Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

Standalone Viewers  
Protein Workshop | Ligand Explorer

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Biological Assembly 2  

 3D View: Structure | Electron Density | Ligand Interaction

Standalone Viewers  
Protein Workshop | Ligand Explorer

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A 

Biological assembly 2 assigned by authors.

Macromolecule Content

• Total Structure Weight: 85301.68 
• Atom Count: 5759 
• Residue Count: 760 
• Unique protein chains: 1

6HSK

Crystal structure of a human HDAC8 L6 loop mutant complexed with Quisinostat

• DOI: 10.2210/pdb6HSK/pdb

• Classification: HYDROLASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli


• Deposited: 2018-10-01 Released: 2018-10-31 
• Deposition Author(s): Marek, M., Shaik, T.B., Ramos-Morales, E., Romier, C.
• Funding Organization(s): European Commission 

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.096 Å
• R-Value Free: 0.189 
• R-Value Work: 0.152 

Literature

Characterization of Histone Deacetylase 8 (HDAC8) Selective Inhibition Reveals Specific Active Site Structural and Functional Determinants.

Marek, M., Shaik, T.B., Heimburg, T., Chakrabarti, A., Lancelot, J., Ramos-Morales, E., Da Veiga, C., Kalinin, D., Melesina, J., Robaa, D., Schmidtkunz, K., Suzuki, T., Holl, R., Ennifar, E., Pierce, R.J., Jung, M., Sippl, W., Romier, C.

(2018) J. Med. Chem. 61: 10000-10016

• PubMed: 30347148 
• DOI: 10.1021/acs.jmedchem.8b01087
• Primary Citation of Related Structures:  
  6HU3, 6HU2, 6HU1, 6HU0, 6HTZ, 6HTT, 6HTI, 6HTH, 6HTG, 6HT8, 6HSZ, 6HSH, 6HSG, 6HSF, 6HRQ, 6HQY


• PubMed Abstract: 
  

Metal-dependent histone deacetylases (HDACs) are key epigenetic regulators that represent promising therapeutic targets for the treatment of numerous human diseases. Yet the currently FDA-approved HDAC inhibitors nonspecifically target at least several of the 11 structurally similar but functionally different HDAC isozymes, which hampers their broad usage in clinical settings. Selective inhibitors targeting single HDAC isozymes are being developed, but precise understanding in molecular terms of their selectivity remains sparse. Here, we show that HDAC8-selective inhibitors adopt a L-shaped conformation required for their binding to a HDAC8-specific pocket formed by HDAC8 catalytic tyrosine and HDAC8 L1 and L6 loops. In other HDAC isozymes, a L1-L6 lock sterically prevents L-shaped inhibitor binding. Shielding of the HDAC8-specific pocket by protein engineering decreases potency of HDAC8-selective inhibitors and affects catalytic activity. Collectively, our results unravel key HDAC8 active site structural and functional determinants important for the design of next-generation chemical probes and epigenetic drugs.

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Organizational Affiliation: 

Department of Chemistry, Osaka Medical College, Takatsuki, 569-8686 Osaka, Japan; [e-mail].,Department of Chemistry, King's College London, Britannia House, 7 Trinity Street, London SE1 1DB, UK; Structural Biology and Biophysics Unit, Fondazione Ri.MED, Via Bandiera, 11, 90133 Palermo, Italy.,Department of Biochemistry and Biophysics, University of California, San Francisco, CA 94143.,Department of Chemistry, University of Illinois at Urbana-Champaign, Champaign, IL, USA.,Heidelberg University Biochemistry Centre, Heidelberg 69120, Germany. Electronic address: [e-mail].,Division of Structural Biology, University of Oxford, Headington, OX3 7BN Oxford, United Kingdom [e-mail] [e-mail] [e-mail].,Center of Biomedical Analysis, Tsinghua University, 100084, Beijing, China.,Department of Chemical Engineering and Biotechnology, University of Applied Sciences Darmstadt, Germany.,Department of Chemistry, Texas A&M University, College Station, TX 77842; [e-mail].,Centre de Biologie Cellulaire de Montpellier, CNRS, University Montpellier, UMR5237, 34090 Montpellier, France.,Institute of Pharmaceutical Sciences, University of Freiburg, Germany.,Faculty of Chemistry, Biological and Chemical Research Centre, University of Warsaw, Żwirki i Wigury 101, 02-089 Warszawa, Poland. Electronic address: [e-mail].,Protein Structure Laboratory, Del Shankel Structural Biology Center , University of Kansas , 2034 Becker Drive , Lawrence , Kansas 66047 , United States.,Beijing Advanced Innovation Center for Food Nutrition and Human Health, College of Food Science & Nutritional Engineering, China Agricultural University, Key Laboratory of Functional Dairy, Ministry of Education, 100083, Beijing, China. [e-mail].,Nanjing Foreign Language School, 210046 Nanjing, China.,Division of Structural Biology, University of Oxford, Headington, OX3 7BN Oxford, United Kingdom.,NEUROFARBA Dept., Sezione di Scienze Farmaceutiche, Università degli Studi di Firenze, Via Ugo Schiff 6, 50019 Sesto Fiorentino, Florence, Italy.,Department of Biochemistry, College of Science, King Saud University, Riyadh, Saudi Arabia.,Department of Pharmaceutical Sciences, College of Pharmacy , University of Kentucky , 789 South Limestone Street , Lexington , Kentucky 40536 , United States.,Global Biotherapeutics Technologies, Pfizer R&D, Grange Castle Business Park, Dublin D22, Ireland.,Newcastle Cancer Centre, Northern Institute for Cancer Research, Medical School, Newcastle University, Paul O'Gorman Building, Framlington Place, Newcastle upon Tyne NE2 4HH, UK. Electronic address: [e-mail].,Department of Biochemistry, University of Illinois at Urbana-Champaign, Champaign, IL, USA.,Department of Molecular and Cell Biology, University of Connecticut, Storrs, United States.,Institute of Biochemistry and Biophysiscs, Polish Academy of Science, Laboratory of Biological NMR, Pawińskiego 5A, 02-106 Warszawa, Poland. Electronic address: [e-mail].,Department of Pulmonary and Critical Care Medicine, Chang Gung Memorial Hospital, Taoyuan, Taiwan.,State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, 430070 Hubei, China.,Laboratory of Genetics and Plant Breeding, School of Agriculture, Forestry and Natural Environment, Aristotle University of Thessaloniki, Thessaloniki, Greece.,School of Pharmaceutical Sciences , Sun Yat-Sen University , Guangzhou 510006 , P.R. China.,School of Biotechnology and Biomolecular Sciences, the University of New South Wales, Sydney, NSW, 2052, Australia. [e-mail].,Department of Biological Sciences, Mount Holyoke College, 50 College Street, South Hadley, MA 01075, USA.,Department of Biochemistry and Biophysics , Oregon State University , Corvallis , Oregon 97331 , United States.,Amgen Research, Department of Cardiometabolic Disorders, Amgen Inc., One Amgen Center Dr., Thousand Oaks, CA 91320, USA.,School of Biotechnology and Biomolecular Sciences, the University of New South Wales, Sydney, NSW, 2052, Australia.,Instituto de Biociências, Letras e Ciências Exatas , Universidade Estadual Paulista , Rua Cristóvão Colombo , 2265 São José do Rio Preto , Brazil.,Department of Chemistry, Institute of Organic Chemistry , University of Hamburg , Martin-Luther-King-Platz 6 , 20146 Hamburg , Germany.,Department of Chemistry, University of Cambridge, CB2 1EW Cambridge, United Kingdom.,CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences (CAS), Beijing, China. [e-mail].,Department of Chemistry, Universität Konstanz, 78464 Konstanz, Germany; [e-mail].,Department of Biology, Massachusetts Institute of Technology, Cambridge, United States.,Department of Chemistry, King's College London, Britannia House, 7 Trinity Street, London SE1 1DB, UK.,Diagnostics and Therapeutics, Georgia State University, Atlanta, Georgia, 30302-3965.,School of Pharmaceutical Sciences; MOE Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology, Tsinghua University, Beijing, 100084, China.,Drug Design Laboratory, Graduate School of Medical Life Science, Yokohama City University, Tsurumi, Yokohama 230-0045, Japan.,School of Medicine, Chang Gung University, Taoyuan, Taiwan.,CREST , Japan Science and Technology Agency (JST) , 4-1-8 Honcho Kawaguchi , 332-0012 Saitama , Japan.,Department of Developmental Biology, Stanford University School of Medicine, Stanford, CA, 94305, USA.,Department of Chemical Engineering and Biotechnology, University of Applied Sciences Darmstadt, Germany; Bioengineering and Biosystems, Institute of Functional Interfaces, Karlsruhe Institute of Technology, Germany.,Department of Physiology, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, 6525 GA Nijmegen, The Netherlands.,Department of Analytical Biochemistry, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Gronostajowa 7, 30-387 Kraków, Poland. Electronic address: [e-mail].,From the Department of Biochemistry, College of Life Science & Biotechnology, Yonsei University, Seoul 03722, South Korea, [e-mail].,Purdue Institute of Inflammation, Immunology and Infectious Disease, Purdue University, West Lafayette, IN 47907, USA.,Institute of Molecular Enzymology, Soochow University, Suzhou, Jiangsu, 215123, China.,Institute of Pharmacy , Martin-Luther-Universität Halle-Wittenberg , Wolfgang-Langenbeck-Straße 4 , 06120 Halle/Saale , Germany.,Institute of Microbiology, Chinese Academy of Sciences, 100101 Beijing, China.,Institute of Applied Biosciences, Centre for Research and Technology Hellas (CERTH), Thessaloniki, Greece.,Human Immunology Unit, Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Oxford, UK. [e-mail].,Department of Biochemistry, Osaka Medical College, Takatsuki, 569-8686 Osaka, Japan.,CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences (CAS), Beijing, China.,Department of Chemical Engineering and Biotechnology, University of Applied Sciences Darmstadt, Germany. Electronic address: [e-mail].,Department of Chemistry, Osaka Medical College, Takatsuki, 569-8686 Osaka, Japan.,Department of Biomolecular Science and Reaction, Institute of Scientific and Industrial Research, Osaka University, Ibaraki, 567-0047 Osaka, Japan.,Konstanz Research School Chemical Biology, Universität Konstanz, 78464 Konstanz, Germany.,Department of Biology, School of Arts & Sciences, University of Richmond , Richmond, Virginia 23173, United States.,Department of Chemistry and Chemical Biology, Cornell University, NE-CAT, Advanced Photon Source, Argonne, Illinois, USA.,Department of Pathology, NYU School of Medicine, New York, New York, USA.,Beijing Advanced Innovation Center for Food Nutrition and Human Health, College of Food Science & Nutritional Engineering, China Agricultural University, Key Laboratory of Functional Dairy, Ministry of Education, 100083, Beijing, China.,Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, Victoria, Australia.,University of Wyoming School of Pharmacy, 1000 E. University Ave., HS 596, Laramie, WY, 82071, USA.,Division of Biomedical Sciences, School of Medicine , University of California Riverside , 900 University Avenue , Riverside , California 92521 , United States.,Department of Ophthalmology, University of California, San Francisco, CA 94158.,Department of Biochemistry and Molecular Genetics, University of Alabama at Birmingham, Birmingham, Alabama, USA.,Department of Biochemistry and Molecular Pharmacology, NYU School of Medicine, New York, New York, USA [e-mail].,Department of Molecular Biosciences , The University of Texas at Austin , Austin , Texas 78712 , United States.,Picobiology Institute, Graduate School of Life Science, University of Hyogo, 3-2-1 Kouto, Kamigori-cho, Ako-gun, Hyogo 678-1297, Japan.,Department of Chemistry, Georgia State University, Atlanta, Georgia, 30302-3965.,Amgen Research, Department of Cardiometabolic Disorders, Amgen Inc., One Amgen Center Dr., Thousand Oaks, CA 91320, USA. [e-mail].,College of Life Sciences, Nankai University, 300071 Tianjin, China.,Departamento de Química, Centro de Investigación en Síntesis Química, Universidad de La Rioja, La Rioja, Spain.,School of Medicine, Chang Gung University, Taoyuan, Taiwan. [e-mail].,Amgen Research, Department of Pharmacokinetics and Drug Metabolism, Amgen Inc., One Amgen Center Dr., Thousand Oaks, CA 91320, USA.,Department of Biological Chemistry , University of Michigan , Ann Arbor , Michigan 48109 , United States.,Institut de Génétique et Biologie Moléculaire et Cellulaire (IGBMC), Département de Biologie Structurale Intégrative , Université de Strasbourg, Centre National de la Recherche Scientifique (CNRS UMR7104), Institut National de la Santé et de la Recherche Médicale (INSERM U1258) , 1 rue Laurent Fries , 67404 Illkirch Cedex , France.,Molecular Biophysics Unit, Indian Institute of Science , Bangalore, Karnataka 560012, India.,California Institute for Quantitative Biology (QB3), University of California, Berkeley, CA 94720.,Department of Microbiology, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Gronostajowa 7, 30-387 Kraków, Poland; Małopolska Centre of Biotechnology, Jagiellonian University, Gronostajowa 7a, 30-387 Kraków, Poland. Electronic address: [e-mail].,Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, VA, 22908, USA.,Institute of Pharmaceutical Sciences , Albert-Ludwigs-Universität Freiburg , Albertstraße 25 , 79104 Freiburg , Germany.,National Leading Research Laboratory of Drug Resistance Proteomics, Department of Biological Sciences, Myongji University, 116 Myongjiro, Yongin, Gyeonggido 17058, Republic of Korea. Electronic address: [e-mail].,Chapman University School of Pharmacy (CUSP), Harry and Diane Rinker Health Science Campus, Chapman University, Irvine, CA, 92618, USA.,Protein Crystal Analysis Division, Structure Analysis Promotion Group, Japan Synchrotron Radiation Research Institute, Sayo-gun, 679-5198 Hyogo, Japan.,Physics Department, and Biodesign Center for Applied Structural Discovery, Arizona State University, Tempe, Arizona 85287.,National Laboratory of Biomacromolecules, CAS Center for Excellence in Macromoleculers, Institute of Biophysics, Chinese Academy of Sciences, 100101 Beijing, China; University of Chinese Academy of Sciences, 100049 Beijing, China.,Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720; [e-mail] [e-mail].,Department of Chemical and Systems Biology, Stanford University School of Medicine, Stanford, CA, 94305, USA.,School of Biological Sciences, Monash University, Melbourne, Australia.,Department of Engineering Physics, Tsinghua University, Beijing 100086, China.,Unité Dynamique Structurale des Macromolécules, Institut Pasteur, UMR 3528, CNRS, 75015 Paris, France.,Neurimmune AG, Wagistrasse 13, 8952 Schlieren, Switzerland; Institute for Regenerative Medicine, University of Zurich, Wagistrasse 12, 8952 Schlieren, Switzerland.,From the Department of Microbiology and Immunology, School of Biomedical Sciences, University of Otago, Dunedin 9054, New Zealand, [e-mail].,Institute of Molecular Enzymology, Soochow University, Suzhou, Jiangsu, 215123, China. [e-mail].,Clinical and Research Center of Infectious Diseases, The National Clinical Key Department of Infectious Disease, Beijing Ditan Hospital, Capital Medical University, Beijing, China.,From Global Biotherapeutics Technologies, Pfizer R&D, Cambridge, Massachusetts 02140 and [e-mail].,Expression Génétique Microbienne , UMR 8261, CNRS, Université Paris, Institut de Biologie Physico-Chimique , 13 rue Pierre et Marie Curie , 75005 Paris , France.,Department of Biochemistry, Brandeis University, Waltham, United States.,Advanced Photon Technology Division, RIKEN SPring-8 Center, Sayo-gun, 679-5148 Hyogo, Japan.,From Global Biotherapeutics Technologies, Pfizer R&D, Cambridge, Massachusetts 02140 and.,Department of Medicine, University of Massachusetts Medical School, Worcester, Massachusetts, USA.,State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei Collaborative Innovation Center for Green Transformation of Bio-resources, Environmental Microbial Technology Center of Hubei Province, Hubei Key Laboratory of Industrial Biotechnology, College of Life Sciences, Hubei University, Wuhan, 430062, China.,Department of Biochemistry, College of Natural and Agricultural Sciences , University of California Riverside , 900 University Avenue , Riverside , California 92521 , United States.,Department of Chemistry and Biochemistry, Center for Biomolecular Structure and Organization, University of Maryland, College Park, MD, 20742, USA. [e-mail].,Department of Chemistry , Louisiana State University , 229A Choppin Hall , Baton Rouge , Louisiana 70803 , United States.,Amgen Research, Comparative Biology and Safety Sciences, Amgen Inc., 360 Binney St., Cambridge, MA 02141, USA.,Department of Chemistry, Texas A&M University, College Station, TX 77842.,Department of Chemistry, Stanford University, Stanford, CA, 94305-5080, USA.,From the Department of Biochemistry, College of Life Science & Biotechnology, Yonsei University, Seoul 03722, South Korea.,From the Department of Microbiology and Immunology, School of Biomedical Sciences, University of Otago, Dunedin 9054, New Zealand.,Biotechnology and Drug Design, Georgia State University, Atlanta, Georgia, 30302-3965.,Division of Microbiology and Immunology, Department of Pathology, University of Utah School of Medicine, Salt Lake City, United States.,College of Veterinary Medicine, China Agricultural University, Beijing, China.,Heidelberg University Biochemistry Centre, Heidelberg 69120, Germany.,Division of Pediatric Infectious Diseases, Department of Pediatrics, Chang Gung Memorial Hospital, Taoyuan, Taiwan.,Department of Chemistry , University of Kansas , Multidisciplinary Research Building, 2030 Becker Drive , Lawrence , Kansas 66047 , United States.,NMR Research Center, Indian Institute of Science , Bangalore, Karnataka 560012, India.,Newcastle Cancer Centre, Northern Institute for Cancer Research, Medical School, Newcastle University, Paul O'Gorman Building, Framlington Place, Newcastle upon Tyne NE2 4HH, UK. Electronic address: [e-mail].,National Center for Biotechnology, Astana, 010000, Kazakhstan; Department of Chemistry, School of Science and Technology, Nazarbayev University, Astana, 010000, Kazakhstan.,Department of Analytical Biochemistry, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Gronostajowa 7, 30-387 Kraków, Poland. Electronic address: [e-mail].,Griffith Institute for Drug Discovery, Griffith University, Don Young Road, Nathan, Brisbane, Queensland 4111, Australia.,Beijing Advanced Innovation Center for Food Nutrition and Human Health, State Key Laboratory of Agrobiotechnology, China Agricultural University, Beijing 100193, China. Electronic address: [e-mail].,Research School of Chemistry, The Australian National University, Canberra, Australia.,CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences (CAS), Beijing, China. [e-mail].,Department of Medicinal Chemistry and Molecular Pharmacology, College of Pharmacy, Purdue University, West Lafayette, IN 47907, USA.,Newcastle Cancer Centre, Northern Institute for Cancer Research, Medical School, Newcastle University, Paul O'Gorman Building, Framlington Place, Newcastle upon Tyne NE2 4HH, UK.,Industrial Enzymes National Engineering Laboratory, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China.,Center for translational Immunology, Chinese Academy of Medical Science Oxford Institute, Nuffield Department of Medicine, Oxford University, Oxford, UK.,Genomics Research Center, Academia Sinica, Taipei, Taiwan.,Laboratory of Enzyme Technology, Department of Biotechnology, School of Food, Biotechnology and Development, Agricultural University of Athens, Athens, Greece.,Howard Hughes Medical Institute, Massachusetts Institute of Technology, Cambridge, United States.,National Laboratory of Macromolecules, Institute of Biophysics, Chinese Academy of Science, 100101 Beijing, China.,Institute of Pharmaceutical Chemistry, University Frankfurt, Germany.,School of Food Science and Technology, National Engineering Research Center of Seafood, Dalian Polytechnic University, 116034, Dalian, China. [e-mail].,School of Life and Environmental Sciences, Deakin University, Melbourne, Victoria, Australia.,Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720.,School of Life Sciences, University of Science and Technology of China, Anhui, 230026, China.,Department of Microbiology and Immunology, University of Michigan Medical School, 5641 Medical Science Building II, 1150 West Medical Center Drive, Ann Arbor, MI 48109-0620, USA.,Centre for Translational and Chemical Biology, School of Biological Sciences, University of Edinburgh, Michael Swann Building, Max Born Crescent, Edinburgh EH9 3BF, U.K.,Ministry of Education Key Laboratory of Protein Science, School of Medicine, Tsinghua University, 100084 Beijing, China; [e-mail] [e-mail] [e-mail].,Amgen Research, Department of Therapeutic Discovery, Amgen Inc., 7990 Enterprise Street, Burnaby, BC V5A 1V7, Canada.,Beijing Key Laboratory of Emerging Infectious Diseases, Beijing, China.,Department of Biochemistry, University of Illinois at Urbana-Champaign, Champaign, IL, USA. [e-mail].,Beijing Advanced Innovation Center for Food Nutrition and Human Health, State Key Laboratory of Agrobiotechnology, China Agricultural University, Beijing 100193, China.,Tsinghua University Affiliated High School, 100084 Beijing, China.,CNRS, Inserm, CHU Lille, Institut Pasteur de Lille, U1019-UMR 8204-CIIL-Centre d'Infection et d'Immunité de Lille , Université de Lille , F-59000 Lille , France.,Howard Hughes Medical Institute, Oregon Health & Science University, Portland, Oregon, United States of America.,Dipartimento di Chimica , Polo Scientifico e Tecnologico , Universita' degli Studi di Firenze , Via della Lastruccia 3, 13, I-50019 Sesto Fiorentino , Firenze , Italy.,Department of Molecular Membrane Biology, Max Planck Institute of Biophysics, 60438 Frankfurt am Main, Germany.,Department of Chemistry, Massachusetts Institute of Technology, Cambridge, United States.,Amgen Research, Department of Cardiometabolic Disorders, Amgen Inc., 1120 Veterans Blvd., South San Francisco, CA 94080, USA.,Biogen, 225 Binney Street, Cambridge, MA 02142, USA. Electronic address: [e-mail].,Department of Cardiovascular Surgery, Min-Sheng General Hospital, Taoyuan, Taiwan.,Institute of Pharmaceutical and Medicinal Chemistry , University of Münster , Corrensstraße 48 , 48149 Münster , Germany.,Department of Biochemistry , Duke University , Durham , North Carolina 27710 , United States.,Architecture et Réactivité de l'ARN, Institut de Biologie Moléculaire et Cellulaire (IBMC), UPR 9004 du CNRS , Université de Strasbourg , 15 Rue René Descartes , 67084 Strasbourg Cedex , France.,Division of Biological and Environmental Sciences and Engineering, King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Saudi Arabia. Electronic address: [e-mail].,Photon Science, SLAC National Accelerator Laboratory, Menlo Park, CA, 94025-7015, USA.,Griffith Institute for Drug Discovery, Griffith University, Don Young Road, Nathan, Brisbane, Queensland 4111, Australia. Electronic address: [e-mail].,School of Life Sciences, Tsinghua University, 100084 Beijing, China.,Centre for Translational and Chemical Biology, School of Biological Sciences, University of Edinburgh, Michael Swann Building, Max Born Crescent, Edinburgh EH9 3BF, U.K. [e-mail].,The Commonwealth Scientific and Industrial Research Organisation, Land and Water Flagship, Canberra, Australian Capital Territory, Australia, and [e-mail].,Division of Hematology, The Children's Hospital of Philadelphia , Philadelphia, Pennsylvania 19104, United States.,Aix Marseille Univ, CNRS, Laboratoire de Bioénergétique et Ingénierie des Protéines, Marseille, France.,Beijing Advanced Innovation Center for Structural Biology, MOE Key Laboratory for Protein Science, Tsinghua-Peking Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing, 100084, China. [e-mail].,Howard Hughes Medical Institute, University of California, Berkeley, CA 94720.,The Ohio State University College of Medicine, 473 W 12th Ave, Columbus, OH, 43210, USA.,Howard Hughes Medical Institute, University of California, San Francisco, CA 94143.,Ministry of Education Key Laboratory of Protein Science, School of Medicine, Tsinghua University, 100084 Beijing, China.,Department of Chemistry and Biochemistry , University of Berne , Freiestrasse 3 , 3012 Berne , Switzerland . Email: [e-mail].,Department of Structural Biology, Stanford University School of Medicine, Stanford, CA, 94305, USA.,Maurice Wilkins Centre for Molecular Biodiscovery, The University of Auckland, Private Bag 92019, Auckland 1042, New Zealand.,Division of Infectious Diseases, Department of Medicine, Chang Gung Memorial Hospital, Taoyuan, Taiwan.,IMCA-CAT , Hauptman Woodward Medical Research Institute , 9700 South Cass Avenue, Building 435A , Argonne , Illinois 60439 , United States.,Sorbonne Universités, Université Pierre et Marie Curie, 75006 Paris, France.,Bioengineering and Biosystems, Institute of Functional Interfaces, Karlsruhe Institute of Technology, Germany.,Centre de Recherches sur les Macromolécules Végétales , UPR5301 , CNRS and Université Grenoble Alpes , 601 rue de la Chimie , F38041 Grenoble , France.,Department of Biological Sciences, Markey Center for Structural Biology, Purdue University, West Lafayette, IN 47907, USA.,Department of Biology, School of Science and Technology, Nazarbayev University, Astana, 010000, Kazakhstan.,Department of Chemistry, Universität Konstanz, 78464 Konstanz, Germany.,Complex Systems Division, Beijing Computational Science Research Center, 10 East Xibeiwang Road, Haidian District, Beijing 100193, China, [e-mail].,Beijing Advanced Innovation Center for Structural Biology, MOE Key Laboratory for Protein Science, Tsinghua-Peking Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing, 100084, China.,Department of Biology, Universität Konstanz, 78464 Konstanz, Germany.,Turku Centre for Biotechnology, University of Turku and Åbo Akademi University, Turku, Finland.,National Center for Biotechnology, Astana, 010000, Kazakhstan.,The Commonwealth Scientific and Industrial Research Organisation, Land and Water Flagship, Canberra, Australian Capital Territory, Australia, and.,Department of Molecular Membrane Biology, Max Planck Institute of Biophysics, 60438 Frankfurt am Main, Germany. Electronic address: [e-mail].,Amgen Research, Department of Therapeutic Discovery, Amgen Inc., 1120 Veterans Blvd., South San Francisco, CA 94080, USA.,Department of Chemistry, School of Science and Technology, Nazarbayev University, Astana, 010000, Kazakhstan. Electronic address: [e-mail].,Institute of Biological Chemistry, Academia Sinica, Taipei, 11529, Taiwan.,Center for Influenza Research and Early-Warning, Chinese Academy of Sciences, Beijing, China. [e-mail].,Global Biotherapeutics Technologies, Pfizer R&D, Grange Castle Business Park, Dublin D22, Ireland [e-mail].,Vollum Institute, Oregon Health & Science University, Portland, Oregon, United States of America.,Human Immunology Unit, Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Oxford, UK.,Bio-inspired Solar Energy Program, Canadian Institute for Advanced Research, Toronto, Canada.,Department of Microbiology, Immunology and Tropical Medicine and Research Center for Neglected Diseases of Poverty, School of Medicine and Health Sciences, George Washington University , Washington D.C. 20037, United States.,Department of Chemistry , The University of Texas at Austin , Austin , Texas 78712 , United States.,Graduate School of Medical Science , Kyoto Prefectural University of Medicine , 1-5 Shimogamohangi-Cho, Sakyo-Ku , 606-0823 Kyoto , Japan.,Department of Biochemistry and Molecular Pharmacology, NYU School of Medicine, New York, New York, USA.,Departamento de Bioquímica e Imunologia, Instituto de Ciências Biológicas , Universidade Federal de Minas Gerais , Av. Antônio Carlos , 6627 Belo Horizonte , Brazil.,School of Biology, Centers for Georgia State University, Atlanta, Georgia, 30302-3965.,Department of Biochemistry, University of Illinois at Urbana-Champaign, Champaign, IL, USA. [e-mail].,Center for Influenza Research and Early-Warning, Chinese Academy of Sciences, Beijing, China. [e-mail].,Center for Biophysics and Computational Biology, University of Illinois at Urbana-Champaign, Champaign, IL, USA. [e-mail].,Research School of Chemistry, The Australian National University, Canberra, Australia, [e-mail].,Department of Chemistry, School of Science and Technology, Nazarbayev University, Astana, 010000, Kazakhstan.,CSIRO, 343 Royal Parade, Parkville, Melbourne, Victoria 3052, Australia.,Department of Chemistry and Biochemistry , Utah State University , Logan , Utah 84322 , United States.,Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720; [e-mail] [e-mail].,Department of Biochemistry and Biophysics, University of California, San Francisco, CA 94143; [e-mail] [e-mail] [e-mail].,Unité Récepteurs-canaux, Institut Pasteur, UMR 3571, CNRS, 75015 Paris, France.,Howard Hughes Medical Institute, University of Illinois at Urbana-Champaign, Champaign, IL, USA. [e-mail].,Department of Physiology, University of California, San Francisco, CA 94143 [e-mail] [e-mail] [e-mail].,Unité Dynamique Structurale des Macromolécules, Institut Pasteur, UMR 3528, CNRS, 75015 Paris, France; [e-mail].,National Leading Research Laboratory of Drug Resistance Proteomics, Department of Biological Sciences, Myongji University, 116 Myongjiro, Yongin, Gyeonggido 17058, Republic of Korea.,The Pirbright Institute, Pirbright, Woking, UK.,Centre for Biodiscovery and Molecular Development of Therapeutics, Australian Institute of Tropical Health and Medicine, James Cook University , Cairns 4870, Queensland Australia.,Amgen Research, Department of Therapeutic Discovery, Amgen Inc., One Amgen Center Dr., Thousand Oaks, CA 91320, USA.,Shenzhen Key Laboratory of Pathogen and Immunity, Shenzhen Third People's Hospital, Shenzhen, China. [e-mail].,Department of Chemical and Systems Biology, Stanford University School of Medicine, Stanford, CA, 94305, USA. [e-mail].,Department of Cell and Molecular Biology, Uppsala University, Biomedical Center, PO Box 596, SE-751 24 Uppsala, Sweden.,Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, CA 94158.,Departamento de Microbiología, Facultad de Salud , Universidad del Valle , Calle 4B No. 36-00 Cali , Colombia.,Center for translational Immunology, Chinese Academy of Medical Science Oxford Institute, Nuffield Department of Medicine, Oxford University, Oxford, UK. [e-mail].,Biogen, 225 Binney Street, Cambridge, MA 02142, USA.,Department of Chemistry and Biochemistry, Knoebel Institute for Healthy Aging , University of Denver , Denver , Colorado 80208 , United States.,Institute of Infectious Diseases, Beijing Ditan Hospital, Capital Medical University, Beijing, China.,Department of Chemistry, King's College London, Britannia House, 7 Trinity Street, London SE1 1DB, UK. Electronic address: [e-mail].,Hubei Colorectal Cancer Clinical Research Center, Hubei Cancer Hospital, 430071 Wuhan, China.,Pediatric Dentistry and Microbiology, University of Alabama at Birmingham, Birmingham, Alabama, USA.,National Laboratory of Biomacromolecules, CAS Center for Excellence in Macromoleculers, Institute of Biophysics, Chinese Academy of Sciences, 100101 Beijing, China.,Department of Chemistry and Biochemistry, Center for Biomolecular Structure and Organization, University of Maryland, College Park, MD, 20742, USA.,Cell Signalling Unit, p53 Signal Transduction Laboratories, Institute of Genetics and Molecular Medicine, University of Edinburgh Cancer Research Centre, Edinburgh EH4 2XR, U.K.,Department of Chemistry, University of Illinois at Urbana-Champaign, Champaign, IL, USA. [e-mail].,Drug Discovery Center for Infectious Disease, College of Pharmacy, Nankai University, 300071 Tianjin, China.,Biogen, 225 Binney Street, Cambridge, MA 02142, USA; Neurimmune AG, Wagistrasse 13, 8952 Schlieren, Switzerland. Electronic address: [e-mail].,Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, United States.,Complex Systems Division, Beijing Computational Science Research Center, 10 East Xibeiwang Road, Haidian District, Beijing 100193, China.,Centre for Biomolecular Spectroscopy and Randall Division of Cell and Molecular Biophysics, King's College London, New Hunt's House, Guy's Campus, London SE1 1UL, UK.,Shenzhen Key Laboratory of Pathogen and Immunity, Shenzhen Third People's Hospital, Shenzhen, China. [e-mail].,Department of Molecular Membrane Biology, Max Planck Institute of Biophysics, 60438 Frankfurt am Main, Germany; National Laboratory of Biomacromolecules, CAS Center for Excellence in Macromoleculers, Institute of Biophysics, Chinese Academy of Sciences, 100101 Beijing, China; Hisun Pharmaceutical (Hangzhou) Co. Ltd, 311404 Hangzhou, China; Institute of Oceanology, Chinese Academy of Sciences, 266071 Qingdao, China. Electronic address: [e-mail].,Laboratoire de Chimie des Processus Biologiques, CNRS-UMR 8229, Collège De France , Université Pierre et Marie Curie , 11 place Marcelin Berthelot , 75231 Paris Cedex 05 , France.,State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, 430070 Hubei, China; [e-mail] [e-mail] [e-mail].,Institute of Biosciences and Technology, Texas A&M Health Science Center, Houston, TX 77030.,National Laboratory of Biomacromolecules, CAS Center for Excellence in Macromoleculers, Institute of Biophysics, Chinese Academy of Sciences, 100101 Beijing, China; School of Medicine, Tsinghua University, 100084 Beijing, China.,Departamento de Microbiologia, Instituto de Ciências Biomédicas , Universidade de São Paulo , Avenida Prof. Lineu Prestes , 1374 São Paulo , Brazil.,Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720.,Department of Systems Biology and Division of Life Sciences, Yonsei University, Seoul 03722, South Korea.,Department of Biochemistry and Molecular Genetics, University of Alabama at Birmingham, Birmingham, Alabama, USA [e-mail].,Department of Microbiology and Immunology, University of Rochester School of Medicine and Dentistry, Rochester, NY 14642, USA.,Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, California 94025, and.,Laboratoire de Biochimie Théorique, CNRS UPR9080 , Institut de Biologie Physico-Chimique , 13 rue Pierre et Marie Curie , 75005 Paris , France.,Neurimmune AG, Wagistrasse 13, 8952 Schlieren, Switzerland.,Division of Pediatric Infectious Diseases, Department of Pediatrics, Chang Gung Memorial Hospital, Taoyuan, Taiwan. [e-mail].

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
Histone deacetylase 8	A, B	380	Homo sapiens	Mutation(s): 0  Gene Names: HDAC8 (HDACL1) EC: 3.5.1.98
Find proteins for Q9BY41 (Homo sapiens) Go to Gene View: HDAC8 Go to UniProtKB:  Q9BY41

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram & Interactions
K	A, B	POTASSIUM ION K NPYPAHLBTDXSSS-UHFFFAOYSA-N
ZN	A, B	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
GOK	A, B	2-[4-[[(1-methylindol-3-yl)methylamino]methyl]piperidin-1-yl]-~{N}-oxidanyl-pyrimidine-5-carboxamide C21 H26 N6 O2 PAWIYAYFNXQGAP-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.096 Å
• R-Value Free: 0.189 
• R-Value Work: 0.152 
• Space Group: P 3₂

Unit Cell:

Length (Å)	Angle (°)
a = 106.390	α = 90.00
b = 106.390	β = 90.00
c = 82.030	γ = 120.00

Software Package:

Software Name	Purpose
PHENIX	refinement
PHENIX	phasing
XDS	data reduction
XDS	data scaling

Structure Validation

Entry History & Funding Information

Deposition Data

• Deposited Date: 2018-10-01 
• Released Date: 2018-10-31 
• Deposition Author(s): Marek, M., Shaik, T.B., Ramos-Morales, E., Romier, C.

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Funding Organization	Location	Grant Number
European Commission	France	241865
European Commission	France	602080

Revision History 

• Version 1.0: 2018-10-31
  Type: Initial release
• Version 1.1: 2018-11-07
  Type: Data collection, Database references
• Version 1.2: 2018-11-14
  Type: Data collection, Structure summary
• Version 1.3: 2018-11-28
  Type: Data collection, Database references