3SFF

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

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.221 
  • R-Value Work: 0.177 

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:  

  • 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: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Histone deacetylase 8
A
378Homo sapiensMutation(s): 0 
Gene Names: HDAC8 (HDACL1)
EC: 3.5.1.98
Find proteins for Q9BY41 (Homo sapiens)
Go to Gene View: HDAC8
Go to UniProtKB:  Q9BY41
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
K
Query on K
Download SDF File 
Download CCD File 
A
POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N
 Ligand Interaction
ZN
Query on ZN
Download SDF File 
Download CCD File 
A
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
0DI
Query on 0DI
Download SDF File 
Download CCD File 
A
(2R)-2-amino-3-(3-chlorophenyl)-1-[4-(2,5-difluorobenzoyl)piperazin-1-yl]propan-1-one
C20 H20 Cl F2 N3 O2
NASCAWUSOSJBJH-GOSISDBHSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
0DIIC50: 200 nM (100) BINDINGDB
0DIIC50: 200 nM BINDINGMOAD
0DIIC50: 200 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.221 
  • R-Value Work: 0.177 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 57.812α = 90.00
b = 53.668β = 108.99
c = 61.338γ = 90.00
Software Package:
Software NamePurpose
PHASERphasing
HKL-2000data collection
SCALEPACKdata scaling
HKL-2000data reduction
BUSTERrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots


View more in-depth experimental data

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
    Type: Database references