4CBT

Design, synthesis, and biological evaluation of potent and selective Class IIa HDAC inhibitors as a potential therapy for Huntington's disease


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.03 Å
  • R-Value Free: 0.273 
  • R-Value Work: 0.211 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Design, synthesis, and biological evaluation of potent and selective class IIa histone deacetylase (HDAC) inhibitors as a potential therapy for Huntington's disease.

Burli, R.W.Luckhurst, C.A.Aziz, O.Matthews, K.L.Yates, D.Lyons, K.A.Beconi, M.McAllister, G.Breccia, P.Stott, A.J.Penrose, S.D.Wall, M.Lamers, M.Leonard, P.Muller, I.Richardson, C.M.Jarvis, R.Stones, L.Hughes, S.Wishart, G.Haughan, A.F.O'Connell, C.Mead, T.McNeil, H.Vann, J.Mangette, J.Maillard, M.Beaumont, V.Munoz-Sanjuan, I.Dominguez, C.

(2013) J. Med. Chem. 56: 9934-9954

  • DOI: 10.1021/jm4011884
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Inhibition of class IIa histone deacetylase (HDAC) enzymes have been suggested as a therapeutic strategy for a number of diseases, including Huntington's disease. Catalytic-site small molecule inhibitors of the class IIa HDAC4, -5, -7, and -9 were de ...

    Inhibition of class IIa histone deacetylase (HDAC) enzymes have been suggested as a therapeutic strategy for a number of diseases, including Huntington's disease. Catalytic-site small molecule inhibitors of the class IIa HDAC4, -5, -7, and -9 were developed. These trisubstituted diarylcyclopropanehydroxamic acids were designed to exploit a lower pocket that is characteristic for the class IIa HDACs, not present in other HDAC classes. Selected inhibitors were cocrystallized with the catalytic domain of human HDAC4. We describe the first HDAC4 catalytic domain crystal structure in a "closed-loop" form, which in our view represents the biologically relevant conformation. We have demonstrated that these molecules can differentiate class IIa HDACs from class I and class IIb subtypes. They exhibited pharmacokinetic properties that should enable the assessment of their therapeutic benefit in both peripheral and CNS disorders. These selective inhibitors provide a means for evaluating potential efficacy in preclinical models in vivo.


    Organizational Affiliation

    BioFocus , Chesterford Research Park, Saffron Walden, Essex, CB10 1XL, United Kingdom.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
HISTONE DEACETYLASE 4
A, B, C
395Homo sapiensMutation(s): 0 
Gene Names: HDAC4 (KIAA0288)
EC: 3.5.1.98
Find proteins for P56524 (Homo sapiens)
Go to Gene View: HDAC4
Go to UniProtKB:  P56524
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download SDF File 
Download CCD File 
A, B, C
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
9F4
Query on 9F4

Download SDF File 
Download CCD File 
A, B, C
(1R,2R,3R)-2-[4-(5-fluoranylpyrimidin-2-yl)phenyl]-N-oxidanyl-3-phenyl-cyclopropane-1-carboxamide
C20 H16 F N3 O2
QHCRWOYXPXJUJS-KZNAEPCWSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
9F4IC50: 50 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.03 Å
  • R-Value Free: 0.273 
  • R-Value Work: 0.211 
  • Space Group: P 32
Unit Cell:
Length (Å)Angle (°)
a = 104.410α = 90.00
b = 104.410β = 90.00
c = 88.440γ = 120.00
Software Package:
Software NamePurpose
REFMACrefinement
PHASERphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Revision History 

  • Version 1.0: 2013-12-11
    Type: Initial release
  • Version 1.1: 2014-01-15
    Type: Database references
  • Version 1.2: 2018-02-07
    Type: Database references, Structure summary