1T64

Crystal Structure of human HDAC8 complexed with Trichostatin A


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.221 
  • R-Value Work: 0.172 
  • R-Value Observed: 0.172 

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
  • Primary Citation of Related Structures:  
    1T69, 1T67, 1T64, 1VKG

  • 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:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Histone deacetylase 8AB377Homo 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
Expand
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
TSN
Query on TSN

Download CCD File 
A, B
TRICHOSTATIN A
C17 H22 N2 O3
RTKIYFITIVXBLE-QEQCGCAPSA-N
 Ligand Interaction
ZN
Query on ZN

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

Download CCD File 
A, B
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
NA
Query on NA

Download CCD File 
A, B
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
TSNIC50:  125   nM  BindingDB
TSNKi:  145   nM  BindingDB
TSNIC50:  213   nM  BindingDB
TSNIC50:  196   nM  BindingDB
TSNIC50:  160   nM  BindingDB
TSNIC50:  165   nM  BindingDB
TSNIC50:  170   nM  BindingDB
TSN-TΔS:  1.1200000047683716   kJ/mol  BindingDB
TSNIC50:  1020   nM  BindingDB
TSNIC50:  960   nM  BindingDB
TSNKi:  130   nM  BindingDB
TSNIC50:  100   nM  BindingDB
TSNΔG:  36   kJ/mol  BindingDB
TSNΔH:  48.970001220703125   kJ/mol  BindingDB
TSNIC50:  1380   nM  BindingDB
TSNIC50:  90   nM  BindingDB
TSNIC50:  3.0999999046325684   nM  BindingDB
TSNIC50:  1360   nM  BindingDB
TSNIC50:  566   nM  BindingDB
TSNIC50:  609   nM  BindingDB
TSNKi:  45   nM  BindingDB
TSNIC50:  472   nM  BindingDB
TSNΔH:  36.86000061035156   kJ/mol  BindingDB
TSNKi:  70   nM  BindingDB
TSNIC50:  770   nM  BindingDB
TSNIC50:  40   nM  BindingDB
TSNIC50:  4550   nM  BindingDB
TSN-TΔS:  0.8899999856948853   kJ/mol  BindingDB
TSNIC50:  300   nM  BindingDB
TSNIC50:  40   nM  BindingDB
TSNΔH:  37   kJ/mol  BindingDB
TSNKd:  490   nM  BindingDB
TSN-TΔS:  0.07999999821186066   kJ/mol  BindingDB
TSNIC50:  1.3799999952316284   nM  BindingDB
TSNIC50:  70.0999984741211   nM  BindingDB
TSNIC50:  25   nM  BindingDB
TSNIC50:  390   nM  BindingDB
TSNKd:  390   nM  BindingDB
TSNIC50:  360   nM  BindingDB
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.221 
  • R-Value Work: 0.172 
  • R-Value Observed: 0.172 
  • Space Group: P 43
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 81.014α = 90
b = 81.014β = 90
c = 114.178γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
SCALEPACKdata scaling
MOLREPphasing

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: Advisory, Version format compliance