6FYZ

Development and characterization of a CNS-penetrant benzhydryl hydroxamic acid class IIa histone deacetylase inhibitor


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.15 Å
  • R-Value Free: 0.228 
  • R-Value Work: 0.193 
  • R-Value Observed: 0.194 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Development and characterization of a CNS-penetrant benzhydryl hydroxamic acid class IIa histone deacetylase inhibitor.

Luckhurst, C.A.Aziz, O.Beaumont, V.Burli, R.W.Breccia, P.Maillard, M.C.Haughan, A.F.Lamers, M.Leonard, P.Matthews, K.L.Raphy, G.Stott, A.J.Munoz-Sanjuan, I.Thomas, B.Wall, M.Wishart, G.Yates, D.Dominguez, C.

(2019) Bioorg Med Chem Lett 29: 83-88

  • DOI: 10.1016/j.bmcl.2018.11.009
  • Primary Citation of Related Structures:  
    6FYZ

  • PubMed Abstract: 
  • We have identified a potent, cell permeable and CNS penetrant class IIa histone deacetylase (HDAC) inhibitor 22, with >500-fold selectivity over class I HDACs (1,2,3) and ∼150-fold selectivity over HDAC8 and the class IIb HDAC6 isoform. Dose escalation pharmacokinetic analysis demonstrated that upon oral administration, compound 22 can reach exposure levels in mouse plasma, muscle and brain in excess of cellular class IIa HDAC IC 50 levels for ∼8 h ...

    We have identified a potent, cell permeable and CNS penetrant class IIa histone deacetylase (HDAC) inhibitor 22, with >500-fold selectivity over class I HDACs (1,2,3) and ∼150-fold selectivity over HDAC8 and the class IIb HDAC6 isoform. Dose escalation pharmacokinetic analysis demonstrated that upon oral administration, compound 22 can reach exposure levels in mouse plasma, muscle and brain in excess of cellular class IIa HDAC IC 50 levels for ∼8 h. Given the interest in aberrant class IIa HDAC function for a number of neurodegenerative, neuromuscular, cardiac and oncology indications, compound 22 (also known as CHDI-390576) provides a selective and potent compound to query the role of class IIa HDAC biology, and the impact of class IIa catalytic site occupancy in vitro and in vivo.


    Organizational Affiliation

    CHDI Management/CHDI Foundation Inc., 6080 Center Drive, Suite 700, Los Angeles, CA 90045, United States.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Histone deacetylase 4A, B, C395Homo sapiensMutation(s): 0 
Gene Names: HDAC4KIAA0288
EC: 3.5.1.98
Find proteins for P56524 (Homo sapiens)
Explore P56524 
Go to UniProtKB:  P56524
NIH Common Fund Data Resources
PHAROS:  P56524
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
EBEKd:  39   nM  Binding MOAD
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.15 Å
  • R-Value Free: 0.228 
  • R-Value Work: 0.193 
  • R-Value Observed: 0.194 
  • Space Group: P 32
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 105.53α = 90
b = 105.53β = 90
c = 88.86γ = 120
Software Package:
Software NamePurpose
REFMACrefinement
iMOSFLMdata reduction
SCALEPACKdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2018-12-05
    Type: Initial release
  • Version 1.1: 2018-12-26
    Changes: Data collection, Database references