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- PDB-8cj7: HDAC6 selective degraded (difluoromethyl)-1,3,4-oxadiazole substr... -

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Basic information

Entry
Database: PDB / ID: 8cj7
TitleHDAC6 selective degraded (difluoromethyl)-1,3,4-oxadiazole substrate inhibitor
ComponentsHistone deacetylase 6
KeywordsHYDROLASE / inhibitor / small molecule hydrazide / HDAC6 / oxadiazole / histone
Function / homology
Function and homology information


Aggrephagy / tubulin deacetylase activity / swimming behavior / definitive hemopoiesis / protein lysine deacetylase activity / regulation of tubulin deacetylation / histone deacetylase activity / potassium ion binding / histone deacetylase complex / hematopoietic progenitor cell differentiation ...Aggrephagy / tubulin deacetylase activity / swimming behavior / definitive hemopoiesis / protein lysine deacetylase activity / regulation of tubulin deacetylation / histone deacetylase activity / potassium ion binding / histone deacetylase complex / hematopoietic progenitor cell differentiation / angiogenesis / negative regulation of transcription by RNA polymerase II / 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
IODIDE ION / : / Chem-UTO / Histone deacetylase 6
Similarity search - Component
Biological speciesDanio rerio (zebrafish)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.51 Å
AuthorsSandmark, J. / Ek, M. / Ripa, L.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: J.Med.Chem. / Year: 2023
Title: Selective and Bioavailable HDAC6 2-(Difluoromethyl)-1,3,4-oxadiazole Substrate Inhibitors and Modeling of Their Bioactivation Mechanism.
Authors: Ripa, L. / Sandmark, J. / Hughes, G. / Shamovsky, I. / Gunnarsson, A. / Johansson, J. / Llinas, A. / Collins, M. / Jung, B. / Noven, A. / Pemberton, N. / Mogemark, M. / Xiong, Y. / Li, Q. / ...Authors: Ripa, L. / Sandmark, J. / Hughes, G. / Shamovsky, I. / Gunnarsson, A. / Johansson, J. / Llinas, A. / Collins, M. / Jung, B. / Noven, A. / Pemberton, N. / Mogemark, M. / Xiong, Y. / Li, Q. / Tangefjord, S. / Ek, M. / Astrand, A.
History
DepositionFeb 12, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 18, 2023Provider: repository / Type: Initial release
Revision 1.1Nov 1, 2023Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Histone deacetylase 6
B: Histone deacetylase 6
C: Histone deacetylase 6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)122,64120
Polymers120,8563
Non-polymers1,78517
Water11,422634
1
A: Histone deacetylase 6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,2339
Polymers40,2851
Non-polymers9488
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Histone deacetylase 6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,8526
Polymers40,2851
Non-polymers5675
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Histone deacetylase 6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,5565
Polymers40,2851
Non-polymers2714
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)95.977, 84.062, 96.132
Angle α, β, γ (deg.)90.00, 110.25, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 3 molecules ABC

#1: Protein Histone deacetylase 6


Mass: 40285.484 Da / Num. of mol.: 3
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

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Non-polymers , 5 types, 651 molecules

#2: Chemical
ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: K
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Zn
#4: Chemical ChemComp-UTO / 6-[(5-pyridin-2-yl-1,2$l^{4},3,4-tetrazacyclopenta-1,3-dien-2-yl)methyl]pyridine-3-carbohydrazide


Mass: 296.287 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C13H12N8O / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical
ChemComp-IOD / IODIDE ION


Mass: 126.904 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: I
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 634 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 3.01 Å3/Da / Density % sol: 59.14 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 20% PEG3350, 0.2 M NaI, 0.1 M Bis-Tris-Propane pH 7.5,10% ethylene glycol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.97624 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jan 25, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97624 Å / Relative weight: 1
ReflectionResolution: 1.52→90.2 Å / Num. obs: 116637 / % possible obs: 89.7 % / Redundancy: 3.3 % / CC1/2: 0.995 / Net I/σ(I): 7.4
Reflection shellResolution: 1.52→1.72 Å / Num. unique obs: 5831 / CC1/2: 0.604

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Processing

Software
NameClassification
BUSTERrefinement
Aimlessdata scaling
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.51→90.19 Å / Cor.coef. Fo:Fc: 0.91 / Cor.coef. Fo:Fc free: 0.901 / SU R Cruickshank DPI: 0.129 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.131 / SU Rfree Blow DPI: 0.119 / SU Rfree Cruickshank DPI: 0.118
RfactorNum. reflection% reflectionSelection details
Rfree0.227 5598 4.8 %RANDOM
Rwork0.206 ---
obs0.207 116662 51.8 %-
Displacement parametersBiso mean: 26.36 Å2
Baniso -1Baniso -2Baniso -3
1-0.1185 Å20 Å24.148 Å2
2---2.3218 Å20 Å2
3---2.2033 Å2
Refine analyzeLuzzati coordinate error obs: 0.27 Å
Refinement stepCycle: 1 / Resolution: 1.51→90.19 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8272 0 59 634 8965
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.018618HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.9911705HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d2935SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes1493HARMONIC5
X-RAY DIFFRACTIONt_it8618HARMONIC20
X-RAY DIFFRACTIONt_nbd0SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion3.56
X-RAY DIFFRACTIONt_other_torsion15.78
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion1107SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact10699SEMIHARMONIC4
LS refinement shellResolution: 1.51→1.64 Å / Total num. of bins used: 50
RfactorNum. reflection% reflection
Rfree0.2331 123 5.27 %
Rwork0.2137 2211 -
all0.2148 2334 -
obs--4.77 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.49170.10880.02911.543-0.03110.6693-0.02680.003-0.0077-0.09850.0343-0.0661-0.01510.001-0.0075-0.15320.00680.0861-0.16540.0018-0.09874.4042-17.28520.4102
20.60980.097-0.19981.5470.110.6799-0.03230.0158-0.0293-0.1470.0034-0.03280.0427-0.01720.0289-0.01760.00890.076-0.19660.0024-0.1777-20.2413-7.041242.5683
32.0860.3442-0.25313.79410.40230.6835-0.10120.0318-0.04230.10970.0291.0142-0.0102-0.06470.0722-0.346-0.00080.106-0.30050.05060.4266-43.63225.9483-0.5812
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{ A|* }
2X-RAY DIFFRACTION2{ B|* }
3X-RAY DIFFRACTION3{ C|* }

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