Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 42.13 kDa 
• Atom Count: 2757 
• Residue Count: 358 
• Unique protein chains: 1

1T69

Crystal Structure of human HDAC8 complexed with SAHA

• DOI: 10.2210/pdb1T69/pdb

• Classification: HYDROLASE
• Organism(s): Homo sapiens
• Expression System: Spodoptera frugiperda
• Mutation(s): No 


• Deposited: 2004-05-05 Released: 2004-07-27 
• Deposition Author(s): 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.

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Experimental Data Snapshot

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

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

• PubMed: 15242608 
• 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 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.

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Organizational Affiliation: 

Celera, 180 Kimball Way, South San Francisco, CA 94080 USA. [e-mail]

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
Histone deacetylase 8	A	377	Homo sapiens	Mutation(s): 0  Gene Names: HDAC8, HDACL1, CDA07 EC: 3.5.1.98
Find proteins for Q9BY41 (Homo sapiens) Explore Q9BY41  Go to UniProtKB:  Q9BY41
NIH Common Fund Data Resources
PHAROS  Q9BY41 GTEx  ENSG00000147099

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SHH	A	OCTANEDIOIC ACID HYDROXYAMIDE PHENYLAMIDE C14 H20 N2 O3 WAEXFXRVDQXREF-UHFFFAOYSA-N
ZN	A	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

External Ligand Annotations
ID	Binding Affinity (Sequence Identity %)
SHH	IC50:  15   nM  BindingDB
SHH	IC50:  3700   nM  BindingDB
SHH	Ki :  480   nM  PDBBind
SHH	IC50:  4890   nM  BindingDB
SHH	IC50:  12   nM  BindingDB
SHH	ΔG:  35   kJ/mol  BindingDB
SHH	IC50:  10000   nM  BindingDB
SHH	IC50:  7469   nM  BindingDB
SHH	IC50:  3295.010009765625   nM  BindingDB
SHH	Kd:  580   nM  BindingDB
SHH	IC50:  7300   nM  BindingDB
SHH	IC50:  45   nM  BindingDB
SHH	IC50:  55   nM  BindingDB
SHH	IC50:  131   nM  BindingDB
SHH	IC50:  120   nM  BindingDB
SHH	IC50:  119   nM  BindingDB
SHH	-TΔS:  0.2199999988079071   kJ/mol  BindingDB
SHH	IC50:  145   nM  BindingDB
SHH	IC50:  1000   nM  BindingDB
SHH	IC50:  110   nM  BindingDB
SHH	IC50:  105   nM  BindingDB
SHH	Ki:  2000   nM  BindingDB
SHH	IC50:  100   nM  BindingDB
SHH	IC50:  102   nM  BindingDB
SHH	IC50:  260   nM  BindingDB
SHH	Kd:  6800   nM  BindingDB
SHH	Ki:  396   nM  BindingDB
SHH	IC50:  240   nM  BindingDB
SHH	IC50:  243   nM  BindingDB
SHH	IC50:  232   nM  BindingDB
SHH	IC50:  306   nM  BindingDB
SHH	IC50:  310   nM  BindingDB
SHH	IC50:  290   nM  BindingDB
SHH	IC50:  300   nM  BindingDB
SHH	IC50:  272   nM  BindingDB
SHH	IC50:  280   nM  BindingDB
SHH	IC50:  180   nM  BindingDB
SHH	IC50:  172   nM  BindingDB
SHH	IC50:  500   nM  BindingDB
SHH	IC50:  660   nM  BindingDB
SHH	Ki:  700   nM  BindingDB
SHH	IC50:  1   nM  BindingDB
SHH	IC50:  540   nM  BindingDB
SHH	IC50:  8.800000190734863   nM  BindingDB
SHH	ΔH:  45.599998474121094   kJ/mol  BindingDB
SHH	IC50:  300   nM  BindingDB
SHH	-TΔS:  10.140000343322754   kJ/mol  BindingDB
SHH	IC50:  440   nM  BindingDB
SHH	IC50:  400   nM  BindingDB
SHH	IC50:  410   nM  BindingDB
SHH	IC50:  1020   nM  BindingDB
SHH	IC50:  960   nM  BindingDB
SHH	IC50:  1260   nM  BindingDB
SHH	IC50:  1200   nM  BindingDB
SHH	IC50:  1100   nM  BindingDB
SHH	IC50:  1140   nM  BindingDB
SHH	ΔH:  37.5099983215332   kJ/mol  BindingDB
SHH	IC50:  780   nM  BindingDB
SHH	Kd:  1200   nM  BindingDB
SHH	IC50:  700   nM  BindingDB
SHH	IC50:  820   nM  BindingDB
SHH	IC50:  827   nM  BindingDB
SHH	IC50:  1989   nM  BindingDB
SHH	IC50:  2000   nM  BindingDB
SHH	Ki:  205   nM  BindingDB
SHH	IC50:  1860   nM  BindingDB
SHH	IC50:  1890   nM  BindingDB
SHH	IC50:  10   nM  BindingDB
SHH	Kd:  2900   nM  BindingDB
SHH	Ki:  173   nM  BindingDB
SHH	IC50:  2290   nM  BindingDB
SHH	IC50:  2185   nM  BindingDB
SHH	IC50:  1480   nM  BindingDB
SHH	IC50:  1500   nM  BindingDB
SHH	IC50:  1524   nM  BindingDB
SHH	IC50:  5.5   nM  BindingDB
SHH	IC50:  1406   nM  BindingDB
SHH	IC50:  1337   nM  BindingDB
SHH	IC50:  1375   nM  BindingDB
SHH	IC50:  1680   nM  BindingDB
SHH	IC50:  1700   nM  BindingDB
SHH	IC50:  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 = 80.761	α = 90
b = 80.761	β = 90
c = 105.615	γ = 120

Software Package:

Software Name	Purpose
HKL-2000	data collection
SCALEPACK	data scaling
MOLREP	phasing
REFMAC	refinement
HKL-2000	data reduction

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2004-05-05 
• Released Date: 2004-07-27 
Deposition Author(s): 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.

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