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

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Basic information

Entry
Database: PDB / ID: 9ggh
TitleCrystal structure of Danio rerio histone deacetylase 6 catalytic domain 2 (CD2) in complex with N-((6-(Hydroxyamino)-6-oxohexyl)oxy)-4-(4-(pyrrolidin-1-yl)phenyl)thiazole-2-carboxamide
ComponentsHistone deacetylase 6
KeywordsHYDROLASE / Histone deacetylase / zinc enzyme / inhibitor
Function / homology
Function and homology information


Aggrephagy / 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 ...Aggrephagy / 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
: / Histone deacetylase 6
Similarity search - Component
Biological speciesDanio rerio (zebrafish)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.14 Å
AuthorsHebeis, M. / Fischer, F. / Kurz, T. / Span, I.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: J.Med.Chem. / Year: 2024
Title: Deciphering the Therapeutic Potential of Novel Pentyloxyamide-Based Class I, IIb HDAC Inhibitors against Therapy-Resistant Leukemia.
Authors: Fischer, F. / Schliehe-Diecks, J. / Tu, J.W. / Gangnus, T. / Ho, Y.L. / Hebeis, M. / Alves Avelar, L.A. / Scharov, K. / Watrin, T. / Kemkes, M. / Stachura, P. / Daugs, K. / Biermann, L. / ...Authors: Fischer, F. / Schliehe-Diecks, J. / Tu, J.W. / Gangnus, T. / Ho, Y.L. / Hebeis, M. / Alves Avelar, L.A. / Scharov, K. / Watrin, T. / Kemkes, M. / Stachura, P. / Daugs, K. / Biermann, L. / Kremeyer, J. / Horstick, N. / Span, I. / Pandyra, A.A. / Borkhardt, A. / Gohlke, H. / Kassack, M.U. / Burckhardt, B.B. / Bhatia, S. / Kurz, T.
History
DepositionAug 13, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 4, 2024Provider: repository / Type: Initial release
Revision 1.1Dec 11, 2024Group: Database references / Category: citation / citation_author
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_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Dec 25, 2024Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Histone deacetylase 6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,0317
Polymers40,2851
Non-polymers7466
Water52229
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area200 Å2
ΔGint-67 kcal/mol
Surface area13240 Å2
MethodPISA
Unit cell
Length a, b, c (Å)42.711, 87.033, 178.864
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-805-

ZN

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Components

#1: Protein Histone deacetylase 6


Mass: 40285.484 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Danio rerio (zebrafish) / Gene: hdac6 / Production host: Escherichia coli (E. coli) / References: UniProt: F8W4B7
#2: Chemical ChemComp-A1IKY / ~{N}-[6-(oxidanylamino)-6-oxidanylidene-hexoxy]-4-(4-pyrrolidin-1-ylphenyl)-1,3-thiazolidine-2-carboxamide


Mass: 418.510 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H26N4O4S / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Zn
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 29 / 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: 2.06 Å3/Da / Density % sol: 40.38 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop
Details: 0.1 M sodium acetate, 0.1 M sodium formate, 22 % PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: MASSIF-3 / Wavelength: 0.9677 Å
DetectorType: DECTRIS EIGER X 4M / Detector: PIXEL / Date: Jan 31, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9677 Å / Relative weight: 1
ReflectionResolution: 2.14→44.76 Å / Num. obs: 18936 / % possible obs: 99.7 % / Redundancy: 7.5 % / CC1/2: 0.994 / Net I/σ(I): 6.5
Reflection shellResolution: 2.14→2.2 Å / Num. unique obs: 1480 / CC1/2: 0.203

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Processing

Software
NameVersionClassification
autoPROCdata processing
XDSdata reduction
Aimlessdata scaling
PHASERphasing
REFMAC5.5refinement
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.14→44.76 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.929 / SU B: 14.649 / SU ML: 0.171 / Cross valid method: THROUGHOUT / ESU R: 0.295 / ESU R Free: 0.214 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: U VALUES : WITH TLS ADDED HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT U VALUES : RESIDUAL ONLY
RfactorNum. reflection% reflectionSelection details
Rfree0.24722 947 5 %RANDOM
Rwork0.20751 ---
obs0.2094 17948 99.67 %-
Solvent computationIon probe radii: 0.7 Å / Shrinkage radii: 0.7 Å / VDW probe radii: 1.1 Å / Solvent model: MASK
Displacement parametersBiso mean: 41.061 Å2
Baniso -1Baniso -2Baniso -3
1--2.95 Å20 Å2-0 Å2
2---1.8 Å2-0 Å2
3---4.75 Å2
Refinement stepCycle: LAST / Resolution: 2.14→44.76 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2759 0 34 29 2822
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0162868
X-RAY DIFFRACTIONr_bond_other_d0.0010.0162627
X-RAY DIFFRACTIONr_angle_refined_deg1.011.793891
X-RAY DIFFRACTIONr_angle_other_deg0.3931.5566050
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.9715.28375
X-RAY DIFFRACTIONr_dihedral_angle_2_deg6.91416.258
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.78910455
X-RAY DIFFRACTIONr_chiral_restr0.0460.2420
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.023405
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02675
X-RAY DIFFRACTIONr_mcbond_it0.271.7381416
X-RAY DIFFRACTIONr_mcbond_other0.271.7381416
X-RAY DIFFRACTIONr_mcangle_it0.493.1261767
X-RAY DIFFRACTIONr_mcangle_other0.493.1261768
X-RAY DIFFRACTIONr_scbond_it0.2431.7961452
X-RAY DIFFRACTIONr_scbond_other0.2431.7961453
X-RAY DIFFRACTIONr_scangle_other0.4373.2852124
X-RAY DIFFRACTIONr_long_range_B_refined2.39416.783156
X-RAY DIFFRACTIONr_long_range_B_other2.39216.773155
LS refinement shellResolution: 2.14→2.193 Å
RfactorNum. reflection% reflection
Rfree0.396 62 -
Rwork0.394 1256 -
obs--97.49 %
Refinement TLS params.Method: refined / Origin x: -5.236 Å / Origin y: -13.38 Å / Origin z: 19.933 Å
111213212223313233
T0.2754 Å20.0052 Å20.0084 Å2-0.3114 Å20.0154 Å2--0.007 Å2
L1.4102 °20.2449 °20.0671 °2-1.7287 °20.1523 °2--0.9724 °2
S0.0449 Å °-0.0793 Å °-0.0806 Å °-0.0163 Å °-0.0265 Å °-0.0649 Å °0.003 Å °0.0093 Å °-0.0183 Å °

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