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 
  • R-Value Observed: 0.171 

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Ligand Structure Quality Assessment 


This is version 1.2 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

  • DOI: 10.1021/acs.jmedchem.8b01013
  • Primary Citation of Related Structures:  
    6DVM, 6DVL, 6DVO, 6DVN

  • PubMed Abstract: 
  • Four crystal structures are presented of histone deacetylase 6 (HDAC6) complexes with para-substituted phenylhydromaxamate inhibitors, including bulky peptoids. These structures provide insight regarding the design of capping groups that confer selectivity for binding to HDAC6, specifically with regard to interactions in a pocket formed by the L1 loop ...

    Four crystal structures are presented of histone deacetylase 6 (HDAC6) complexes with para-substituted phenylhydromaxamate inhibitors, including bulky peptoids. These structures provide insight regarding the design of capping groups that confer selectivity for binding to HDAC6, specifically with regard to interactions in a pocket formed by the L1 loop. Capping group interactions may also influence hydroxamate-Zn 2+ coordination with monodentate or bidentate geometry.


    Organizational Affiliation

    Roy and Diana Vagelos Laboratories, Department of Chemistry , University of Pennsylvania , 231 South 34th Street , Philadelphia , Pennsylvania 19104-6323 , United States.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Hdac6 proteinA364Danio rerioMutation(s): 0 
Gene Names: hdac6
UniProt
Find proteins for F8W4B7 (Danio rerio)
Explore F8W4B7 
Go to UniProtKB:  F8W4B7
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 5 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
HBV (Subject of Investigation/LOI)
Query on HBV

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

Download Ideal Coordinates CCD File 
E [auth A]PROLINE
C5 H9 N O2
ONIBWKKTOPOVIA-BYPYZUCNSA-N
 Ligand Interaction
ZN
Query on ZN

Download Ideal Coordinates CCD File 
B [auth A]ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
EDO
Query on EDO

Download Ideal Coordinates CCD File 
G [auth A], H [auth A], I [auth A], J [auth A], K [auth A], L [auth A], M [auth A], N [auth A]1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
K
Query on K

Download Ideal Coordinates CCD File 
C [auth A], D [auth A]POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N
 Ligand Interaction
Binding Affinity Annotations 
IDSourceBinding Affinity
HBV Binding MOAD:  6DVO IC50: 60 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.98 Å
  • R-Value Free: 0.216 
  • R-Value Work: 0.168 
  • R-Value Observed: 0.171 
  • Space Group: P 65
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 97.23α = 90
b = 97.23β = 90
c = 78.9γ = 120
Software Package:
Software NamePurpose
Aimlessdata scaling
PHENIXrefinement
PDB_EXTRACTdata extraction
iMOSFLMdata reduction
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment  



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI)United StatesGM49758

Revision History  (Full details and data files)

  • Version 1.0: 2018-08-29
    Type: Initial release
  • Version 1.1: 2018-09-26
    Changes: Data collection, Database references
  • Version 1.2: 2019-12-18
    Changes: Author supporting evidence