7UK2 | pdb_00007uk2

Crystal structure of Danio rerio histone deacetylase 6 catalytic domain 2 complexed with NN-390

• PDB DOI: https://doi.org/10.2210/pdb7UK2/pdb

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


• Deposited: 2022-03-31 Released: 2022-11-02 
• 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: 1.60 Å
• R-Value Free: 
  0.222 (Depositor), 0.225 (DCC) 
• R-Value Work: 
  0.199 (Depositor), 0.204 (DCC) 
• R-Value Observed: 
  0.200 (Depositor) 

Starting Model: experimental

Literature

High Efficacy and Drug Synergy of HDAC6-Selective Inhibitor NN-429 in Natural Killer (NK)/T-Cell Lymphoma.

Garcha, H.K., Nawar, N., Sorger, H., Erdogan, F., Aung, M.M.K., Sedighi, A., Manaswiyoungkul, P., Seo, H.S., Schonefeldt, S., Poloske, D., Dhe-Paganon, S., Neubauer, H.A., Mustjoki, S.M., Herling, M., de Araujo, E.D., Moriggl, R., Gunning, P.T.

(2022) Pharmaceuticals (Basel) 15

• PubMed: 36355493 
• DOI: https://doi.org/10.3390/ph15111321
• Primary Citation Related Structures: 
  7UK2


• PubMed Abstract: 
  

  NK/T-cell lymphoma (NKTCL) and γδ T-cell non-Hodgkin lymphomas (γδ T-NHL) are highly aggressive lymphomas that lack rationally designed therapies and rely on repurposed chemotherapeutics from other hematological cancers. Histone deacetylases (HDACs) have been targeted in a range of malignancies, including T-cell lymphomas. This study represents exploratory findings of HDAC6 inhibition in NKTCL and γδ T-NHL through a second-generation inhibitor NN-429. With nanomolar in vitro HDAC6 potency and high in vitro and in cellulo selectivity for HDAC6, NN-429 also exhibited long residence time and improved pharmacokinetic properties in contrast to older generation inhibitors. Following unique selective cytotoxicity towards γδ T-NHL and NKTCL, NN-429 demonstrated a synergistic relationship with the clinical agent etoposide and potential synergies with doxorubicin, cytarabine, and SNS-032 in these disease models, opening an avenue for combination treatment strategies.

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Organizational Affiliation: 
• Department of Chemical and Physical Sciences, University of Toronto Mississauga, 3359 Mississauga Road, Mississauga, ON L5L 1C6, Canada.
Department of Chemistry, University of Toronto, 80 St. George Street, Toronto, ON M5S 3H6, Canada.
Institute of Animal Breeding and Genetics, University of Veterinary Medicine Vienna, 1210 Vienna, Austria.
Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA.
Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02215, USA.
Translational Immunology Research Program and Department of Clinical Chemistry and Hematology, University of Helsinki, 00014 Helsinki, Finland.
Hematology Research Unit, Helsinki University Hospital Comprehensive Cancer Center, 00290 Helsinki, Finland.
iCAN Digital Precision Cancer Medicine Flagship, 00014 Helsinki, Finland.
Department of Hematology, Cellular Therapy, and Hemostaseology, University of Leipzig, 04109 Leipzig, Germany.

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: 40.29 kDa 
• Atom Count: 3,241 
• Modeled Residue Count: 353 
• Deposited Residue Count: 357 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Hdac6 protein	A	357	Danio rerio	Mutation(s): 0  Gene Names: hdac6
UniProt
Find proteins for F8W4B7 (Danio rerio) Explore F8W4B7  Go to UniProtKB:  F8W4B7

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
O2L (Subject of Investigation/LOI)	B [auth A]	N-hydroxy-4-{[(propan-2-yl)(2,3,4,5-tetrafluorobenzene-1-sulfonyl)amino]methyl}benzamide C17 H16 F4 N2 O4 S SJWJGLIJTRUXIZ-UHFFFAOYSA-N
ZN	C [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
K	D [auth A], E [auth A]	POTASSIUM ION K NPYPAHLBTDXSSS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.60 Å
• R-Value Free:  0.222 (Depositor), 0.225 (DCC) 
• R-Value Work:  0.199 (Depositor), 0.204 (DCC) 
• R-Value Observed: 0.200 (Depositor) 

Space Group: P 2 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 51.263	α = 90
b = 83.135	β = 90
c = 93.276	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
xia2	data scaling
PHASER	phasing
PDB_EXTRACT	data extraction
xia2	data reduction

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2022-11-02 
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: 2022-11-02
  Type: Initial release
  
• Version 1.1: 2022-11-30
  Changes: Database references
• Version 1.2: 2023-10-25
  Changes: Data collection, Refinement description