3ZNR

HDAC7 bound with inhibitor TMP269


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.4 Å
  • R-Value Free: 0.241 
  • R-Value Work: 0.212 

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:  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 ...

    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: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
HISTONE DEACETYLASE 7
A, B, C
423Homo sapiensGene Names: HDAC7 (HDAC7A)
EC: 3.5.1.98
Find proteins for Q8WUI4 (Homo sapiens)
Go to Gene View: HDAC7
Go to UniProtKB:  Q8WUI4
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
K
Query on K

Download SDF File 
Download CCD File 
A, B, C
POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N
 Ligand Interaction
ZN
Query on ZN

Download SDF File 
Download CCD File 
A, B, C
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
NU9
Query on NU9

Download SDF File 
Download CCD File 
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
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
NU9IC50: 4.1 nM (100) BINDINGDB
NU9Ki: 36 nM BINDINGMOAD
NU9Ki: 36 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.4 Å
  • R-Value Free: 0.241 
  • R-Value Work: 0.212 
  • Space Group: P 32
Unit Cell:
Length (Å)Angle (°)
a = 81.393α = 90.00
b = 81.393β = 90.00
c = 149.265γ = 120.00
Software Package:
Software NamePurpose
HKLdata scaling
PHASERphasing
HKLdata reduction
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

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