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

Literature

Macromolecules
Sequence Display for 3MAX

Classification: HYDROLASE

Total Structure Weight: 127895.75

Macromolecule Entities
Molecule Chains Length Organism Details
Histone deacetylase 2 A, B, C 367 Homo sapiens EC#: 3.5.1.98 IUBMB
Gene Name(s): HDAC2 Gene View
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG

Small Molecules
Ligands 5 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
LLX
Query on LLX

A, B, C N-(4-aminobiphenyl-3-yl)benzamide
C19 H16 N2 O
ZWLFHHHQRUYIBT-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
NHE
Query on NHE

A 2-[N-CYCLOHEXYLAMINO]ETHANE SULFONIC ACID
N-CYCLOHEXYLTAURINE; CHES (Synonym)
C8 H17 N O3 S
MKWKNSIESPFAQN-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
ZN
Query on ZN

A, B, C ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
CA
Query on CA

A, B, C CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
NA
Query on NA

A, B, C SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
External Ligand Annotations
ID Binding Affinity (Sequence Identity %)
LLX IC50: 27 - 1200 nM (93 - 99) BindingDB

IC50: 27 nM  BindingMOAD
IC50: 900 nM  PDBbind

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.05 Å
  • R-Value Free: 0.204
  • R-Value Work: 0.164
  • Space Group: P 21 21 21

Unit Cell:

Length (Å) Angle (°)
a = 92.31 α = 90.00
b = 97.23 β = 90.00
c = 138.85 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2010-03-24
  • Released Date: 2010-04-28
  • Deposition author(s): Skene, R.J., Jennings, A.J.

Revision History

  • 2011-07-13
    Type: Version format compliance