Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | 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 
• Modelled Residue Count: 358 
• Deposited Residue Count: 377 
• Unique protein chains: 1

1T69

Crystal Structure of human HDAC8 complexed with SAHA

• PDB 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
• 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.

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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	Image
Histone deacetylase 8	A	377	Homo sapiens	Mutation(s): 0  Gene Names: HDAC8, HDACL1, CDA07 EC: 3.5.1.98
UniProt & NIH Common Fund Data Resources
Find proteins for Q9BY41 (Homo sapiens) Explore Q9BY41  Go to UniProtKB:  Q9BY41
PHAROS:  Q9BY41

Small Molecules

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

Binding Affinity Annotations
ID	Source	Binding Affinity
SHH	PDBBind:  1T69	Ki: 480 (nM) from 1 assay(s)
	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)

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