3SFH

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.70 Å
  • R-Value Free: 0.244 
  • R-Value Work: 0.175 
  • R-Value Observed: 0.179 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

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: 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 ...

    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



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Histone deacetylase 8A378Homo sapiensMutation(s): 0 
Gene Names: HDAC8HDACL1CDA07
EC: 3.5.1.98
Find proteins for Q9BY41 (Homo sapiens)
Explore Q9BY41 
Go to UniProtKB:  Q9BY41
NIH Common Fund Data Resources
PHAROS  Q9BY41
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
1DI
Query on 1DI

Download CCD File 
A
(2R)-2-amino-3-(2,4-dichlorophenyl)-1-(1,3-dihydro-2H-isoindol-2-yl)propan-1-one
C17 H16 Cl2 N2 O
JFWNERIMAUEHNN-MRXNPFEDSA-N
 Ligand Interaction
ZN
Query on ZN

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A
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
ACT
Query on ACT

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A
ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
 Ligand Interaction
K
Query on K

Download CCD File 
A
POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
1DIIC50:  1090   nM  BindingDB
1DIIC50:  90   nM  BindingDB
1DIIC50 :  90   nM  PDBBind
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.70 Å
  • R-Value Free: 0.244 
  • R-Value Work: 0.175 
  • R-Value Observed: 0.179 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 57.643α = 90
b = 53.366β = 109.47
c = 60.893γ = 90
Software Package:
Software NamePurpose
HKL-2000data collection
PHASERphasing
CNXrefinement
HKL-2000data reduction
SCALEPACKdata scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

  • Deposited Date: 2011-06-13 
  • Released Date: 2011-07-20 
  • Deposition Author(s): Stams, T., Vash, B.

Revision History 

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