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

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Basic information

Entry
Database: PDB / ID: 9efr
TitleCrystal structure of Danio rerio histone deacetylase 6 catalytic domain 2 complexed with TO-600
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


negative regulation of cellular component organization / positive regulation of cellular component organization / regulation of biological quality / tubulin deacetylase activity / mitochondrion localization / swimming behavior / definitive hemopoiesis / regulation of microtubule-based process / protein lysine deacetylase activity / potassium ion binding ...negative regulation of cellular component organization / positive regulation of cellular component organization / regulation of biological quality / tubulin deacetylase activity / mitochondrion localization / swimming behavior / definitive hemopoiesis / regulation of microtubule-based process / protein lysine deacetylase activity / potassium ion binding / response to stress / hematopoietic progenitor cell differentiation / transferase activity / actin binding / chromatin organization / angiogenesis / perikaryon / axon / dendrite / centrosome / zinc ion binding / nucleus / cytoplasm
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: 1.24 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)80,50311
Polymers79,4502
Non-polymers1,0539
Water14,196788
1
A: Hdac6 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,2325
Polymers39,7251
Non-polymers5074
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Hdac6 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,2716
Polymers39,7251
Non-polymers5465
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)75.140, 92.600, 96.490
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: 39724.973 Da / Num. of mol.: 2 / Fragment: catalytic domain 2 (UNP residues 290-646)
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-A1BHX / N-hydroxy-4-({(propane-2-sulfonyl)[(pyridin-3-yl)methyl]amino}methyl)benzamide


Mass: 363.431 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C17H21N3O4S / 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.: 5 / Source method: obtained synthetically / Formula: K
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 788 / 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: 2.11 Å3/Da / Density % sol: 41.78 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / Details: 15% PEG 3350, 0.2M magnesium formate dihydrate

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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: Dec 20, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 1.24→59.28 Å / Num. obs: 157108 / % possible obs: 82.6 % / Redundancy: 6.2 % / CC1/2: 0.999 / Rmerge(I) obs: 0.055 / Rpim(I) all: 0.023 / Rrim(I) all: 0.06 / Net I/σ(I): 14.2
Reflection shellResolution: 1.24→1.26 Å / Redundancy: 3.3 % / Rmerge(I) obs: 1.453 / Num. unique obs: 2656 / CC1/2: 0.308 / Rpim(I) all: 0.909 / Rrim(I) all: 1.725

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Processing

Software
NameVersionClassification
PHENIX1.20_4459refinement
xia2data scaling
xia2data reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.24→59.28 Å / Cross valid method: THROUGHOUT
RfactorNum. reflection% reflection
Rwork0.1984 --
obs-157037 82.47 %
Refinement stepCycle: LAST / Resolution: 1.24→59.28 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5546 0 57 788 6391

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