3C0Z

Crystal structure of catalytic domain of human histone deacetylase HDAC7 in complex with SAHA

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.243 
  • R-Value Work: 0.197 
  • R-Value Observed: 0.199 

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Literature

Human HDAC7 harbors a class IIa histone deacetylase-specific zinc binding motif and cryptic deacetylase activity.

Schuetz, A., Min, J., Allali-Hassani, A., Schapira, M., Shuen, M., Loppnau, P., Mazitschek, R., Kwiatkowski, N.P., Lewis, T.A., Maglathin, R.L., McLean, T.H., Bochkarev, A., Plotnikov, A.N., Vedadi, M., Arrowsmith, C.H.

(2008) J Biol Chem 283: 11355-11363

  • DOI: 10.1074/jbc.M707362200
  • Primary Citation of Related Structures:  
    3C0Y, 3C0Z, 3C10

  • PubMed Abstract: 

    • Histone deacetylases (HDACs) are protein deacetylases that play a role in repression of gene transcription and are emerging targets in cancer therapy. Here, we characterize the structure and enzymatic activity of the catalytic domain of human HDAC7 (cdHDAC7) ...

    Histone deacetylases (HDACs) are protein deacetylases that play a role in repression of gene transcription and are emerging targets in cancer therapy. Here, we characterize the structure and enzymatic activity of the catalytic domain of human HDAC7 (cdHDAC7). Although HDAC7 normally exists as part of a multiprotein complex, we show that cdHDAC7 has a low level of deacetylase activity which can be inhibited by known HDAC inhibitors. The crystal structures of human cdHDAC7 and its complexes with two hydroxamate inhibitors are the first structures of the catalytic domain of class IIa HDACs and demonstrate significant differences with previously reported class I and class IIb-like HDAC structures. We show that cdHDAC7 has an additional class IIa HDAC-specific zinc binding motif adjacent to the active site which is likely to participate in substrate recognition and protein-protein interaction and may provide a site for modulation of activity. Furthermore, a different active site topology results in modified catalytic properties and in an enlarged active site pocket. Our studies provide mechanistic insights into class IIa HDACs and facilitate the design of specific modulators.

    Organizational Affiliation: 

    Structural Genomics Consortium, University of Toronto, Toronto, Ontario M5G 1L5, Canada.



Macromolecules
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(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Histone deacetylase 7aA, B, C423Homo sapiensMutation(s): 0 
Gene Names: HDAC7A, HDAC7
EC: 3.5.1.98
UniProt & NIH Common Fund Data Resources
Find proteins for Q8WUI4 (Homo sapiens)
Explore Q8WUI4 
Go to UniProtKB:  Q8WUI4
PHAROS:  Q8WUI4
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8WUI4
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SHH
Query on SHH
Download Ideal Coordinates CCD File 
H [auth A],
M [auth B],
R [auth C]		OCTANEDIOIC ACID HYDROXYAMIDE PHENYLAMIDE
C14 H20 N2 O3
WAEXFXRVDQXREF-UHFFFAOYSA-N		 Ligand Interaction
ZN
Query on ZN
Download Ideal Coordinates CCD File 
D [auth A],
E [auth A],
I [auth B],
J [auth B],
N [auth C],
D [auth A],
E [auth A],
I [auth B],
J [auth B],
N [auth C],
O [auth C]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N		 Ligand Interaction
K
Query on K
Download Ideal Coordinates CCD File 
F [auth A],
G [auth A],
K [auth B],
L [auth B],
P [auth C],
F [auth A],
G [auth A],
K [auth B],
L [auth B],
P [auth C],
Q [auth C]
POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N		 Ligand Interaction
Binding Affinity Annotations 
IDSourceBinding Affinity
SHH BindingDB:  3C0Z Ki: 129 (nM) from 1 assay(s)
Kd: 3.60e+4 (nM) from 1 assay(s)
IC50: min: 1, max: 1.00e+4 (nM) from 13 assay(s)
PDBBind:  3C0Z IC50: 1.13e+5 (nM) from 1 assay(s)
Binding MOAD:  3C0Z IC50: 1.13e+5 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.243 
  • R-Value Work: 0.197 
  • R-Value Observed: 0.199 
  • Space Group: P 32
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 81.825α = 90
b = 81.825β = 90
c = 148.867γ = 120
Software Package:
Software NamePurpose
REFMACrefinement
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
ARP/wARPmodel building

Structure Validation

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Ligand Structure Quality Assessment 


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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2008-02-19
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance