Crystal structure of human histone deacetylase 6 catalytic domain 2 in complex with trichostatin A

Experimental Data Snapshot

  • Resolution: 2.79 Å
  • R-Value Free: 0.275 
  • R-Value Work: 0.213 
  • R-Value Observed: 0.216 

wwPDB Validation   3D Report Full Report

This is version 2.2 of the entry. See complete history


Histone deacetylase 6 structure and molecular basis of catalysis and inhibition.

Hai, Y.Christianson, D.W.

(2016) Nat Chem Biol 12: 741-747

  • DOI: https://doi.org/10.1038/nchembio.2134
  • Primary Citation of Related Structures:  
    5EDU, 5EEF, 5EEI, 5EEK, 5EEM, 5EEN, 5EF7, 5EF8, 5EFB, 5EFG, 5EFH, 5EFJ, 5EFK, 5EFN

  • PubMed Abstract: 

    Histone deacetylase 6 (HDAC6) is a critical target for drug design because of its role in oncogenic transformation and cancer metastasis, and is unique among all histone deacetylases in that it contains tandem catalytic domains designated CD1 and CD2. We now report the crystal structures of CD2 from Homo sapiens HDAC6 and of CD1 and CD2 from Danio rerio HDAC6. We correlated these structures with activity measurements using 13 different substrates. The catalytic activity of CD2 from both species exhibited broad substrate specificity, whereas that of CD1 was highly specific for substrates bearing C-terminal acetyllysine residues. Crystal structures of substrate complexes yielded unprecedented snapshots of the catalytic mechanism. Additionally, crystal structures of complexes with eight different inhibitors, including belinostat and panobinostat (currently used in cancer chemotherapy), the macrocyclic tetrapeptide HC toxin, and the HDAC6-specific inhibitor N-hydroxy-4-(2-((2-hydroxyethyl)(phenyl)amino)-2-oxoethyl)benzamide, revealed surprising new insight regarding changes in Zn(2+) coordination and isozyme-specific inhibition.

  • Organizational Affiliation

    Radcliffe Institute for Advanced Study and Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts, USA.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Maltose-binding periplasmic protein, Histone deacetylase 6 chimeraA [auth B],
B [auth A]
745Escherichia coliHomo sapiens
This entity is chimeric
Mutation(s): 0 
Gene Names: malEZ5632ECs5017HDAC6KIAA0901JM21
EC: (PDB Primary Data), 3.5.1 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for P0AEX9 (Escherichia coli (strain K12))
Explore P0AEX9 
Go to UniProtKB:  P0AEX9
Find proteins for Q9UBN7 (Homo sapiens)
Explore Q9UBN7 
Go to UniProtKB:  Q9UBN7
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupsQ9UBN7P0AEX9
Sequence Annotations
  • Reference Sequence


Entity ID: 2
MoleculeChains Length2D Diagram Glycosylation3D Interactions
C, D
Glycosylation Resources
GlyTouCan:  G07411ON
GlyCosmos:  G07411ON
Small Molecules
Binding Affinity Annotations 
IDSourceBinding Affinity
TSN BindingDB:  5EDU Ki: min: 0.13, max: 3 (nM) from 5 assay(s)
IC50: min: 0.4, max: 3600 (nM) from 53 assay(s)
EC50: 5.2 (nM) from 1 assay(s)
Biologically Interesting Molecules (External Reference) 1 Unique
Experimental Data & Validation

Experimental Data

  • Resolution: 2.79 Å
  • R-Value Free: 0.275 
  • R-Value Work: 0.213 
  • R-Value Observed: 0.216 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 49.262α = 90
b = 149.032β = 90
c = 216.333γ = 90
Software Package:
Software NamePurpose
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesGM 49758

Revision History  (Full details and data files)

  • Version 1.0: 2016-07-27
    Type: Initial release
  • Version 1.1: 2016-08-10
    Changes: Database references
  • Version 1.2: 2016-09-07
    Changes: Database references
  • Version 1.3: 2017-09-13
    Changes: Author supporting evidence, Derived calculations
  • Version 1.4: 2019-12-25
    Changes: Author supporting evidence
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Atomic model, Data collection, Derived calculations, Non-polymer description, Structure summary
  • Version 2.1: 2020-12-30
    Changes: Structure summary
  • Version 2.2: 2023-09-27
    Changes: Data collection, Database references, Refinement description