6DVO

Crystal structure of Danio rerio histone deacetylase 6 catalytic domain 2 in complex with Bavarostat


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.98 Å
  • R-Value Free: 0.216 
  • R-Value Work: 0.168 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Histone Deacetylase 6-Selective Inhibitors and the Influence of Capping Groups on Hydroxamate-Zinc Denticity.

Porter, N.J.Osko, J.D.Diedrich, D.Kurz, T.Hooker, J.M.Hansen, F.K.Christianson, D.W.

(2018) J. Med. Chem. 61: 8054-8060


Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Hdac6 protein
A
364Danio rerioMutation(s): 0 
Gene Names: hdac6
Find proteins for F8W4B7 (Danio rerio)
Go to UniProtKB:  F8W4B7
Small Molecules
Ligands 5 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
K
Query on K

Download SDF File 
Download CCD File 
A
POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N
 Ligand Interaction
ZN
Query on ZN

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Download CCD File 
A
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
HBV
Query on HBV

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Download CCD File 
A
3-fluoro-N-hydroxy-4-[(methyl{[(3s,5s,7s)-tricyclo[3.3.1.1~3,7~]decan-1-yl]methyl}amino)methyl]benzamide
Bavarostat
C20 H27 F N2 O2
IGZQZELTOHAHNW-PVGDPBLGSA-N
 Ligand Interaction
EDO
Query on EDO

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Download CCD File 
A
1,2-ETHANEDIOL
ETHYLENE GLYCOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
PRO
Query on PRO

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Download CCD File 
A
PROLINE
C5 H9 N O2
ONIBWKKTOPOVIA-BYPYZUCNSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.98 Å
  • R-Value Free: 0.216 
  • R-Value Work: 0.168 
  • Space Group: P 65
Unit Cell:
Length (Å)Angle (°)
a = 97.230α = 90.00
b = 97.230β = 90.00
c = 78.900γ = 120.00
Software Package:
Software NamePurpose
iMOSFLMdata reduction
PHENIXrefinement
PHASERphasing
PDB_EXTRACTdata extraction
Aimlessdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Human Genome Research InstituteUnited StatesGM49758

Revision History 

  • Version 1.0: 2018-08-29
    Type: Initial release
  • Version 1.1: 2018-09-26
    Type: Data collection, Database references