6DVO

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

• PDB DOI: https://doi.org/10.2210/pdb6DVO/pdb

• Classification: hydrolase/hydrolase inhibitor
• Organism(s): Danio rerio
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2018-06-24 Released: 2018-08-29 
• Deposition Author(s): Porter, N.J., Christianson, D.W.
• Funding Organization(s): National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI)

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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 

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

• PubMed: 30118224 
• DOI: https://doi.org/10.1021/acs.jmedchem.8b01013
• Primary Citation of Related Structures:  
  6DVL, 6DVM, 6DVN, 6DVO


• 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. Capping group interactions may also influence hydroxamate-Zn ²⁺ coordination with monodentate or bidentate geometry.

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Organizational Affiliation: 

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

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 41.39 kDa 
• Atom Count: 3,087 
• Modelled Residue Count: 352 
• Deposited Residue Count: 364 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Hdac6 protein	A	364	Danio rerio	Mutation(s): 0  Gene Names: hdac6
UniProt
Find proteins for F8W4B7 (Danio rerio) Explore F8W4B7  Go to UniProtKB:  F8W4B7

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
HBV	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
PRO	E [auth A]	PROLINE C5 H9 N O2 ONIBWKKTOPOVIA-BYPYZUCNSA-N
ZN	B [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
EDO	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
K	C [auth A], D [auth A]	POTASSIUM ION K NPYPAHLBTDXSSS-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding 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 = 97.23	α = 90
b = 97.23	β = 90
c = 78.9	γ = 120

Software Package:

Software Name	Purpose
Aimless	data scaling
PHENIX	refinement
PDB_EXTRACT	data extraction
iMOSFLM	data reduction
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2018-08-29 
Deposition Author(s): Porter, N.J., Christianson, D.W.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI)	United States	GM49758

Revision History  

• 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
• Version 1.3: 2023-10-11
  Changes: Data collection, Database references, Derived calculations, Refinement description