3F07

Crystal Structure Analysis of Human HDAC8 complexed with APHA in a new monoclinic crystal form


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.3 Å
  • R-Value Free: 0.260
  • R-Value Work: 0.216

Literature

Macromolecules
Sequence Display for 3F07

Classification: HYDROLASE

Total Structure Weight: 130589.66

Macromolecule Entities
Molecule Chains Length Organism Details
Histone deacetylase 8 A, B, C 388 Homo sapiens EC#: 3.5.1.98 IUBMB
Gene Name(s): HDAC8 Gene View HDACL1 CDA07
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG

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

A, B (2E)-N-hydroxy-3-[1-methyl-4-(phenylacetyl)- 1H-pyrrol-2-yl]prop-2-enamide
APHA Compound 8; 3-(1-Methyl-4-phenylacetyl- 1H-2-pyrrolyl)-N-hydroxypropenamide (Synonym)
C16 H16 N2 O3
UFQOXIMRSMFQRI-BQYQJAHWSA-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)
K
Query on K

A, B, C POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
External Ligand Annotations
ID Binding Affinity (Sequence Identity %)
AGE N/A in BindingDB
N/A in BindingMoad
IC50: 2900 nM  PDBbind

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.3 Å
  • R-Value Free: 0.260
  • R-Value Work: 0.216
  • Space Group: P 1 21 1

Unit Cell:

Length (Å) Angle (°)
a = 88.38 α = 90.00
b = 90.17 β = 94.74
c = 92.27 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2008-10-24
  • Released Date: 2008-12-30
  • Deposition author(s): Dowling, D.P., Gantt, S.L., Gattis, S.G., Fierke, C.A., Christianson, D.W.

Revision History

  • Version 1_0: 2008-12-30

    Type: Initial release

  • Version 1_1: 2011-07-13

    Type: Version format compliance