3MAX

Crystal Structure of Human HDAC2 complexed with an N-(2-aminophenyl)benzamide


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.05 Å
  • R-Value Free: 0.204 
  • R-Value Work: 0.164 
  • R-Value Observed: 0.166 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Exploration of the HDAC2 foot pocket: Synthesis and SAR of substituted N-(2-aminophenyl)benzamides.

Bressi, J.C.Jennings, A.J.Skene, R.Wu, Y.Melkus, R.De Jong, R.O'Connell, S.Grimshaw, C.E.Navre, M.Gangloff, A.R.

(2010) Bioorg Med Chem Lett 20: 3142-3145

  • DOI: 10.1016/j.bmcl.2010.03.091
  • Primary Citation of Related Structures:  
    3MAX

  • PubMed Abstract: 
  • A series of N-(2-amino-5-substituted phenyl)benzamides (3-21) were designed, synthesized and evaluated for their inhibition of HDAC2 and their cytotoxicity in HCT116 cancer cells. Multiple compounds from this series demonstrated time-dependent bindin ...

    A series of N-(2-amino-5-substituted phenyl)benzamides (3-21) were designed, synthesized and evaluated for their inhibition of HDAC2 and their cytotoxicity in HCT116 cancer cells. Multiple compounds from this series demonstrated time-dependent binding kinetics that is rationalized using a co-complex crystal structure of HDAC2 and N-(4-aminobiphenyl-3-yl)benzamide (6).


    Organizational Affiliation

    Takeda San Diego, San Diego, CA 92121, USA.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Histone deacetylase 2ABC367Homo 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
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  • Reference Sequence
Small Molecules
Ligands 5 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
LLX
Query on LLX

Download CCD File 
A, B, C
N-(4-aminobiphenyl-3-yl)benzamide
C19 H16 N2 O
ZWLFHHHQRUYIBT-UHFFFAOYSA-N
 Ligand Interaction
NHE
Query on NHE

Download CCD File 
A
2-[N-CYCLOHEXYLAMINO]ETHANE SULFONIC ACID
C8 H17 N O3 S
MKWKNSIESPFAQN-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 %)
LLXIC50:  140   nM  BindingDB
LLXIC50:  1200   nM  BindingDB
LLXIC50:  350   nM  BindingDB
LLXIC50 :  900   nM  PDBBind
LLXIC50:  60   nM  BindingDB
LLXIC50:  52   nM  BindingDB
LLXIC50:  410   nM  BindingDB
LLXIC50:  27   nM  Binding MOAD
LLXIC50:  780   nM  BindingDB
LLXIC50:  27   nM  BindingDB
LLXIC50:  900   nM  BindingDB
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.05 Å
  • R-Value Free: 0.204 
  • R-Value Work: 0.164 
  • R-Value Observed: 0.166 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 92.311α = 90
b = 97.227β = 90
c = 138.849γ = 90
Software Package:
Software NamePurpose
HKL-2000data collection
MOLREPphasing
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2010-04-28
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance