5WGK

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.822 Å
  • R-Value Free: 0.173 
  • R-Value Work: 0.149 

wwPDB Validation  3D Report Full Report


This is version 1.2 of the entry. See complete history

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

  • DOI: 10.1073/pnas.1718823114
  • Primary Citation of Related Structures:  5WGI, 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 Zn2+-dependent class IIb enzyme HDAC6 regulates microtubule function by deacetylating α-t ...

    Histone deacetylases (HDACs) regulate myriad cellular processes by catalyzing the hydrolysis of acetyl-l-lysine residues in histone and nonhistone proteins. The Zn2+-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 Zn2+ 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 Zn2+-binding conformers for the inhibitor: a major conformer (70%) with canonical bidentate hydroxamate-Zn2+ coordination geometry and a minor conformer (30%) with monodentate hydroxamate-Zn2+ 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.


    Organizational Affiliation

    Roy and Diana Vagelos Laboratories, Department of Chemistry, University of Pennsylvania, Philadelphia, PA 19104-6323.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
Molecule Chains Sequence Length Organism Details
Hdac6 protein
A
364 Danio rerio Gene Names: hdac6
Find proteins for A7YT55 (Danio rerio)
Go to UniProtKB:  A7YT55
Small Molecules
Ligands 6 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
K
Query on K

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

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Download CCD File 
A
N-hydroxy-4-{[(2-hydroxyethyl)(phenylacetyl)amino]methyl}benzamide
C18 H20 N2 O4
GTFAUKGKYICUDS-UHFFFAOYSA-N
 Ligand Interaction
ZN
Query on ZN

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

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A
IODIDE ION
I
XMBWDFGMSWQBCA-UHFFFAOYSA-M
 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
PEG
Query on PEG

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A
DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.822 Å
  • R-Value Free: 0.173 
  • R-Value Work: 0.149 
  • Space Group: P 2 21 21
Unit Cell:
Length (Å) Angle (°)
a = 51.670 α = 90.00
b = 83.970 β = 90.00
c = 94.570 γ = 90.00
Software Package:
Software Name Purpose
Aimless data scaling
iMOSFLM data reduction
PHASER phasing
PHENIX refinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding Organization Country Grant Number
National Institutes of Health/National Institute of General Medical Sciences United States GM49758

Revision History 

  • Version 1.0: 2017-12-06
    Type: Initial release
  • Version 1.1: 2017-12-20
    Type: Database references
  • Version 1.2: 2018-01-03
    Type: Database references