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Yorodumi- PDB-7js8: STRUCTURE OF HUMAN HDAC2 IN COMPLEX WITH AN ETHYL KETONE INHIBITO... -
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-Basic information
Entry | Database: PDB / ID: 7js8 | ||||||
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Title | STRUCTURE OF HUMAN HDAC2 IN COMPLEX WITH AN ETHYL KETONE INHIBITOR CONTAINING A SPIRO-BICYCLIC GROUP (COMPOUND 22) | ||||||
Components | Histone deacetylase 2 | ||||||
Keywords | HYDROLASE / HISTONE DEACETYLASE / HYDROLASE-HYDROLASE INHIBITOR COMPLEX | ||||||
Function / homology | Function and homology information protein de-2-hydroxyisobutyrylase activity / positive regulation of male mating behavior / negative regulation of peptidyl-lysine acetylation / p75NTR negatively regulates cell cycle via SC1 / epidermal cell differentiation / negative regulation of dendritic spine development / histone decrotonylase activity / fungiform papilla formation / behavioral response to ethanol / negative regulation of MHC class II biosynthetic process ...protein de-2-hydroxyisobutyrylase activity / positive regulation of male mating behavior / negative regulation of peptidyl-lysine acetylation / p75NTR negatively regulates cell cycle via SC1 / epidermal cell differentiation / negative regulation of dendritic spine development / histone decrotonylase activity / fungiform papilla formation / behavioral response to ethanol / negative regulation of MHC class II biosynthetic process / NuRD complex / positive regulation of interleukin-1 production / regulation of cell fate specification / negative regulation of stem cell population maintenance / EGR2 and SOX10-mediated initiation of Schwann cell myelination / negative regulation of transcription by competitive promoter binding / ESC/E(Z) complex / regulation of stem cell differentiation / STAT3 nuclear events downstream of ALK signaling / cellular response to dopamine / histone deacetylase / cardiac muscle hypertrophy / protein lysine deacetylase activity / positive regulation of signaling receptor activity / response to caffeine / Hydrolases; Acting on carbon-nitrogen bonds, other than peptide bonds; In linear amides / histone deacetylase activity / embryonic digit morphogenesis / positive regulation of oligodendrocyte differentiation / positive regulation of stem cell population maintenance / Sin3-type complex / Notch-HLH transcription pathway / dendrite development / eyelid development in camera-type eye / odontogenesis of dentin-containing tooth / positive regulation of proteolysis / RNA Polymerase I Transcription Initiation / response to amyloid-beta / histone deacetylase complex / hair follicle placode formation / Regulation of MECP2 expression and activity / NF-kappaB binding / positive regulation of collagen biosynthetic process / response to hyperoxia / positive regulation of epithelial to mesenchymal transition / FOXO-mediated transcription of oxidative stress, metabolic and neuronal genes / heterochromatin formation / MECP2 regulates neuronal receptors and channels / cellular response to retinoic acid / positive regulation of tyrosine phosphorylation of STAT protein / Regulation of TP53 Activity through Acetylation / cellular response to transforming growth factor beta stimulus / response to amphetamine / heat shock protein binding / SUMOylation of chromatin organization proteins / negative regulation of cell migration / response to cocaine / ERCC6 (CSB) and EHMT2 (G9a) positively regulate rRNA expression / response to nicotine / Regulation of PTEN gene transcription / promoter-specific chromatin binding / HDACs deacetylate histones / negative regulation of transforming growth factor beta receptor signaling pathway / circadian regulation of gene expression / protein modification process / NoRC negatively regulates rRNA expression / negative regulation of DNA-binding transcription factor activity / NOTCH1 Intracellular Domain Regulates Transcription / cellular response to hydrogen peroxide / Constitutive Signaling by NOTCH1 PEST Domain Mutants / Constitutive Signaling by NOTCH1 HD+PEST Domain Mutants / histone deacetylase binding / positive regulation of tumor necrosis factor production / negative regulation of neuron projection development / cellular response to heat / Factors involved in megakaryocyte development and platelet production / histone binding / RNA polymerase II-specific DNA-binding transcription factor binding / Potential therapeutics for SARS / response to lipopolysaccharide / chromosome, telomeric region / chromatin remodeling / response to xenobiotic stimulus / negative regulation of DNA-templated transcription / chromatin binding / positive regulation of cell population proliferation / chromatin / negative regulation of apoptotic process / positive regulation of DNA-templated transcription / negative regulation of transcription by RNA polymerase II / enzyme binding / positive regulation of transcription by RNA polymerase II / protein-containing complex / RNA binding / nucleoplasm / nucleus / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.634 Å | ||||||
Authors | Klein, D.J. / Yu, W. | ||||||
Citation | Journal: J.Med.Chem. / Year: 2021 Title: Discovery of Ethyl Ketone-Based Highly Selective HDACs 1, 2, 3 Inhibitors for HIV Latency Reactivation with Minimum Cellular Potency Serum Shift and Reduced hERG Activity. Authors: Yu, W. / Liu, J. / Clausen, D. / Yu, Y. / Duffy, J.L. / Wang, M. / Xu, S. / Deng, L. / Suzuki, T. / Chung, C.C. / Myers, R.W. / Klein, D.J. / Fells, J.I. / Holloway, M.K. / Wu, J. / Wu, G. / ...Authors: Yu, W. / Liu, J. / Clausen, D. / Yu, Y. / Duffy, J.L. / Wang, M. / Xu, S. / Deng, L. / Suzuki, T. / Chung, C.C. / Myers, R.W. / Klein, D.J. / Fells, J.I. / Holloway, M.K. / Wu, J. / Wu, G. / Howell, B.J. / Barnard, R.J.O. / Kozlowski, J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7js8.cif.gz | 258.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7js8.ent.gz | 215.7 KB | Display | PDB format |
PDBx/mmJSON format | 7js8.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/js/7js8 ftp://data.pdbj.org/pub/pdb/validation_reports/js/7js8 | HTTPS FTP |
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-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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2 |
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3 |
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Unit cell |
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-Components
-Protein , 1 types, 3 molecules ABC
#1: Protein | Mass: 43061.988 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: HDAC2 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q92769, histone deacetylase |
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-Non-polymers , 6 types, 1173 molecules
#2: Chemical | #3: Chemical | ChemComp-SO4 / #4: Chemical | ChemComp-CA / #5: Chemical | ChemComp-PEG / #6: Chemical | #7: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | Y |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.52 Å3/Da / Density % sol: 51.18 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop Details: 25% PEG 3350, 0.2 M ammonium sulfate, 0.1 M Hepes pH 7.5 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 4, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.634→139 Å / Num. obs: 158991 / % possible obs: 99.9 % / Redundancy: 6.6 % / CC1/2: 0.999 / Net I/σ(I): 16.9 |
Reflection shell | Resolution: 1.634→1.639 Å / Num. unique obs: 1553 / CC1/2: 0.758 |
-Processing
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS / Resolution: 1.634→23.6 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.948 / SU R Cruickshank DPI: 0.08 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.086 / SU Rfree Blow DPI: 0.082 / SU Rfree Cruickshank DPI: 0.079
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Displacement parameters | Biso max: 140.01 Å2 / Biso mean: 27.61 Å2 / Biso min: 7.28 Å2
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Refine analyze | Luzzati coordinate error obs: 0.19 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.634→23.6 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.634→1.65 Å / Rfactor Rfree error: 0
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