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 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.2 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: https://doi.org/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. 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

    Charles River Discovery (previously BioFocus), Chesterford Research Park, Saffron Walden, Essex CB10 1XL, United Kingdom.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Histone deacetylase 4
A, B, C
395Homo sapiensMutation(s): 0 
Gene Names: HDAC4KIAA0288
EC: 3.5.1.98
UniProt & NIH Common Fund Data Resources
Find proteins for P56524 (Homo sapiens)
Explore P56524 
Go to UniProtKB:  P56524
PHAROS:  P56524
GTEx:  ENSG00000068024 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP56524
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
EBE (Subject of Investigation/LOI)
Query on EBE

Download Ideal Coordinates CCD File 
D [auth A],
H [auth B],
L [auth C]
(2~{S})-2-(2-fluorophenyl)-2-[4-(2-methylpyrimidin-5-yl)phenyl]-~{N}-oxidanyl-ethanamide
C19 H16 F N3 O2
SFXMVIQZYOMYOF-SFHVURJKSA-N
ZN
Query on ZN

Download Ideal Coordinates CCD File 
E [auth A]
F [auth A]
I [auth B]
J [auth B]
M [auth C]
E [auth A],
F [auth A],
I [auth B],
J [auth B],
M [auth C],
N [auth C]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
NA
Query on NA

Download Ideal Coordinates CCD File 
G [auth A],
K [auth B],
O [auth C]
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
Binding Affinity Annotations 
IDSourceBinding Affinity
EBE BindingDB:  6FYZ Kd: 80 (nM) from 1 assay(s)
IC50: 36 (nM) from 1 assay(s)
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



Ligand Structure Quality Assessment 


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
  • Version 1.2: 2024-01-17
    Changes: Data collection, Database references, Derived calculations, Refinement description