9EGU

Crystal structure of Danio rerio histone deacetylase 6 catalytic domain 2 complexed with TO-599

• PDB DOI: https://doi.org/10.2210/pdb9EGU/pdb

• Classification: METAL BINDING PROTEIN
• Organism(s): Danio rerio
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2024-11-21 Released: 2024-12-04 
• Deposition Author(s): Erdogan, F., Seo, H.-S., Dhe-Paganon, S.
• Funding Organization(s): Natural Sciences and Engineering Research Council (NSERC, Canada), Canadian Institutes of Health Research (CIHR), Canada Research Chairs, Ontario Research Fund, Canada Foundation for Innovation

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.27 Å
• R-Value Free: 0.221 
• R-Value Work: 0.208 
• R-Value Observed: 0.209 

Starting Model: experimental

Literature

Bisected Cap Group Modifications Provides Basis for Improved Pharmacokinetics of HDAC Inhibitors

Olaoye, O., Erdogan, F., Gunning, P.T.

To be published.

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: 80.47 kDa 
• Atom Count: 6,332 
• Modelled Residue Count: 714 
• Deposited Residue Count: 714 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Hdac6 protein	A, B	357	Danio rerio	Mutation(s): 0  Gene Names: hdac6
UniProt
Find proteins for A7YT55 (Danio rerio) Explore A7YT55  Go to UniProtKB:  A7YT55

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
A1BH9 (Subject of Investigation/LOI)	C [auth A], F [auth B]	N-hydroxy-4-({[(pyridin-3-yl)methyl](thiophene-3-sulfonyl)amino}methyl)benzamide C18 H17 N3 O4 S2 PMNUORLLCSPXOC-UHFFFAOYSA-N
ZN	D [auth A], G [auth B]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
K	E [auth A], H [auth B]	POTASSIUM ION K NPYPAHLBTDXSSS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.27 Å
• R-Value Free: 0.221 
• R-Value Work: 0.208 
• R-Value Observed: 0.209 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 74.79	α = 90
b = 91.19	β = 90
c = 96.16	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
xia2	data scaling
xia2	data reduction
PHENIX	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2024-12-04 
Deposition Author(s): Erdogan, F., Seo, H.-S., Dhe-Paganon, S.

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Funding Organization	Location	Grant Number
Natural Sciences and Engineering Research Council (NSERC, Canada)	Canada	RGPIN-2014-05767
Canadian Institutes of Health Research (CIHR)	Canada	MOP-130424
Canada Research Chairs	Canada	950-232042
Ontario Research Fund	Canada	34876
Canada Foundation for Innovation	Canada	33536

Revision History  

• Version 1.0: 2024-12-04
  Type: Initial release