1VKG

Crystal Structure of Human HDAC8 complexed with CRA-19156

Structural Biology Knowledgebase: 1VKG SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.2 Å
  • R-Value Free: 0.304
  • R-Value Work: 0.237

Literature

Macromolecules
Sequence Display for 1VKG

Classification: hydrolase

Total Structure Weight: 84617.45

Macromolecule Entities
Molecule Chains Length Organism Details
Histone deacetylase 8 A, B 377 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
CRI
Query on CRI

A, B 5-(4-METHYL-BENZOYLAMINO)-BIPHENYL-3,4'-DICARBOXYLIC ACID 3- DIMETHYLAMIDE-4'-HYDROXYAMIDE
C24 H23 N3 O4
DOPFUKKMSDUVTQ-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
ZN
Query on ZN

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

A, B SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.2 Å
  • R-Value Free: 0.304
  • R-Value Work: 0.237
  • Space Group: P 21 21 21
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 82.63 α = 90.00
b = 92.71 β = 90.00
c = 98.76 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2004-05-13
  • Released Date: 2004-07-27
  • Deposition author(s): Somoza, J.R., Skene, R.J., Katz, B.A., Mol, C., Ho, J.D., Jennings, A.J., Luong, C., Arvai, A., Buggy, J.J., Chi, E., Tang, J., Sang, B.-C., Verner, E., Wynands, R., Leahy, E.M., Dougan, D.R., Snell, G., Navre, M., Knuth, M.W., Swanson, R.V., McRee, D.E., Tari, L.W.

Revision History

  • 2011-07-13
    Type: Version format compliance | Details: compliance with PDB Exchange Dictionary V4