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- PDB-9efc: Crystal structure of Danio rerio histone deacetylase 6 catalytic ... -

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Basic information

Entry
Database: PDB / ID: 9efc
TitleCrystal structure of Danio rerio histone deacetylase 6 catalytic domain 2 complexed with TO-588
ComponentsHdac6 protein
KeywordsMETAL BINDING PROTEIN / potassium ion binding / alkali metal ion binding / ion binding / cation binding / metal ion binding / catalytic activity / hydrolase activity / deacetylase activity / protein deacetylase activity / acting on a protein / acting on carbon-nitrogen (but not peptide) bonds / in linear amides / tubulin deacetylase activity / zinc ion binding / transition metal ion binding
Function / homology
Function and homology information


tubulin deacetylase activity / swimming behavior / definitive hemopoiesis / protein lysine deacetylase activity / histone deacetylase activity / potassium ion binding / histone deacetylase complex / hematopoietic progenitor cell differentiation / epigenetic regulation of gene expression / angiogenesis / zinc ion binding
Similarity search - Function
Ubiquitin Carboxyl-terminal Hydrolase-like zinc finger / Zinc finger, UBP-type / Zn-finger in ubiquitin-hydrolases and other protein / Zinc finger UBP-type profile. / : / Histone deacetylase family / Histone deacetylase domain / Histone deacetylase domain superfamily / Histone deacetylase domain / Ureohydrolase domain superfamily / Zinc finger, RING/FYVE/PHD-type
Similarity search - Domain/homology
: / : / Protein deacetylase HDAC6
Similarity search - Component
Biological speciesDanio rerio (zebrafish)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.26 Å
AuthorsErdogan, F. / Seo, H.-S. / Dhe-Paganon, S.
Funding support Canada, 5items
OrganizationGrant numberCountry
Natural Sciences and Engineering Research Council (NSERC, Canada)RGPIN-2014-05767 Canada
Canadian Institutes of Health Research (CIHR)MOP-130424 Canada
Canada Research Chairs950-232042 Canada
Ontario Research Fund34876 Canada
Canada Foundation for Innovation33536 Canada
CitationJournal: J.Med.Chem. / Year: 2025
Title: Improved Pharmacokinetic Profiles of HDAC6 Inhibitors via Cap Group Modifications.
Authors: 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- ...Authors: 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.
History
DepositionNov 20, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 4, 2024Provider: repository / Type: Initial release
Revision 1.1Aug 13, 2025Group: Database references / Category: citation
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.year
Revision 1.2Sep 10, 2025Group: Database references / Category: citation / citation_author / Item: _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.3Sep 24, 2025Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Hdac6 protein
B: Hdac6 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)80,58210
Polymers79,6242
Non-polymers9588
Water14,106783
1
A: Hdac6 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,2915
Polymers39,8121
Non-polymers4794
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Hdac6 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,2915
Polymers39,8121
Non-polymers4794
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)75.080, 92.110, 96.450
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Hdac6 protein / Histone Deacetylase 6


Mass: 39812.051 Da / Num. of mol.: 2 / Fragment: catalytic domain 2 (UNP residues 289-646)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Danio rerio (zebrafish) / Gene: hdac6 / Production host: Escherichia coli (E. coli) / References: UniProt: A7YT55
#2: Chemical ChemComp-A1BHY / N-hydroxy-4-({(methanesulfonyl)[(pyridin-3-yl)methyl]amino}methyl)benzamide


Mass: 335.378 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C15H17N3O4S / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#4: Chemical
ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: K
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 783 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.1 Å3/Da / Density % sol: 41.33 %
Crystal growTemperature: 277 K / Method: vapor diffusion / Details: 25% PEG 400, 0.2M MgCl2, 0.1M Na Caco. 5.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.9792 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Oct 6, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 1.26→66.61 Å / Num. obs: 172572 / % possible obs: 95.7 % / Redundancy: 6.4 % / CC1/2: 0.999 / Rmerge(I) obs: 0.097 / Net I/σ(I): 8.7
Reflection shellResolution: 1.26→1.348 Å / Num. unique obs: 6051 / CC1/2: 0.283

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Processing

Software
NameVersionClassification
PHENIX1.20_4459refinement
xia2data scaling
PHENIXphasing
xia2data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.26→66.61 Å / Cross valid method: THROUGHOUT
RfactorNum. reflection% reflection
Rwork0.1881 --
obs-172473 95.39 %
Refinement stepCycle: LAST / Resolution: 1.26→66.61 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5532 0 52 783 6367

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