9EGF | pdb_00009egf

Crystal structure of Danio rerio histone deacetylase 6 catalytic domain 2 complexed with TO-589

  • 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

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.25 Å
  • R-Value Free: 
    0.221 (Depositor), 0.219 (DCC) 
  • R-Value Work: 
    0.200 (Depositor), 0.200 (DCC) 
  • R-Value Observed: 
    0.201 (Depositor) 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history


Literature

Improved Pharmacokinetic Profiles of HDAC6 Inhibitors via Cap Group Modifications.

Olaoye, O.O.Erdogan, F.Gracia-Hernandez, M.Garcha, H.K.Sedighi, A.Ashraf, Q.F.Nawar, N.Geletu, M.Seo, H.S.Abdallah, D.I.Abdeldayem, A.Hassan, M.M.Dhe-Paganon, S.de Araujo, E.D.Villagra, A.Gunning, P.T.

(2025) J Med Chem 68: 18216-18229

  • DOI: https://doi.org/10.1021/acs.jmedchem.5c00479
  • Primary Citation of Related Structures:  
    9EFC, 9EFR, 9EFX, 9EGF, 9EGU

  • PubMed Abstract: 

    Hydroxamic acid (HA)-based HDAC inhibitors often suffer from poor pharmacokinetic (PK) profiles, limiting their in vivo applications. Cap group modification offers a promising strategy to address these challenges. Here, we optimized the cap group of TO-317, a selective HDAC6 inhibitor with a bisected cap structure, generating 26 analogs with comparable or improved HDAC6 binding affinity and selectivity. Replacing the redundant tetrafluorobenzene sulfonamide cap while retaining the essential picolyl cap group preserved the critical H614 hydrogen bond, as confirmed by X-ray crystallography (1.24-1.27 Å resolution) of five analogs. Analog 14 , featuring a 2-chlorobenzene sulfonamide cap, demonstrated a 120-fold enhancement in plasma concentration in mice compared to that of TO-317. Preclinical studies showed that analog 14 achieved 56% tumor growth inhibition in an SM1 melanoma murine model without observed toxicity. These findings highlight cap group optimization as a powerful approach to enhance HA-based HDAC inhibitors for advanced preclinical and clinical development.


  • Organizational Affiliation
    • Department of Chemical and Physical Sciences, University of Toronto Mississauga, 3359 Mississauga Rd N., Mississauga, Ontario L5L 1C6, Canada.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Hdac6 protein
A, B
357Danio rerioMutation(s): 0 
Gene Names: hdac6
UniProt
Find proteins for F8W4B7 (Danio rerio)
Explore F8W4B7 
Go to UniProtKB:  F8W4B7
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupF8W4B7
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
A1BH8 (Subject of Investigation/LOI)
Query on A1BH8

Download Ideal Coordinates CCD File 
C [auth A],
F [auth B]
4-({(ethanesulfonyl)[(pyridin-3-yl)methyl]amino}methyl)-N-hydroxybenzamide
C16 H19 N3 O4 S
GABRQLARJXNUJD-UHFFFAOYSA-N
ZN
Query on ZN

Download Ideal Coordinates CCD File 
D [auth A],
G [auth B]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
K
Query on K

Download Ideal Coordinates CCD File 
E [auth A],
H [auth B]
POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.25 Å
  • R-Value Free:  0.221 (Depositor), 0.219 (DCC) 
  • R-Value Work:  0.200 (Depositor), 0.200 (DCC) 
  • R-Value Observed: 0.201 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 75.37α = 90
b = 91.82β = 90
c = 96.63γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
xia2data scaling
xia2data reduction
PHENIXphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Natural Sciences and Engineering Research Council (NSERC, Canada)CanadaRGPIN-2014-05767
Canadian Institutes of Health Research (CIHR)CanadaMOP-130424
Canada Research ChairsCanada950-232042
Ontario Research FundCanada34876
Canada Foundation for InnovationCanada33536

Revision History  (Full details and data files)

  • Version 1.0: 2024-12-04
    Type: Initial release
  • Version 1.1: 2025-08-13
    Changes: Database references
  • Version 1.2: 2025-09-10
    Changes: Database references
  • Version 1.3: 2025-09-24
    Changes: Database references