Crystal Structure of human HDAC8 complexed with SAHA

Experimental Data Snapshot

  • Resolution: 2.91 Å
  • R-Value Free: 0.310 
  • R-Value Work: 0.249 

wwPDB Validation   3D Report Full Report

This is version 1.3 of the entry. See complete history


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: https://doi.org/10.1016/j.str.2004.04.012
  • Primary Citation of Related Structures:  
    1T64, 1T67, 1T69, 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 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

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Histone deacetylase 8377Homo sapiensMutation(s): 0 
Gene Names: HDAC8HDACL1CDA07
EC: (UniProt), 3.5.1 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for Q9BY41 (Homo sapiens)
Explore Q9BY41 
Go to UniProtKB:  Q9BY41
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9BY41
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on SHH

Download Ideal Coordinates CCD File 
C14 H20 N2 O3
Query on ZN

Download Ideal Coordinates CCD File 
B [auth A]ZINC ION
Binding Affinity Annotations 
IDSourceBinding Affinity
SHH BindingDB:  1T69 Ki: min: 173, max: 1.57e+4 (nM) from 8 assay(s)
Kd: min: 580, max: 6800 (nM) from 4 assay(s)
IC50: min: 1, max: 1.00e+4 (nM) from 82 assay(s)
-TΔS: min: 0.22, max: 10.14 (kJ/mol) from 2 assay(s)
ΔH: min: -4.56e+1, max: -3.75e+1 (kJ/mol) from 2 assay(s)
ΔG: -3.50e+1 (kJ/mol) from 1 assay(s)
PDBBind:  1T69 Ki: 480 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • 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
HKL-2000data reduction

Structure Validation

View Full Validation Report

Entry History 

Revision History  (Full details and data files)

  • 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
  • Version 1.3: 2023-08-23
    Changes: Data collection, Database references, Derived calculations, Refinement description