5IX0

HDAC2 WITH LIGAND BRD7232

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.72 Å
  • R-Value Free: 0.200 
  • R-Value Work: 0.180 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history. 

Literature

Kinetic and structural insights into the binding of histone deacetylase 1 and 2 (HDAC1, 2) inhibitors.

Wagner, F.F., Weiwer, M., Steinbacher, S., Schomburg, A., Reinemer, P., Gale, J.P., Campbell, A.J., Fisher, S.L., Zhao, W.N., Reis, S.A., Hennig, K.M., Thomas, M., Muller, P., Jefson, M.R., Fass, D.M., Haggarty, S.J., Zhang, Y.L., Holson, E.B.

(2016) Bioorg.Med.Chem. 24: 4008-4015

  • DOI: 10.1016/j.bmc.2016.06.040
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    • The structure-activity and structure-kinetic relationships of a series of novel and selective ortho-aminoanilide inhibitors of histone deacetylases (HDACs) 1 and 2 are described. Different kinetic and thermodynamic selectivity profiles were obtained ...

    The structure-activity and structure-kinetic relationships of a series of novel and selective ortho-aminoanilide inhibitors of histone deacetylases (HDACs) 1 and 2 are described. Different kinetic and thermodynamic selectivity profiles were obtained by varying the moiety occupying an 11Å channel leading to the Zn(2+) catalytic pocket of HDACs 1 and 2, two paralogs with a high degree of structural similarity. The design of these novel inhibitors was informed by two ligand-bound crystal structures of truncated hHDAC2. BRD4884 and BRD7232 possess kinetic selectivity for HDAC1 versus HDAC2. We demonstrate that the binding kinetics of HDAC inhibitors can be tuned for individual isoforms in order to modulate target residence time while retaining functional activity and increased histone H4K12 and H3K9 acetylation in primary mouse neuronal cell culture assays. These chromatin modifiers, with tuned binding kinetic profiles, can be used to define the relation between target engagement requirements and the pharmacodynamic response of HDACs in different disease applications.

    Organizational Affiliation: 

    Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, 75 Ames Street, Cambridge, MA, USA. Electronic address: fwagner@broadinstitute.org.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Histone deacetylase 2
A, B, C
369Homo sapiensMutation(s): 0 
Gene Names: HDAC2
EC: 3.5.1.98
Find proteins for Q92769 (Homo sapiens)
Go to Gene View: HDAC2
Go to UniProtKB:  Q92769
Small Molecules
Ligands 8 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PG5
Query on PG5
Download SDF File 
Download CCD File 
A, B
1-METHOXY-2-[2-(2-METHOXY-ETHOXY]-ETHANE
C8 H18 O4
YFNKIDBQEZZDLK-UHFFFAOYSA-N
 Ligand Interaction
ZN
Query on ZN
Download SDF File 
Download CCD File 
A, B, C
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
CA
Query on CA
Download SDF File 
Download CCD File 
A, B, C
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
EDO
Query on EDO
Download SDF File 
Download CCD File 
B, C
1,2-ETHANEDIOL
ETHYLENE GLYCOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
PG4
Query on PG4
Download SDF File 
Download CCD File 
A, C
TETRAETHYLENE GLYCOL
C8 H18 O5
UWHCKJMYHZGTIT-UHFFFAOYSA-N
 Ligand Interaction
PGE
Query on PGE
Download SDF File 
Download CCD File 
A, B, C
TRIETHYLENE GLYCOL
C6 H14 O4
ZIBGPFATKBEMQZ-UHFFFAOYSA-N
 Ligand Interaction
PEG
Query on PEG
Download SDF File 
Download CCD File 
A, B, C
DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
 Ligand Interaction
6EZ
Query on 6EZ
Download SDF File 
Download CCD File 
A, B, C
(3-exo)-N-(4-amino-4'-fluoro[1,1'-biphenyl]-3-yl)-8-oxabicyclo[3.2.1]octane-3-carboxamide
C20 H21 F N2 O2
SBKJRDAJADZOCH-XGBSXSJOSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.72 Å
  • R-Value Free: 0.200 
  • R-Value Work: 0.180 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 92.195α = 90.00
b = 97.473β = 90.00
c = 139.254γ = 90.00
Software Package:
Software NamePurpose
REFMACrefinement
MOLREPphasing
XDSdata reduction
XSCALEdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots


View more in-depth experimental data

Entry History 

Deposition Data

  • Deposited Date: 2016-03-23 
  • Released Date: 2016-08-31 
  • Deposition Author(s): Steinbacher, S.

Revision History 

  • Version 1.0: 2016-08-31
    Type: Initial release