3ZNS

HDAC7 bound with TFMO inhibitor tmp942

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.45 Å
  • R-Value Free: 0.225 
  • R-Value Work: 0.186 
  • R-Value Observed: 0.188 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history. 


Literature

Selective Class Iia Histone Deacetylase Inhibition Via a Non-Chelating Zinc Binding Group

Lobera, M., Madauss, K.P., Pohlhaus, D.T., Wright, Q.G., Trocha, M., Schmidt, D.R., Baloglu, E., Trump, R.P., Head, M.S., Hofmann, G.A., Murray-Thompson, M., Schwartz, B., Chakravorty, S., Wu, Z., Mander, P.K., Kruidenier, L., Reid, R.A., Burkhart, W., Turunen, B.J., Rong, J.X., Wagner, C., Moyer, M.B., Wells, C., Hong, X., Moore, J.T., Williams, J.D., Soler, D., Ghosh, S., Nolan, M.A.

(2013) Nat Chem Biol 9: 319

  • DOI: 10.1038/nchembio.1223
  • Primary Citation of Related Structures:  
    3ZNR, 3ZNS

  • PubMed Abstract: 

    • In contrast to studies on class I histone deacetylase (HDAC) inhibitors, the elucidation of the molecular mechanisms and therapeutic potential of class IIa HDACs (HDAC4, HDAC5, HDAC7 and HDAC9) is impaired by the lack of potent and selective chemical pro ...

    In contrast to studies on class I histone deacetylase (HDAC) inhibitors, the elucidation of the molecular mechanisms and therapeutic potential of class IIa HDACs (HDAC4, HDAC5, HDAC7 and HDAC9) is impaired by the lack of potent and selective chemical probes. Here we report the discovery of inhibitors that fill this void with an unprecedented metal-binding group, trifluoromethyloxadiazole (TFMO), which circumvents the selectivity and pharmacologic liabilities of hydroxamates. We confirm direct metal binding of the TFMO through crystallographic approaches and use chemoproteomics to demonstrate the superior selectivity of the TFMO series relative to a hydroxamate-substituted analog. We further apply these tool compounds to reveal gene regulation dependent on the catalytic active site of class IIa HDACs. The discovery of these inhibitors challenges the design process for targeting metalloenzymes through a chelating metal-binding group and suggests therapeutic potential for class IIa HDAC enzyme blockers distinct in mechanism and application compared to current HDAC inhibitors.

    Organizational Affiliation: 

    Tempero Pharmaceuticals, Cambridge, Massachusetts, USA.



Macromolecules
Find similar proteins by: 
(by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
HISTONE DEACETYLASE 7 A, B, C423Homo sapiensMutation(s): 0 
Gene Names: HDAC7, HDAC7A
EC: 3.5.1.98
Find proteins for Q8WUI4 (Homo sapiens)
Explore Q8WUI4 
Go to UniProtKB:  Q8WUI4
NIH Common Fund Data Resources
PHAROS:  Q8WUI4
GTEx:  ENSG00000061273
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.45 Å
  • R-Value Free: 0.225 
  • R-Value Work: 0.186 
  • R-Value Observed: 0.188 
  • Space Group: P 32
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 81.57α = 90
b = 81.57β = 90
c = 150.101γ = 120
Software Package:
Software NamePurpose
REFMACrefinement
HKLdata reduction
HKLdata scaling
PHASERphasing

Structure Validation

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View more in-depth experimental data

Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2013-03-27
    Type: Initial release
  • Version 1.1: 2013-04-03
    Changes: Database references
  • Version 1.2: 2013-05-01
    Changes: Database references