Entry | Database: PDB / ID: 8g45 |
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Title | Structure of HDAC6 zinc-finger ubiquitin binding domain in complex with SGC-UBD253 chemical probe |
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Components | Histone deacetylase 6 |
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Keywords | HYDROLASE/INHIBITOR / Inhibitor / chemical probe / HDAC6 / histone deacetylase / HYDROLASE / Structural Genomics / Structural Genomics Consortium / SGC / HYDROLASE-INHIBITOR complex |
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Function / homology | Function and homology information
negative regulation of hydrogen peroxide metabolic process / cellular response to topologically incorrect protein / polyubiquitinated misfolded protein transport / positive regulation of cellular response to oxidative stress / erythrocyte enucleation / negative regulation of aggrephagy / positive regulation of cholangiocyte proliferation / response to misfolded protein / negative regulation of oxidoreductase activity / regulation of microtubule-based movement ...negative regulation of hydrogen peroxide metabolic process / cellular response to topologically incorrect protein / polyubiquitinated misfolded protein transport / positive regulation of cellular response to oxidative stress / erythrocyte enucleation / negative regulation of aggrephagy / positive regulation of cholangiocyte proliferation / response to misfolded protein / negative regulation of oxidoreductase activity / regulation of microtubule-based movement / parkin-mediated stimulation of mitophagy in response to mitochondrial depolarization / negative regulation of protein-containing complex disassembly / protein-containing complex disassembly / negative regulation of axon extension involved in axon guidance / regulation of establishment of protein localization / positive regulation of tubulin deacetylation / tubulin deacetylation / Cilium Assembly / regulation of autophagy of mitochondrion / peptidyl-lysine deacetylation / tubulin deacetylase activity / collateral sprouting / Transcriptional regulation by RUNX2 / lysosome localization / negative regulation of protein acetylation / misfolded protein binding / negative regulation of microtubule depolymerization / ubiquitin-dependent protein catabolic process via the multivesicular body sorting pathway / protein deacetylation / cilium disassembly / response to growth factor / dendritic spine morphogenesis / histone deacetylase / aggresome assembly / regulation of androgen receptor signaling pathway / protein lysine deacetylase activity / positive regulation of signaling receptor activity / cellular response to misfolded protein / aggresome / cellular response to parathyroid hormone stimulus / positive regulation of dendrite morphogenesis / Hydrolases; Acting on carbon-nitrogen bonds, other than peptide bonds; In linear amides / regulation of fat cell differentiation / microtubule associated complex / negative regulation of gene expression, epigenetic / histone deacetylase activity / response to corticosterone / dynein complex binding / axonal transport of mitochondrion / Notch-HLH transcription pathway / positive regulation of epithelial cell migration / beta-tubulin binding / cell leading edge / response to dexamethasone / protein quality control for misfolded or incompletely synthesized proteins / RUNX2 regulates osteoblast differentiation / histone deacetylase complex / response to immobilization stress / alpha-tubulin binding / cilium assembly / HSF1 activation / polyubiquitin modification-dependent protein binding / regulation of macroautophagy / negative regulation of protein-containing complex assembly / inclusion body / axon cytoplasm / response to amphetamine / multivesicular body / positive regulation of synaptic transmission, glutamatergic / transcription corepressor binding / ciliary basal body / ubiquitin binding / regulation of autophagy / caveola / negative regulation of proteolysis / actin filament organization / Late endosomal microautophagy / intracellular protein transport / Hsp90 protein binding / protein destabilization / regulation of protein stability / tau protein binding / NOTCH1 Intracellular Domain Regulates Transcription / beta-catenin binding / Constitutive Signaling by NOTCH1 PEST Domain Mutants / Constitutive Signaling by NOTCH1 HD+PEST Domain Mutants / autophagy / histone deacetylase binding / Aggrephagy / Chaperone Mediated Autophagy / cellular response to hydrogen peroxide / protein polyubiquitination / positive regulation of peptidyl-serine phosphorylation / actin binding / cellular response to heat / microtubule binding / perikaryon / microtubule / RNA polymerase II cis-regulatory region sequence-specific DNA binding / axonSimilarity 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-typeSimilarity search - Domain/homology |
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Biological species | Homo sapiens (human) |
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Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.62 Å |
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Authors | Harding, R.J. / Franzoni, I. / Mann, M.K. / Szewczyk, M. / Mirabi, B. / Owens, D.D.G. / Ackloo, S. / Scheremetjew, A. / Juarez-Ornelas, K.A. / Sanichar, R. ...Harding, R.J. / Franzoni, I. / Mann, M.K. / Szewczyk, M. / Mirabi, B. / Owens, D.D.G. / Ackloo, S. / Scheremetjew, A. / Juarez-Ornelas, K.A. / Sanichar, R. / Baker, R.J. / Dank, C. / Brown, P.J. / Barsyte-Lovejoy, D. / Santhakumar, V. / Schapira, M. / Lautens, M. / Arrowsmith, C.H. / Structural Genomics Consortium (SGC) |
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Funding support | 1items Organization | Grant number | Country |
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Other government | | |
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Citation | Journal: J.Med.Chem. / Year: 2023 Title: Discovery and Characterization of a Chemical Probe Targeting the Zinc-Finger Ubiquitin-Binding Domain of HDAC6. Authors: Harding, R.J. / Franzoni, I. / Mann, M.K. / Szewczyk, M.M. / Mirabi, B. / Ferreira de Freitas, R. / Owens, D.D.G. / Ackloo, S. / Scheremetjew, A. / Juarez-Ornelas, K.A. / Sanichar, R. / ...Authors: Harding, R.J. / Franzoni, I. / Mann, M.K. / Szewczyk, M.M. / Mirabi, B. / Ferreira de Freitas, R. / Owens, D.D.G. / Ackloo, S. / Scheremetjew, A. / Juarez-Ornelas, K.A. / Sanichar, R. / Baker, R.J. / Dank, C. / Brown, P.J. / Barsyte-Lovejoy, D. / Santhakumar, V. / Schapira, M. / Lautens, M. / Arrowsmith, C.H. |
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History | Deposition | Feb 8, 2023 | Deposition site: RCSB / Processing site: RCSB |
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Revision 1.0 | May 3, 2023 | Provider: repository / Type: Initial release |
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Revision 1.1 | Aug 9, 2023 | Group: 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_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year |
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Revision 1.2 | Aug 16, 2023 | Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / citation Item: _citation.journal_volume / _citation.page_first / _citation.page_last |
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