2VQQ

STRUCTURE OF HDAC4 CATALYTIC DOMAIN (A DOUBLE CYSTEINE-TO-ALANINE MUTANT) BOUND TO A TRIFLUOROMETHYLKETONE INHBITOR

Structural Biology Knowledgebase: 2VQQ SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.221
  • R-Value Work: 0.194

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 2VQQ

Classification: HYDROLASE

Total Structure Weight: 90249.54

Macromolecule Entities
Molecule Chains Length Organism Details
HISTONE DEACETYLASE 4 A, B 413 Homo sapiens EC#: 3.5.1.98 IUBMB
Fragment: CATALYTIC DOMAIN, RESIDUES 648-1057
Mutation: C25A, C56A
Gene Name(s): HDAC4 Gene View KIAA0288

Small Molecules
Ligands 4 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
K
Query on K

A, B POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N
Ligand Explorer
 
JSmol
SO4
Query on SO4

A, B SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
Ligand Explorer
 
JSmol
TFG
Query on TFG

A, B 2,2,2-TRIFLUORO-1-{5-[(3-PHENYL-5,6-DIHYDROIMIDAZO[1,2- A]PYRAZIN-7(8H)-YL)CARBONYL]THIOPHEN-2-YL}ETHANE- 1,1-DIOL
C19 H16 F3 N3 O3 S
OFBFUNBBOQCNFX-UHFFFAOYSA-N
Ligand Explorer
 
JSmol
ZN
Query on ZN

A, B ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
Ligand Explorer
 
JSmol
External Ligand Annotations
ID Binding Affinity (Sequence Identity %)
TFG N/A in BindingDB
IC50: 367 nM  BindingMOAD
N/A in PDBbind

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.221
  • R-Value Work: 0.194
  • Space Group: P 1 21 1
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 85.61 α = 90.00
b = 70.67 β = 108.08
c = 88.20 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2008-03-18
  • Released Date: 2008-07-08
  • Deposition author(s): Bottomley, M.J., Lo Surdo, P., Di Giovine, P., Cirillo, A., Scarpelli, R., Ferrigno, F., Jones, P., Neddermann, P., De Francesco, R., Steinkuhler, C., Gallinari, P., Carfi, A.

Revision History

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