Crystal Structure of Human HDAC8 Inhibitor Complex, an Amino Acid Derived Inhibitor

Experimental Data Snapshot

  • Resolution: 2.00 Å
  • R-Value Free: 0.221 
  • R-Value Work: 0.177 
  • R-Value Observed: 0.179 

wwPDB Validation   3D Report Full Report

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Human HDAC isoform selectivity achieved via exploitation of the acetate release channel with structurally unique small molecule inhibitors.

Whitehead, L.Dobler, M.R.Radetich, B.Zhu, Y.Atadja, P.W.Claiborne, T.Grob, J.E.McRiner, A.Pancost, M.R.Patnaik, A.Shao, W.Shultz, M.Tichkule, R.Tommasi, R.A.Vash, B.Wang, P.Stams, T.

(2011) Bioorg Med Chem 19: 4626-4634

  • DOI: https://doi.org/10.1016/j.bmc.2011.06.030
  • Primary Citation of Related Structures:  
    3SFF, 3SFH

  • PubMed Abstract: 

    Herein we report the discovery of a family of novel yet simple, amino-acid derived class I HDAC inhibitors that demonstrate isoform selectivity via access to the internal acetate release channel. Isoform selectivity criteria is discussed on the basis of X-ray crystallography and molecular modeling of these novel inhibitors bound to HDAC8, potentially revealing insights into the mechanism of enzymatic function through novel structural features revealed at the atomic level.

  • Organizational Affiliation

    Novartis Institutes for Biomedical Research, 100 Technology Square & 250 Massachusetts Avenue, Cambridge, MA 02139, USA. lewis.whitehead@novartis.com

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Histone deacetylase 8378Homo sapiensMutation(s): 0 
Gene Names: HDAC8HDACL1CDA07
EC: (PDB Primary Data), 3.5.1 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for Q9BY41 (Homo sapiens)
Explore Q9BY41 
Go to UniProtKB:  Q9BY41
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9BY41
Sequence Annotations
  • Reference Sequence
Small Molecules
Binding Affinity Annotations 
IDSourceBinding Affinity
0DI BindingDB:  3SFF IC50: 200 (nM) from 1 assay(s)
PDBBind:  3SFF IC50: 200 (nM) from 1 assay(s)
Binding MOAD:  3SFF IC50: 200 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Resolution: 2.00 Å
  • R-Value Free: 0.221 
  • R-Value Work: 0.177 
  • R-Value Observed: 0.179 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 57.812α = 90
b = 53.668β = 108.99
c = 61.338γ = 90
Software Package:
Software NamePurpose
HKL-2000data collection
HKL-2000data reduction
SCALEPACKdata scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2011-07-20
    Type: Initial release
  • Version 1.1: 2011-08-03
    Changes: Database references