3ZNR

HDAC7 bound with inhibitor TMP269


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 0.241 
  • R-Value Work: 0.212 
  • R-Value Observed: 0.214 

wwPDB Validation   3D Report Full Report


This is version 1.3 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: https://doi.org/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 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)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
HISTONE DEACETYLASE 7
A, B, C
423Homo sapiensMutation(s): 0 
EC: 3.5.1.98 (PDB Primary Data), 3.5.1 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for Q8WUI4 (Homo sapiens)
Explore Q8WUI4 
Go to UniProtKB:  Q8WUI4
PHAROS:  Q8WUI4
GTEx:  ENSG00000061273 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8WUI4
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
NU9
Query on NU9

Download Ideal Coordinates CCD File 
H [auth A]N-{[4-(4-phenyl-1,3-thiazol-2-yl)tetrahydro-2H-pyran-4-yl]methyl}-3-[5-(trifluoromethyl)-1,2,4-oxadiazol-3-yl]benzamide
C25 H21 F3 N4 O3 S
HORXBWNTEDOVKN-UHFFFAOYSA-N
ZN
Query on ZN

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

Download Ideal Coordinates CCD File 
F [auth A]
G [auth A]
K [auth B]
L [auth B]
O [auth C]
F [auth A],
G [auth A],
K [auth B],
L [auth B],
O [auth C],
P [auth C]
POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N
Binding Affinity Annotations 
IDSourceBinding Affinity
NU9 PDBBind:  3ZNR Ki: 36 (nM) from 1 assay(s)
BindingDB:  3ZNR Ki: min: 36, max: 46 (nM) from 2 assay(s)
IC50: min: 32.4, max: 153 (nM) from 6 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 0.241 
  • R-Value Work: 0.212 
  • R-Value Observed: 0.214 
  • Space Group: P 32
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 81.393α = 90
b = 81.393β = 90
c = 149.265γ = 120
Software Package:
Software NamePurpose
REFMACrefinement
HKLdata reduction
HKLdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • 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: Atomic model, Database references
  • Version 1.3: 2024-05-08
    Changes: Data collection, Database references, Derived calculations, Other