5WGK | pdb_00005wgk

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

• PDB DOI: https://doi.org/10.2210/pdb5WGK/pdb

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


• Deposited: 2017-07-14 Released: 2017-12-06 
• Deposition Author(s): Porter, N.J., Christianson, D.W.
• Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.82 Å
• R-Value Free: 
  0.173 (Depositor), 0.176 (DCC) 
• R-Value Work: 
  0.149 (Depositor), 0.153 (DCC) 
• R-Value Observed: 
  0.150 (Depositor) 

Starting Model: experimental

Literature

Unusual zinc-binding mode of HDAC6-selective hydroxamate inhibitors.

Porter, N.J., Mahendran, A., Breslow, R., Christianson, D.W.

(2017) Proc Natl Acad Sci U S A 114: 13459-13464

• PubMed: 29203661 
• DOI: https://doi.org/10.1073/pnas.1718823114
• Primary Citation Related Structures: 
  5WGI, 5WGK, 5WGL, 5WGM


• PubMed Abstract: 
  

  Histone deacetylases (HDACs) regulate myriad cellular processes by catalyzing the hydrolysis of acetyl-l-lysine residues in histone and nonhistone proteins. The Zn ²⁺ -dependent class IIb enzyme HDAC6 regulates microtubule function by deacetylating α-tubulin, which suppresses microtubule dynamics and leads to cell cycle arrest and apoptosis. Accordingly, HDAC6 is a target for the development of selective inhibitors that might be useful in new therapeutic approaches for the treatment of cancer, neurodegenerative diseases, and other disorders. Here, we present high-resolution structures of catalytic domain 2 from Danio rerio HDAC6 (henceforth simply "HDAC6") complexed with compounds that selectively inhibit HDAC6 while maintaining nanomolar inhibitory potency: N -hydroxy-4-[( N (2-hydroxyethyl)-2-phenylacetamido)methyl)-benzamide)] (HPB), ACY-1215 (Ricolinostat), and ACY-1083. These structures reveal that an unusual monodentate Zn ²⁺ coordination mode is exploited by sterically bulky HDAC6-selective phenylhydroxamate inhibitors. We additionally report the ultrahigh-resolution structure of the HDAC6-trichostatin A complex, which reveals two Zn ²⁺ -binding conformers for the inhibitor: a major conformer (70%) with canonical bidentate hydroxamate-Zn ²⁺ coordination geometry and a minor conformer (30%) with monodentate hydroxamate-Zn ²⁺ coordination geometry, reflecting a free energy difference of only 0.5 kcal/mol. The minor conformer is not visible in lower resolution structure determinations. Structural comparisons of HDAC6-inhibitor complexes with class I HDACs suggest active site features that contribute to the isozyme selectivity observed in biochemical assays.

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Organizational Affiliation: 
• Roy and Diana Vagelos Laboratories, Department of Chemistry, University of Pennsylvania, Philadelphia, PA 19104-6323.
Department of Chemistry, Columbia University, New York, NY 10027.
Roy and Diana Vagelos Laboratories, Department of Chemistry, University of Pennsylvania, Philadelphia, PA 19104-6323; [e-mail].

Biological Assembly 1  

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

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: immunoprecipitation

Macromolecule Content 

• Total Structure Weight: 43.17 kDa 
• Atom Count: 3,377 
• Modeled Residue Count: 355 
• 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 6 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
AGJ	Q [auth A]	N-hydroxy-4-{[(2-hydroxyethyl)(phenylacetyl)amino]methyl}benzamide C18 H20 N2 O4 GTFAUKGKYICUDS-UHFFFAOYSA-N
IOD	B [auth A], C [auth A], D [auth A], E [auth A], F [auth A], G [auth A], H [auth A], I [auth A], J [auth A], K [auth A], L [auth A]	IODIDE ION I XMBWDFGMSWQBCA-UHFFFAOYSA-M
PEG	FA [auth A]	DI(HYDROXYETHYL)ETHER C4 H10 O3 MTHSVFCYNBDYFN-UHFFFAOYSA-N
ZN	M [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
EDO	AA [auth A], BA [auth A], CA [auth A], DA [auth A], EA [auth A], R [auth A], S [auth A], T [auth A], U [auth A], V [auth A], W [auth A], X [auth A], Y [auth A], Z [auth A]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N
K	N [auth A], O [auth A], P [auth A]	POTASSIUM ION K NPYPAHLBTDXSSS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.82 Å
• R-Value Free:  0.173 (Depositor), 0.176 (DCC) 
• R-Value Work:  0.149 (Depositor), 0.153 (DCC) 
• R-Value Observed: 0.150 (Depositor) 

Space Group: P 2 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 51.67	α = 90
b = 83.97	β = 90
c = 94.57	γ = 90

Software Package:

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

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2017-12-06 
Deposition Author(s): Porter, N.J., Christianson, D.W.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	GM49758

Revision History  

• Version 1.0: 2017-12-06
  Type: Initial release
  
• Version 1.1: 2017-12-20
  Changes: Database references
• Version 1.2: 2018-01-03
  Changes: Database references
• Version 1.3: 2020-01-01
  Changes: Author supporting evidence
• Version 1.4: 2023-10-04
  Changes: Data collection, Database references, Derived calculations, Refinement description