1T69

Crystal Structure of human HDAC8 complexed with SAHA


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.91 Å
  • R-Value Free: 0.310 
  • R-Value Work: 0.249 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Structural Snapshots of Human HDAC8 Provide Insights into the Class I Histone Deacetylases

Somoza, J.R.Skene, R.J.Katz, B.A.Mol, C.Ho, J.D.Jennings, A.J.Luong, C.Arvai, A.Buggy, J.J.Chi, E.Tang, J.Sang, B.-C.Verner, E.Wynands, R.Leahy, E.M.Dougan, D.R.Snell, G.Navre, M.Knuth, M.W.Swanson, R.V.McRee, D.E.Tari, L.W.

(2004) Structure 12: 1325-1334

  • DOI: 10.1016/j.str.2004.04.012
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • Modulation of the acetylation state of histones plays a pivotal role in the regulation of gene expression. Histone deacetylases (HDACs) catalyze the removal of acetyl groups from lysines near the N termini of histones. This reaction promotes the cond ...

    Modulation of the acetylation state of histones plays a pivotal role in the regulation of gene expression. Histone deacetylases (HDACs) catalyze the removal of acetyl groups from lysines near the N termini of histones. This reaction promotes the condensation of chromatin, leading to repression of transcription. HDAC deregulation has been linked to several types of cancer, suggesting a potential use for HDAC inhibitors in oncology. Here we describe the first crystal structures of a human HDAC: the structures of human HDAC8 complexed with four structurally diverse hydroxamate inhibitors. This work sheds light on the catalytic mechanism of the HDACs, and on differences in substrate specificity across the HDAC family. The structure also suggests how phosphorylation of Ser39 affects HDAC8 activity.


    Organizational Affiliation

    Celera, 180 Kimball Way, South San Francisco, CA 94080 USA. john.somoza@celera.com



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Histone deacetylase 8A377Homo sapiensMutation(s): 0 
Gene Names: HDAC8HDACL1CDA07
EC: 3.5.1.98
Find proteins for Q9BY41 (Homo sapiens)
Explore Q9BY41 
Go to UniProtKB:  Q9BY41
NIH Common Fund Data Resources
PHAROS  Q9BY41
Protein Feature View
 ( Mouse scroll to zoom / Hold left click to move )
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SHH
Query on SHH

Download CCD File 
A
OCTANEDIOIC ACID HYDROXYAMIDE PHENYLAMIDE
C14 H20 N2 O3
WAEXFXRVDQXREF-UHFFFAOYSA-N
 Ligand Interaction
ZN
Query on ZN

Download CCD File 
A
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
SHHIC50:  15   nM  BindingDB
SHHIC50:  3700   nM  BindingDB
SHHKi :  480   nM  PDBBind
SHHIC50:  4890   nM  BindingDB
SHHIC50:  12   nM  BindingDB
SHHΔG:  35   kJ/mol  BindingDB
SHHIC50:  10000   nM  BindingDB
SHHIC50:  7469   nM  BindingDB
SHHIC50:  3295.010009765625   nM  BindingDB
SHHKd:  580   nM  BindingDB
SHHIC50:  7300   nM  BindingDB
SHHIC50:  45   nM  BindingDB
SHHIC50:  55   nM  BindingDB
SHHIC50:  131   nM  BindingDB
SHHIC50:  120   nM  BindingDB
SHHIC50:  119   nM  BindingDB
SHH-TΔS:  0.2199999988079071   kJ/mol  BindingDB
SHHIC50:  145   nM  BindingDB
SHHIC50:  1000   nM  BindingDB
SHHIC50:  110   nM  BindingDB
SHHIC50:  105   nM  BindingDB
SHHKi:  2000   nM  BindingDB
SHHIC50:  100   nM  BindingDB
SHHIC50:  102   nM  BindingDB
SHHIC50:  260   nM  BindingDB
SHHKd:  6800   nM  BindingDB
SHHKi:  396   nM  BindingDB
SHHIC50:  240   nM  BindingDB
SHHIC50:  243   nM  BindingDB
SHHIC50:  232   nM  BindingDB
SHHIC50:  306   nM  BindingDB
SHHIC50:  310   nM  BindingDB
SHHIC50:  290   nM  BindingDB
SHHIC50:  300   nM  BindingDB
SHHIC50:  272   nM  BindingDB
SHHIC50:  280   nM  BindingDB
SHHIC50:  180   nM  BindingDB
SHHIC50:  172   nM  BindingDB
SHHIC50:  500   nM  BindingDB
SHHIC50:  660   nM  BindingDB
SHHKi:  700   nM  BindingDB
SHHIC50:  1   nM  BindingDB
SHHIC50:  540   nM  BindingDB
SHHIC50:  8.800000190734863   nM  BindingDB
SHHΔH:  45.599998474121094   kJ/mol  BindingDB
SHHIC50:  300   nM  BindingDB
SHH-TΔS:  10.140000343322754   kJ/mol  BindingDB
SHHIC50:  440   nM  BindingDB
SHHIC50:  400   nM  BindingDB
SHHIC50:  410   nM  BindingDB
SHHIC50:  1020   nM  BindingDB
SHHIC50:  960   nM  BindingDB
SHHIC50:  1260   nM  BindingDB
SHHIC50:  1200   nM  BindingDB
SHHIC50:  1100   nM  BindingDB
SHHIC50:  1140   nM  BindingDB
SHHΔH:  37.5099983215332   kJ/mol  BindingDB
SHHIC50:  780   nM  BindingDB
SHHKd:  1200   nM  BindingDB
SHHIC50:  700   nM  BindingDB
SHHIC50:  820   nM  BindingDB
SHHIC50:  827   nM  BindingDB
SHHIC50:  1989   nM  BindingDB
SHHIC50:  2000   nM  BindingDB
SHHKi:  205   nM  BindingDB
SHHIC50:  1860   nM  BindingDB
SHHIC50:  1890   nM  BindingDB
SHHIC50:  10   nM  BindingDB
SHHKd:  2900   nM  BindingDB
SHHKi:  173   nM  BindingDB
SHHIC50:  2290   nM  BindingDB
SHHIC50:  2185   nM  BindingDB
SHHIC50:  1480   nM  BindingDB
SHHIC50:  1500   nM  BindingDB
SHHIC50:  1524   nM  BindingDB
SHHIC50:  5.5   nM  BindingDB
SHHIC50:  1406   nM  BindingDB
SHHIC50:  1337   nM  BindingDB
SHHIC50:  1375   nM  BindingDB
SHHIC50:  1680   nM  BindingDB
SHHIC50:  1700   nM  BindingDB
SHHIC50:  1600   nM  BindingDB
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.91 Å
  • R-Value Free: 0.310 
  • R-Value Work: 0.249 
  • Space Group: P 31 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 80.761α = 90
b = 80.761β = 90
c = 105.615γ = 120
Software Package:
Software NamePurpose
HKL-2000data collection
SCALEPACKdata scaling
MOLREPphasing
REFMACrefinement
HKL-2000data reduction

Structure Validation

View Full Validation Report



Entry History 

Revision History 

  • Version 1.0: 2004-07-27
    Type: Initial release
  • Version 1.1: 2008-04-30
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance