4LY1

Structure of Human HDAC2 in complex with inhibitor 4-(acetylamino)-N-[2-amino-5-(thiophen-2-yl)phenyl]benzamide


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.57 Å
  • R-Value Free: 0.187 
  • R-Value Work: 0.169 
  • R-Value Observed: 0.170 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Histone Deacetylase (HDAC) Inhibitor Kinetic Rate Constants Correlate with Cellular Histone Acetylation but Not Transcription and Cell Viability.

Lauffer, B.E.Mintzer, R.Fong, R.Mukund, S.Tam, C.Zilberleyb, I.Flicke, B.Ritscher, A.Fedorowicz, G.Vallero, R.Ortwine, D.F.Gunzner, J.Modrusan, Z.Neumann, L.Koth, C.M.Lupardus, P.J.Kaminker, J.S.Heise, C.E.Steiner, P.

(2013) J Biol Chem 288: 26926-26943

  • DOI: 10.1074/jbc.M113.490706
  • Primary Citation of Related Structures:  
    4LXZ, 4LY1

  • PubMed Abstract: 
  • Histone deacetylases (HDACs) are critical in the control of gene expression, and dysregulation of their activity has been implicated in a broad range of diseases, including cancer, cardiovascular, and neurological diseases. HDAC inhibitors (HDACi) em ...

    Histone deacetylases (HDACs) are critical in the control of gene expression, and dysregulation of their activity has been implicated in a broad range of diseases, including cancer, cardiovascular, and neurological diseases. HDAC inhibitors (HDACi) employing different zinc chelating functionalities such as hydroxamic acids and benzamides have shown promising results in cancer therapy. Although it has also been suggested that HDACi with increased isozyme selectivity and potency may broaden their clinical utility and minimize side effects, the translation of this idea to the clinic remains to be investigated. Moreover, a detailed understanding of how HDACi with different pharmacological properties affect biological functions in vitro and in vivo is still missing. Here, we show that a panel of benzamide-containing HDACi are slow tight-binding inhibitors with long residence times unlike the hydroxamate-containing HDACi vorinostat and trichostatin-A. Characterization of changes in H2BK5 and H4K14 acetylation following HDACi treatment in the neuroblastoma cell line SH-SY5Y revealed that the timing and magnitude of histone acetylation mirrored both the association and dissociation kinetic rates of the inhibitors. In contrast, cell viability and microarray gene expression analysis indicated that cell death induction and changes in transcriptional regulation do not correlate with the dissociation kinetic rates of the HDACi. Therefore, our study suggests that determining how the selective and kinetic inhibition properties of HDACi affect cell function will help to evaluate their therapeutic utility.


    Organizational Affiliation

    From the Departments of Neuroscience.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Histone deacetylase 2A, B, C369Homo sapiensMutation(s): 0 
Gene Names: HDAC2
EC: 3.5.1.98
Find proteins for Q92769 (Homo sapiens)
Explore Q92769 
Go to UniProtKB:  Q92769
NIH Common Fund Data Resources
PHAROS  Q92769
Protein Feature View
 ( Mouse scroll to zoom / Hold left click to move )
  • Reference Sequence
Small Molecules
Ligands 6 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
20Y
Query on 20Y

Download CCD File 
A, B, C
4-(acetylamino)-N-[2-amino-5-(thiophen-2-yl)phenyl]benzamide
C19 H17 N3 O2 S
ABZSPJVXTTUFAA-UHFFFAOYSA-N
 Ligand Interaction
NHE
Query on NHE

Download CCD File 
B
2-[N-CYCLOHEXYLAMINO]ETHANE SULFONIC ACID
C8 H17 N O3 S
MKWKNSIESPFAQN-UHFFFAOYSA-N
 Ligand Interaction
PG4
Query on PG4

Download CCD File 
A, B, C
TETRAETHYLENE GLYCOL
C8 H18 O5
UWHCKJMYHZGTIT-UHFFFAOYSA-N
 Ligand Interaction
ZN
Query on ZN

Download CCD File 
A, B, C
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
CA
Query on CA

Download CCD File 
A, B, C
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
NA
Query on NA

Download CCD File 
A, B, C
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
20YKi:  1.5   nM  BindingDB
20YKd:  38.099998474121094   nM  BindingDB
20YIC50:  1   nM  BindingDB
20YIC50:  56.29999923706055   nM  BindingDB
20YIC50:  100   nM  BindingDB
20YIC50:  10.100000381469727   nM  BindingDB
20YIC50:  7   nM  BindingDB
20YKd :  55.20000076293945   nM  PDBBind
20YIC50:  56.29999923706055   nM  Binding MOAD
20YIC50:  40   nM  BindingDB
20YKd:  55.20000076293945   nM  BindingDB
20YIC50:  13   nM  BindingDB
20YKi:  0.20000000298023224   nM  BindingDB
20YIC50:  49   nM  BindingDB
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.57 Å
  • R-Value Free: 0.187 
  • R-Value Work: 0.169 
  • R-Value Observed: 0.170 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 92.034α = 90
b = 97.49β = 90
c = 138.922γ = 90
Software Package:
Software NamePurpose
PHASERphasing
BUSTERrefinement
HKL-2000data reduction
SCALEPACKdata scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2013-08-21
    Type: Initial release
  • Version 1.1: 2013-10-02
    Changes: Database references