5EEN | pdb_00005een

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

• PDB DOI: https://doi.org/10.2210/pdb5EEN/pdb

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


• Deposited: 2015-10-23 Released: 2016-07-27 
• Deposition Author(s): Hai, Y., 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: 1.86 Å
• R-Value Free: 
  0.224 (Depositor), 0.222 (DCC) 
• R-Value Work: 
  0.183 (Depositor), 0.184 (DCC) 
• R-Value Observed: 
  0.185 (Depositor) 

Starting Model: experimental

Literature

Histone deacetylase 6 structure and molecular basis of catalysis and inhibition.

Hai, Y., Christianson, D.W.

(2016) Nat Chem Biol 12: 741-747

• PubMed: 27454933 
• DOI: https://doi.org/10.1038/nchembio.2134
• Primary Citation Related Structures: 
  5EDU, 5EEF, 5EEI, 5EEK, 5EEM, 5EEN, 5EF7, 5EF8, 5EFB, 5EFG, 5EFH, 5EFJ, 5EFK, 5EFN


• PubMed Abstract: 
  

  Histone deacetylase 6 (HDAC6) is a critical target for drug design because of its role in oncogenic transformation and cancer metastasis, and is unique among all histone deacetylases in that it contains tandem catalytic domains designated CD1 and CD2. We now report the crystal structures of CD2 from Homo sapiens HDAC6 and of CD1 and CD2 from Danio rerio HDAC6. We correlated these structures with activity measurements using 13 different substrates. The catalytic activity of CD2 from both species exhibited broad substrate specificity, whereas that of CD1 was highly specific for substrates bearing C-terminal acetyllysine residues. Crystal structures of substrate complexes yielded unprecedented snapshots of the catalytic mechanism. Additionally, crystal structures of complexes with eight different inhibitors, including belinostat and panobinostat (currently used in cancer chemotherapy), the macrocyclic tetrapeptide HC toxin, and the HDAC6-specific inhibitor N-hydroxy-4-(2-((2-hydroxyethyl)(phenyl)amino)-2-oxoethyl)benzamide, revealed surprising new insight regarding changes in Zn(2+) coordination and isozyme-specific inhibition.

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Organizational Affiliation: 
• Roy and Diana Vagelos Laboratories, Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania, USA.
Radcliffe Institute for Advanced Study and Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts, USA.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly 2  

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

Biological assembly 2 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 81.57 kDa 
• Atom Count: 5,965 
• Modeled Residue Count: 710 
• Deposited Residue Count: 728 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Hdac6 protein	A [auth B], B [auth A]	364	Danio rerio	Mutation(s): 0  Gene Names: hdac6 EC: 3.5.1.98
UniProt
Find proteins for F8W4B7 (Danio rerio) Explore F8W4B7  Go to UniProtKB:  F8W4B7

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
5OG	F [auth B], J [auth A]	Belinostat C15 H14 N2 O4 S NCNRHFGMJRPRSK-MDZDMXLPSA-N
ZN	E [auth B], I [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
K	C [auth B], D [auth B], G [auth A], H [auth A]	POTASSIUM ION K NPYPAHLBTDXSSS-UHFFFAOYSA-N
CL	K [auth A], L [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Binding Affinity Annotations
ID	Source	Binding Affinity
5OG	BindingDB:  5EEN	Ki: 1.1 (nM) from 1 assay(s)
		IC50: 1.9 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.86 Å
• R-Value Free:  0.224 (Depositor), 0.222 (DCC) 
• R-Value Work:  0.183 (Depositor), 0.184 (DCC) 
• R-Value Observed: 0.185 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 75.972	α = 90
b = 95.483	β = 90
c = 96.336	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling
PHASER	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2016-07-27 
Deposition Author(s): Hai, Y., 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	GM 49758

Revision History  

• Version 1.0: 2016-07-27
  Type: Initial release
  
• Version 1.1: 2016-08-10
  Changes: Database references
• Version 1.2: 2016-09-07
  Changes: Database references
• Version 1.3: 2017-09-13
  Changes: Author supporting evidence, Derived calculations
• Version 1.4: 2019-12-25
  Changes: Author supporting evidence
• Version 1.5: 2023-09-27
  Changes: Data collection, Database references, Derived calculations, Refinement description