1VKG

Crystal Structure of Human HDAC8 complexed with CRA-19156


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.304 
  • R-Value Work: 0.237 

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:  
    1VKG, 1T69, 1T67, 1T64

  • 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 condensa ...

    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 8 AB377Homo 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 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CRI
Query on CRI

Download Ideal Coordinates CCD File 
A, B
5-(4-METHYL-BENZOYLAMINO)-BIPHENYL-3,4'-DICARBOXYLIC ACID 3-DIMETHYLAMIDE-4'-HYDROXYAMIDE
C24 H23 N3 O4
DOPFUKKMSDUVTQ-UHFFFAOYSA-N
 Ligand Interaction
ZN
Query on ZN

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

Download Ideal Coordinates CCD File 
A, B
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.304 
  • R-Value Work: 0.237 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 82.63α = 90
b = 92.71β = 90
c = 98.76γ = 90
Software Package:
Software NamePurpose
Crystaldata collection
Crystaldata reduction
X-sightmodel building
X-PLORrefinement
CrystalCleardata scaling
X-SIGHTphasing
X-PLORrefinement

Structure Validation

View Full Validation Report



Entry History 

Revision History 

  • Version 1.0: 2004-07-27
    Type: Initial release
  • Version 1.1: 2008-04-26
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance