Enhancer Factor-2 (MEF2) for their recruitment to specific genomic loci. Targeting this interaction presents an alternative approach to inhibiting this class of HDACs. We have used structural and functional approaches to identify and characterize a group of small molecules that indirectly target class IIa HDACs by blocking their interaction with MEF2 on DNA.Weused X-ray crystallography and (19)F NMRto show that these compounds directly bind to MEF2. We have also shown that the small molecules blocked the recruitment of class IIa HDACs to MEF2-targeted genes to enhance the expression of those targets. These compounds can be used as tools to study MEF2 and class IIa HDACs in vivo and as leads for drug development.

    Organizational Affiliation: 

    Molecular and Computational Biology, Department of Biological Sciences, University of Southern California, Los Angeles, CA 90089, USA. jayathil@usc.edu



Macromolecules

Find similar proteins by: 
(by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Myocyte-specific enhancer factor 2AA, B, E [auth C], F [auth D]71Homo sapiensMutation(s): 1 
Gene Names: MEF2A, MEF2
UniProt & NIH Common Fund Data Resources
Find proteins for Q02078 (Homo sapiens)
Explore Q02078 
Go to UniProtKB:  Q02078
PHAROS:  Q02078
GTEx:  ENSG00000068305
Protein Feature View
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  • Reference Sequence
  • Find similar nucleic acids by:  Sequence   |   Structure
    • Entity ID: 2
    MoleculeChainsLengthOrganismImage
    DNA (5'-D(*AP*AP*AP*GP*CP*TP*AP*TP*TP*AP*TP*TP*AP*GP*CP*TP*T)-3')C [auth E], G17N/A
    Protein Feature View
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    • Reference Sequence
    • Find similar nucleic acids by:  Sequence   |   Structure
      • Entity ID: 3
      MoleculeChainsLengthOrganismImage
      DNA (5'-D(*TP*AP*AP*GP*CP*TP*AP*AP*TP*AP*AP*TP*AP*GP*CP*TP*T)-3')D [auth F], H17N/A
      Protein Feature View
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      • Reference Sequence
      Small Molecules
      Ligands 1 Unique
      IDChainsName / Formula / InChI Key2D Diagram3D Interactions
      BXL
      Query on BXL
      Download Ideal Coordinates CCD File 
      		 I [auth A](3E)-N~8~-(2-aminophenyl)-N~1~-phenyloct-3-enediamide
      C20 H23 N3 O2
      WWKBRKDVEBSJBW-LZCJLJQNSA-N      		 Ligand Interaction
      Experimental Data & Validation

      Experimental Data

      • Method: X-RAY DIFFRACTION
      • Resolution: 2.43 Å
      • R-Value Free: 0.251 
      • R-Value Work: 0.230 
      • R-Value Observed: 0.231 
      • Space Group: P 1
      Unit Cell:
      Length ( Å )Angle ( ˚ )
      a = 41.567α = 114.12
      b = 61.622β = 89.99
      c = 61.478γ = 89.95
      Software Package:
      Software NamePurpose
      DENZOdata reduction
      SCALEPACKdata scaling
      PHASERphasing
      PHENIXrefinement
      PDB_EXTRACTdata extraction

      Structure Validation

      View Full Validation Report


      View more in-depth experimental data

      Entry History 

      Deposition Data

      Revision History  (Full details and data files)

      • Version 1.0: 2011-11-02
        Type: Initial release
      • Version 1.1: 2012-02-22
        Changes: Database references
      • Version 1.2: 2012-03-21
        Changes: Database references
      • Version 1.3: 2012-07-25
        Changes: Database references
      • Version 1.4: 2017-11-08
        Changes: Refinement description