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: 2.434 Å
  • R-Value Free: 0.251 
  • R-Value Work: 0.230 

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

  • 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 conser ...

    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: Sequence  |  Structure


Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Myocyte-specific enhancer factor 2A
A, B, C, D
71Homo sapiensMutation(s): 1 
Gene Names: MEF2A (MEF2)
Find proteins for Q02078 (Homo sapiens)
Go to Gene View: MEF2A
Go to UniProtKB:  Q02078
Entity ID: 2
MoleculeChainsLengthOrganism
DNA (5'-D(*AP*AP*AP*GP*CP*TP*AP*TP*TP*AP*TP*TP*AP*GP*CP*TP*T)-3')E,G17N/A
Entity ID: 3
MoleculeChainsLengthOrganism
DNA (5'-D(*TP*AP*AP*GP*CP*TP*AP*AP*TP*AP*AP*TP*AP*GP*CP*TP*T)-3')F,H17N/A
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
BXL
Query on BXL
Download SDF File 
Download CCD File 
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: 2.434 Å
  • R-Value Free: 0.251 
  • R-Value Work: 0.230 
  • 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
PHENIXrefinement
SCALEPACKdata scaling
PHASERphasing
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report or Ramachandran Plots


View more in-depth experimental data

Entry History 

Deposition Data

Revision History 

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