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 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.3 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: 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


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Histone deacetylase 8
A, B
377Homo sapiensMutation(s): 0 
EC: 3.5.1 (UniProt), 3.5.1.98 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for Q9BY41 (Homo sapiens)
Explore Q9BY41 
Go to UniProtKB:  Q9BY41
PHAROS:  Q9BY41
GTEx:  ENSG00000147099 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9BY41
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
TSN
Query on TSN

Download Ideal Coordinates CCD File 
H [auth A],
I [auth A],
O [auth B],
P [auth B]
TRICHOSTATIN A
C17 H22 N2 O3
RTKIYFITIVXBLE-QEQCGCAPSA-N
ZN
Query on ZN

Download Ideal Coordinates CCD File 
C [auth A],
J [auth B]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
CA
Query on CA

Download Ideal Coordinates CCD File 
D [auth A],
E [auth A],
K [auth B],
L [auth B]
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
NA
Query on NA

Download Ideal Coordinates CCD File 
F [auth A],
G [auth A],
M [auth B],
N [auth B]
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
Binding Affinity Annotations 
IDSourceBinding Affinity
TSN BindingDB:  1T64 Ki: min: 45, max: 504 (nM) from 5 assay(s)
Kd: min: 390, max: 490 (nM) from 2 assay(s)
IC50: min: 1.38, max: 4550 (nM) from 56 assay(s)
-TΔS: min: 0.08, max: 1.13 (kJ/mol) from 3 assay(s)
ΔH: min: -4.90e+1, max: -3.69e+1 (kJ/mol) from 3 assay(s)
ΔG: -3.60e+1 (kJ/mol) from 1 assay(s)
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

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Ligand Structure Quality Assessment 


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