6G8M

Yeast 20S proteasome in complex with Cystargolide B Derivative 1


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.7 Å
  • R-Value Free: 0.214 
  • R-Value Work: 0.179 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

Design, synthesis, and evaluation of cystargolide-based beta-lactones as potent proteasome inhibitors.

Niroula, D.Hallada, L.P.Le Chapelain, C.Ganegamage, S.K.Dotson, D.Rogelj, S.Groll, M.Tello-Aburto, R.

(2018) Eur J Med Chem 157: 962-977

  • DOI: 10.1016/j.ejmech.2018.08.052
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The peptidic β-lactone proteasome inhibitors (PIs) cystargolides A and B were used to conduct structure-activity relationship (SAR) studies in order to assess their anticancer potential. A total of 24 different analogs were designed, synthesized and ...

    The peptidic β-lactone proteasome inhibitors (PIs) cystargolides A and B were used to conduct structure-activity relationship (SAR) studies in order to assess their anticancer potential. A total of 24 different analogs were designed, synthesized and evaluated for proteasome inhibition, for cytotoxicity towards several cancer cell lines, and for their ability to enter intact cells. X-ray crystallographic analysis and subunit selectivity was used to determine the specific subunit binding associated with the structural modification of the β-lactone (P 1 ), peptidic core, (P x and P y ), and end-cap (P z ) of our scaffold. The cystargolide derivative 5k, structurally unique at both P y and P 1 , exhibited the most promising inhibitory activity for the β5 subunit of human proteasomes (IC 50  = 3.1 nM) and significant cytotoxicity towards MCF-7 (IC 50  = 416 nM), MDA-MB-231 (IC 50  = 74 nM) and RPMI 8226 (IC 50  = 41 nM) cancer cell lines. Cellular infiltration assays revealed that minor structural modifications have significant effects on the ability of our PIs to inhibit intracellular proteasomes, and we identified 5k as a promising candidate for continued therapeutic studies. Our novel drug lead 5k is a more potent proteasome inhibitor than carfilzomib with mid-to-low nanomolar IC 50 measurements and it is cytotoxic against multiple cancer cell lines at levels approaching those of carfilzomib.


    Organizational Affiliation

    Griffith Institute for Drug Discovery, Griffith University, Nathan, Queensland, Australia.,College of Veterinary Medicine, Northwest A&F University, Yangling 712100, Shanxi, China.,Department of Chemistry, Boston University, Boston, MA 02215, USA.,Department of Bioengineering, James H. Clark Center, Stanford University, Stanford, CA 94305; shannon-au@cuhk.edu.hk wahc@stanford.edu.,Center for Computational and Integrative Biology, Massachusetts General Hospital, Boston, United States.,State Key Laboratory of Membrane Biology, Institute of Molecular Medicine, Peking University, Beijing Key Laboratory of Cardiometabolic Molecular Medicine, Beijing 100871, China; Peking-Tsinghua Center for Life Sciences, Peking University, Beijing 100871, China; Academy for Advanced Interdisciplinary Studies, Peking University, Beijing 100871, China.,Department of Genetics, Harvard Medical School, Boston, United States.,Centre for BioImaging Sciences, National University of Singapore, Singapore 117557.,Department of Chemistry , Massachusetts Institute of Technology , Cambridge , Massachusetts 02139 , United States.,Department of Chemistry and Biochemistry, Utah State University, Logan, Utah 84322.,Takeda California, 10410 Science Center Drive, San Diego, CA, 92121, USA.,Institut für Biophysik, Johann Wolfgang von Goethe-Universität, Max-von-Laue-Str. 1, 60438, Frankfurt, Germany.,Center for Biomolecular Structure and Dynamics, University of Montana, Missoula, MT 59812.,Centre for Microbial Diseases and Immunity Research, University of British Columbia, 2259 Lower Mall Research Station, Vancouver, BC, V6T 1Z4, Canada.,Gene Center and Center for Integrated Protein Science Munich, Department of Biochemistry, University of Munich, Munich, Germany. beckmann@genzentrum.lmu.de.,School of Chemistry and Biomedical Sciences Research Complex, University of St Andrews, Fife, Scotland, United Kingdom.,Department of Molecular Genetics, University of Toronto, Toronto, Ontario M5S 1A8, Canada.,Department of Medical Genetics, University of Cambridge and Cambridge NIHR Biomedical Research Centre, Cambridge, UK.,Sorbonne Université, CNRS, Laboratoire de Réactivité de Surface (LRS), UPMC Univ Paris 06, UMR 7197, Paris, F-75005, France.,HIV Dynamics and Replication Program, National Cancer Institute, National Institutes of Health, Frederick, Maryland, USA.,Howard Hughes Medical Institute, University of California, Los Angeles, Los Angeles, CA, USA; Department of Biological Chemistry, University of California, Los Angeles, Los Angeles, CA, USA.,Simons Electron Microscopy Center, New York Structural Biology Center, New York, NY, USA.,Laboratory of Medicinal Chemistry, Center for Interdisciplinary Research on Medicines (CIRM) , ULiège , Quartier Hôpital, Avenue Hippocrate, 15, B36 , B-4000 Liège , Belgium.,School of Life Science and Technology, Tokyo Institute of Technology, 2-12-1 Ookayama, Meguro, Tokyo 152-8550, Japan. Electronic address: akitao@bio.titech.ac.jp.,Department of Chemistry and Biochemistry, University of Bern, 3012 Bern, Switzerland; Graduate School for Cellular and Biomedical Sciences, University of Bern, 3012 Bern, Switzerland.,Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore 637551.,Department of Biochemistry, University of Toronto, Toronto, Ontario M5S 1A8, Canada.,Center for Structural Genomics of Infectious Diseases, Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA e-filippova@northwestern.edu wf-anderson@northwestern.edu.,Department of Chemistry, Boston University, Boston, MA 02215, USA; Center for Biomedical Mass Spectrometry, Boston University School of Medicine, Boston, MA 02118, USA.,Department of Molecular Biosciences, University of Texas at Austin, Austin, TX 78712, USA.,School of Life Sciences, GIST, 123 Cheomdan-gwagiro, Buk-gu, Gwangju 61005, Republic of Korea.,Crop Science, Bayer AG, 40789 Monheim, Germany.,Departments of Molecular and Cellular Physiology and Structural Biology, Stanford University School of Medicine, Stanford, CA, USA. kcgarcia@stanford.edu.,School of Life Sciences, Faculty of Science, The Chinese University of Hong Kong, Shatin, Hong Kong.,Biozentrum, University of Basel, Basel, Switzerland.,Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, Ontario M5G 1X5, Canada.,Department of Biology, Institute of Molecular Biology and Biophysics, ETH Zürich, 8093 Zürich, Switzerland. Electronic address: allain@mol.biol.ethz.ch.,Laboratory of Molecular Biophysics, National Heart, Lung, and Blood Institute, NIH, Bethesda, MD, USA.,the Division of Hematology, Children's Hospital of Philadelphia, and the Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104.,School of Life Sciences, Faculty of Science, The Chinese University of Hong Kong, Shatin, Hong Kong; shannon-au@cuhk.edu.hk wahc@stanford.edu.,Department of Chemistry, Boston University, Boston, MA 02215, USA. Electronic address: pinghua@bu.edu.,Institute for Molecular Bioscience, The University of Queensland, St. Lucia, Queensland, Australia.,Key Laboratory of Animal Immunology of the Ministry of Agriculture, Henan Provincial Key Laboratory of Animal Immunology, Henan Academy of Agricultural Sciences, Zhengzhou 450002, Henan, China.,Department of Biochemistry and Molecular Genetics, Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA.,Center for Integrated Protein Science at the Department Chemie, Technische Universitat München, Lichtenbergstraße 4, 85748 Garching, Germany.,State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, Shanghai 200438, People's Republic of China.,Department of Molecular Biology and Biotechnology, The University of Sheffield, Firth Court, Western Bank, Sheffield, S10 2TN, UK.,Department of Pediatrics, Hadassah Hebrew University Medical Center, Jerusalem, Israel.,Institute of Structural Biology, Nanyang Technological University, Singapore 639798.,Institute of Structural and Molecular Biology, Department of Biological Sciences, Birkbeck, University of London, London, UK. c.moores@mail.cryst.bbk.ac.uk.,Centro de Análises Proteômicas e Bioquímicas, Pós-Graduação em Ciências Genômicas e Biotecnologia Universidade Católica de Brasília, Brasília, 70790-160, DF, Brazil.,the Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724.,Department of Bioengineering, Rice University, 6100 Main St., Houston, TX 77005, USA. Electronic address: jsuh@rice.edu.,GE Healthcare Life Sciences, Beijing 100176, China.,State Key Laboratory of Membrane Biology, Institute of Molecular Medicine, Peking University, Beijing Key Laboratory of Cardiometabolic Molecular Medicine, Beijing 100871, China.,Department of Bone Marrow Transplantation and Cancer Immunotherapy, Hadassah Hebrew University Medical Center, Jerusalem, Israel.,Department of Microbiology and Immunology, Loyola University Chicago, Health Sciences Division, Stritch School of Medicine, Maywood, Illinois, USA.,Department of Biological Chemistry, University of Michigan Medical School, 1150 W. Medical Center Drive, SPC 5606, Ann Arbor, MI 48109, USA.,Service of Infectious Diseases, University Hospital Geneva, Geneva, Switzerland thilo.kohler@unige.ch.,Pohang Accelerator Laboratory, Pohang, Gyeongbuk 37673, Republic of Korea.,Ubiquitin Signalling Division, The Walter and Eliza Hall Institute of Medical Research, Parkville Melbourne, VIC, Australia.,Biological Science Imaging facility (BSIR), Department of Biology, 89 Chieftan Way, Florida State University, Tallahassee, FL 32306, USA.,Department of Chemistry and Biochemistry, Howard Hughes Medical Institute, David Geffen School of Medicine, Departments of Biological Chemistry and Physiology, and UCLA-DOE Institute, University of California, Los Angeles, California 90095, United States.,S-Inova Biotech, Pós-graduação em Biotecnologia, Universidade Católica Dom Bosco, Campo Grande, 79117-010, MS, Brazil. ocfranco@gmail.com.,Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, CA, USA. kcgarcia@stanford.edu.,Department of Macromolecular Science, Graduate School of Science, Osaka University, 1-1 Machikaneyama-cho, Toyonaka, Osaka 560-0043, Japan. Electronic address: kimada@chem.sci.osaka-u.ac.jp.,School of Biological Sciences and Technology, Chonnam National University, Gwangju 61186, Republic of Korea.,Department of Macromolecular Science, Graduate School of Science, Osaka University, 1-1 Machikaneyama-cho, Toyonaka, Osaka 560-0043, Japan.,Service of Infectious Diseases, University Hospital Geneva, Geneva, Switzerland.,Biosciences Division, SLAC National Accelerator Laboratory, Stanford University, Menlo Park, CA 94025.,Laboratory of Drug Design and Medicinal Chemistry, Showa Pharmaceutical University, 3-3165 Higashi-Tamagawagakuen, Machida, Tokyo 194-8543, Japan.,Department of Biological Sciences, Virginia Tech, Derring Hall, Blacksburg, VA 24061, U.S.A.,Department of Structural & Chemical Biology, Centro de Investigaciones Biológicas, CIB-CSIC 28040 Madrid, Spain. Electronic address: earias@cib.csic.es.,Medical Research Council Laboratory of Molecular Biology, Cambridge, UK damgaard@mrc-lmb.cam.ac.uk dkomander@wehi.edu.au berkun@hadassah.org.il.,Molecular Pathology Post-graduate Program, University of Brasília, Brasília, 70.910-900, DF, Brazil. ocfranco@gmail.com.,Graduate School of Frontier Biosciences, Osaka University, 1-3 Yamadaoka, Suita, Osaka 565-0871, Japan; RIKEN Center for Biosystems Dynamics Research & SPring-8 Center, 1-3 Yamadaoka, Suita, Osaka 565-0871, Japan.,Laboratório de RMN, Instituto de Química, Universidade Federal de Goiás, Goiânia, 74690-900, GO, Brazil.,Jacobs University, Bremen, Germany.,New Drug Development Center, Daegu-Gyeongbuk Medical Innovation Foundation, Daegu 41061, Republic of Korea.,Laboratory of Molecular Pharmacology, GIGA-Molecular Biology of Diseases , ULiège , B34, Quartier Hôpital, Avenue de l'hôpital, 11 , B-4000 Liège , Belgium.,Department of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA; Howard Hughes Medical Institute, California Institute of Technology, Pasadena, CA, USA.,Howard Hughes Medical Institute, University of California, Los Angeles, Los Angeles, CA, USA; Department of Biological Chemistry, University of California, Los Angeles, Los Angeles, CA, USA; Department of Physiology, University of California, Los Angeles, Los Angeles, CA, USA. Electronic address: tgonen@ucla.edu.,School of Life Sciences, Sun Yat-Sen University, 510275 Guangzhou, China.,Department of Biochemistry and Molecular Biology, University of Florida, 1200 Newell Drive, Gainesville, FL 32610, USA.,Centro de Análises Proteômicas e Bioquímicas, Pós-Graduação em Ciências Genômicas e Biotecnologia Universidade Católica de Brasília, Brasília, 70790-160, DF, Brazil. ocfranco@gmail.com.,School of Life Sciences, GIST, 123 Cheomdan-gwagiro, Buk-gu, Gwangju 61005, Republic of Korea; Advanced Photonics Research Institute, GIST, 123 Cheomdan-gwagiro, Buk-gu, Gwangju 61005, Republic of Korea.,Department of Biochemistry, Virginia Tech, Engel Hall, Blacksburg, VA 24061, U.S.A.,Department of Chemistry and Biochemistry, University of Bern, 3012 Bern, Switzerland.,School of Biological and Chemical Sciences, Queen Mary University of London, Mile End Road, London E1 4NS, UK.,Institut für Biologie, Strukturbiologie/Biochemie, Humboldt-Universität zu Berlin, Unter den Linden 6, 10099, Berlin, Germany.,Hebrew University Hadassah Medical School, Jerusalem, Israel.,Synthetic Biology Group, MIT Synthetic Biology Center; The Center for Microbiome Informatics and Therapeutics; Research Laboratory of Electronics, Department of Biological Engineering, and Department of Electrical Engineering and Computer Science, Massachusetts Institute of Technology, Cambridge, 02139, MA, USA.,Institute for Molecular Bioscience, The University of Queensland, St. Lucia, Queensland, Australia roisin.mcmahon@griffith.edu.au pmireland@dstl.gov.uk jlm@griffith.edu.au.,Institute of Molecular Medicine, University of Texas Health Science Center at Houston, 6767 Bertner Avenue, Houston, TX 77225, USA.,Broad Institute of MIT and Harvard, Cambridge, 02139, MA, USA. cfuente@mit.edu.,Marshall Centre for Infectious Disease Research and Training, School of Pathology and Laboratory Medicine, University of Western Australia, Perth, Western Australia, Australia.,Institute of Biological Chemistry, Washington State University, Pullman, Washington 99163.,Agricultural Solutions, BASF, Morrisville, NC 27560; Jelena.zaitseva@agro.basf-se.com.,Department of Biology, Institute of Molecular Biology and Biophysics, ETH Zürich, 8093 Zürich, Switzerland; Monash Biomedicine Discovery Institute, Department of Biochemistry and Molecular Biology, Monash University, Clayton, 3800 VIC, Australia. Electronic address: fionna.loughlin@monash.edu.,Institute of Structural and Molecular Biology, Department of Biological Sciences, Birkbeck, University of London, London, UK. s.manka@mail.cryst.bbk.ac.uk.,Institute of Molecular and Cell Biology, Agency for Science, Technology and Research, Singapore 138673.,Department of Immunology and Microbiology, Scripps Research, La Jolla, California, USA.,College of Veterinary Medicine, Jilin University, Changchun 130062, Jilin, China; Key Laboratory of Animal Immunology of the Ministry of Agriculture, Henan Provincial Key Laboratory of Animal Immunology, Henan Academy of Agricultural Sciences, Zhengzhou 450002, Henan, China; College of Veterinary Medicine, Northwest A&F University, Yangling 712100, Shanxi, China; College of Animal Science and Veterinary Medicine, Henan Agricultural University, Zhengzhou 450002, Henan, China; Jiangsu Co-innovation Center for the Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou 225009, Jiangsu, China. Electronic address: zhanggaiping2003@163.com.,Department of Biochemistry and Center of Excellence in Protein and Enzyme Technology, Faculty of Science, Mahidol University, Bangkok, Thailand.,Department of Chemistry, University of Manitoba, 44 Dysart Rd, R3T 2N2, Winnipeg, MB, Canada.,Defence Science and Technology Laboratory, Chemical, Biological and Radiological Division, Porton Down, Salisbury, Wiltshire, United Kingdom roisin.mcmahon@griffith.edu.au pmireland@dstl.gov.uk jlm@griffith.edu.au.,Keck Biophysics Facility, Northwestern University, Evanston, Illinois, USA.,College of Chemistry, Fuzhou University, Fuzhou 350116, Fujian, China.,Division of Pharmaceutics, College of Pharmacy, The University of Texas at Austin, Austin, TX, USA.,Graduate School of Frontier Biosciences, Osaka University, 1-3 Yamadaoka, Suita, Osaka 565-0871, Japan.,Department of Molecular Biology, Howard Hughes Medical Institute, Massachusetts General Hospital, Boston, United States.,Department of Biological Sciences, Virginia Tech, Derring Hall, Blacksburg, VA 24061, U.S.A. bscharf@vt.edu fschubot@vt.edu.,Broad Institute of MIT and Harvard, Cambridge, 02139, MA, USA.,Department of Biology, Institute of Molecular Biology and Biophysics, ETH Zürich, 8093 Zürich, Switzerland.,Department of Biological Chemistry, University of Michigan Medical School, 1150 W. Medical Center Drive, SPC 5606, Ann Arbor, MI 48109, USA; Program in Cellular and Molecular Biology, University of Michigan, Ann Arbor, MI 48109, USA. Electronic address: uhnsoo@med.umich.edu.,Department of Chemical and Biomolecular Engineering, Rice University, 6100 Main Street, Houston, TX 77005, USA.,School of Biological Sciences, Nanyang Technological University, Singapore 637551; ygao@ntu.edu.sg yangliang@ntu.edu.sg rero@ntu.edu.sg.,Agricultural Solutions, BASF, Morrisville, NC 27560.,Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Institut für Biochemie (CC2), Charitéplatz 1, D-10117 Berlin, Germany.,Institute of Molecular Life Sciences, University of Zurich, 8057 Zurich, Switzerland.,Institut für Chemie, Technische Universität Berlin, Müller-Breslau-Str. 10, 10623, Berlin, Germany.,HIV Dynamics and Replication Program, National Cancer Institute, National Institutes of Health, Frederick, Maryland, USA hughesst@mail.nih.gov.,Center for Advanced Biotechnology and Medicine, Rutgers University, Piscataway, New Jersey, USA.,Department of Chemistry, New Mexico Institute of Mining and Technology, Socorro, NM 87801, USA; Department of Biology, New Mexico Institute of Mining and Technology, Socorro, NM 87801, USA.,CryoEM and Bioimaging Division, Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Stanford University, Menlo Park, CA 94025.,Pacific Northwest National Laboratory, Richland, Washington 99352, and.,Department of Bioengineering, Rice University, 6100 Main St., Houston, TX 77005, USA.,Biostructural Research, Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences , University of Copenhagen , Universitetsparken 2 , DK-2100 Copenhagen , Denmark.,Department of Pharmaceutics, Faculty of Pharmacy, Minia University, Minia, Egypt.,Department of Chemical Engineering, University of Texas at Austin, Austin, TX 78712, USA.,Graduate School of Frontier Biosciences, Osaka University, 1-3 Yamadaoka, Suita, Osaka 565-0871, Japan. Electronic address: tohru@fbs.osaka-u.ac.jp.,Department of Biological Chemistry, University of Michigan Medical School, 1150 W. Medical Center Drive, SPC 5606, Ann Arbor, MI 48109, USA; Program in Cellular and Molecular Biology, University of Michigan, Ann Arbor, MI 48109, USA.,Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA.,State Key Laboratory of Membrane Biology, Institute of Molecular Medicine, Peking University, Beijing Key Laboratory of Cardiometabolic Molecular Medicine, Beijing 100871, China; Peking-Tsinghua Center for Life Sciences, Peking University, Beijing 100871, China.,Porto Reports, Brasília, 72236-011, DF, Brazil.,Institute of Biochemistry II, Goethe University, Frankfurt am Main 60590, Germany.,Hebrew University Hadassah Medical School, Jerusalem, Israel damgaard@mrc-lmb.cam.ac.uk dkomander@wehi.edu.au berkun@hadassah.org.il.,Defence Science and Technology Laboratory, Chemical, Biological and Radiological Division, Porton Down, Salisbury, Wiltshire, United Kingdom.,Novartis Institutes for BioMedical Research, Novartis Campus, 4002, Basel, Switzerland.,The Warren and Katharine Schlinger Laboratory of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California 91125, United States.,Department of Chemistry, New Mexico Institute of Mining and Technology, Socorro, NM 87801, USA. Electronic address: rodolfo.tello-aburto@nmt.edu.,Department of Microbiology and Molecular Medicine, University of Geneva, Geneva, Switzerland.,Gene Center and Center for Integrated Protein Science Munich, Department of Biochemistry, University of Munich, Munich, Germany.,Department of Medical Biology, The University of Melbourne, Melbourne VIC, Australia.,Centro de Ciências Naturais e Humanas, Universidade Federal do ABC, Santo André, São Paulo, 09210-580, Brazil.,State Key Laboratory of Membrane Biology, Institute of Molecular Medicine, Peking University, Beijing Key Laboratory of Cardiometabolic Molecular Medicine, Beijing 100871, China; Peking-Tsinghua Center for Life Sciences, Peking University, Beijing 100871, China. Electronic address: chenlei2016@pku.edu.cn.,S-Inova Biotech, Pós-graduação em Biotecnologia, Universidade Católica Dom Bosco, Campo Grande, 79117-010, MS, Brazil.,Complex Carbohydrate Research Center, University of Georgia, Athens, GA, USA.,Department of Chemistry, Chonnam National University, Gwangju 61186, Republic of Korea.,Monique and Jacques Roboh Department of Genetic Research, Hadassah Hebrew University Medical Center, Jerusalem, Israel.,Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA. Electronic address: jmberger@jhmi.edu.,Pacific Northwest National Laboratory, Richland, Washington 99352, and lance.seefeldt@usu.edu.,Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, MI 48109, USA.,Global Discovery Chemistry, Novartis Institutes for BioMedical Research, Novartis Campus, 4002, Basel, Switzerland.,Crop Science, Bayer US, Durham, NC 27703.,Department of Bioengineering, James H. Clark Center, Stanford University, Stanford, CA 94305.,Department of Immunology and Microbiology, Scripps Research, La Jolla, California, USA erica@scripps.edu.,Department of Molecular Biology and Biotechnology, The University of Sheffield, Firth Court, Western Bank, Sheffield, S10 2TN, UK. Electronic address: d.kelly@sheffield.ac.uk.,Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Institut für Medizinische Physik und Biophysik (CC2), Group Protein X-ray Crystallography and Signal Transduction, Charitéplatz 1, D-10117 Berlin, Germany. Electronic address: patrick.scheerer@charite.de.,Laboratory of Cell and Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, NIH, Bethesda, MD, USA. jennyh@niddk.nih.gov.,Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, CA, USA.,Department of Pathology, School of Medicine, Stanford University, Palo Alto, CA, USA.,Pharmaceutical Research Division, Takeda Pharmaceutical Company Limited, 26-1, Muraoka-higashi 2-chome, Fujisawa, Kanagawa, 251-8555, Japan.,Laboratory of Drug Design and Medicinal Chemistry, Showa Pharmaceutical University, 3-3165 Higashi-Tamagawagakuen, Machida, Tokyo 194-8543, Japan. Electronic address: titoh@ac.shoyaku.ac.jp.,Stanford Blood Center, Palo Alto, CA, USA.,From the School of Life and Environmental Sciences, University of Sydney New South Wales 2006, Australia, joel.mackay@sydney.edu.au.,NAmur MEdicine & Drug Innovation Center (NAMEDIC), NARILIS, UNamur , rue de Bruxelles 61 , B-5000 Namur , Belgium.,From the Department of Chemistry and Biochemistry, Montana State University, Bozeman, Montana 59717, jw.peters@wsu.edu.,Institute of Chemical Biology and Drug Discovery and Department of Chemistry, Stony Brook University, Stony Brook, NY 11794-3400, USA.,Division of Chemical Biology and Medicinal Chemistry, College of Pharmacy, The University of Texas at Austin, Austin, TX, USA.,Biosyntia ApS, Copenhagen, 2100, Denmark.,Sorbonne Université, CNRS, Institut de Biologie Paris-Seine (IBPS), Biogenèse des Signaux Peptidiques (BIOSIPE), UPMC Univ Paris 06, Paris, F-75005, France.,Gene Center and Center for Integrated Protein Science Munich, Department of Biochemistry, University of Munich, Munich, Germany. becker@genzentrum.lmu.de.,Molecular Pathology Post-graduate Program, University of Brasília, Brasília, 70.910-900, DF, Brazil.,Medical Research Council Laboratory of Molecular Biology, Cambridge, UK.,Gene Center and Center for Integrated Protein Science Munich, Department of Biochemistry, University of Munich, Munich, Germany. beatrix@genzentrum.lmu.de.,College of Veterinary Medicine, Jilin University, Changchun 130062, Jilin, China; Key Laboratory of Animal Immunology of the Ministry of Agriculture, Henan Provincial Key Laboratory of Animal Immunology, Henan Academy of Agricultural Sciences, Zhengzhou 450002, Henan, China.,Present address: Hospira Zagreb d.o.o., a Pfizer company, Prudnicka cesta 60, 10291, Prigorje Brdovecko, Croatia.,Institute for Molecular Engineering and Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, IL, USA.,From the School of Life and Environmental Sciences, University of Sydney New South Wales 2006, Australia.,Faculty of Science, Health, Education and Engineering, University of the Sunshine Coast, Sippy Downs, Queensland, Australia.,Laboratory of Cell and Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, NIH, Bethesda, MD, USA.,Department of Chemistry, New Mexico Institute of Mining and Technology, Socorro, NM 87801, USA.,School of Life Sciences, GIST, 123 Cheomdan-gwagiro, Buk-gu, Gwangju 61005, Republic of Korea. Electronic address: misunjin@gist.ac.kr.,Division of Biophysics, Department of Biology, University of Osnabruck, Osnabruck, Germany.,the Department of Biochemistry, University of Otago, Dunedin 9016, New Zealand, and.,Rega Institute for Medical Research and Department of Microbiology and Immunology, Leuven, Belgium.,Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, CA 94158.,Department of Biochemistry , Brandeis University , Waltham , Massachusetts 02454 , United States.,Skaggs Institute for Chemical Biology, Scripps Research, La Jolla, California, USA.,School of Biological Sciences, Nanyang Technological University, Singapore 637551.,Institute for Cell and Molecular Biosciences, Medical School, Newcastle University, Newcastle upon Tyne NE2 4HH, UK.,Donnelly Centre for Cellular and Biomolecular Research, Banting and Best Department of Medical Research, University of Toronto, M5S 3E1 Toronto, Ontario, Canada.,Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Institut für Medizinische Physik und Biophysik (CC2), Group Protein X-ray Crystallography and Signal Transduction, Charitéplatz 1, D-10117 Berlin, Germany.,Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Institut für Biochemie (CC2), Charitéplatz 1, D-10117 Berlin, Germany. Electronic address: hartmut.kuhn@charite.de.,National Synchrotron Light Source II, Brookhaven National Laboratory, Upton, New York, USA.,Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, New Jersey, USA.,Department of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA.,Synthetic Biology Group, MIT Synthetic Biology Center; The Center for Microbiome Informatics and Therapeutics; Research Laboratory of Electronics, Department of Biological Engineering, and Department of Electrical Engineering and Computer Science, Massachusetts Institute of Technology, Cambridge, 02139, MA, USA. cfuente@mit.edu.,Department of Biology, New Mexico Institute of Mining and Technology, Socorro, NM 87801, USA.,Chemical Biology Laboratory, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, Maryland, USA.,Global and Tropical Health Division, Menzies School of Health Research, Darwin, Northern Territory, Australia.,Department of Molecular Biosciences, University of Texas at Austin, Austin, TX 78712, USA; Institute for Cellular and Molecular Biology, University of Texas at Austin, Austin, TX 78712, USA. Electronic address: jzhang@cm.utexas.edu.,Departments of Molecular and Cellular Physiology and Structural Biology, Stanford University School of Medicine, Stanford, CA, USA.,Nano Life Science Institute (WPI-NanoLSI), Kanazawa University, Kakuma-machi, Kanazawa 920-1192, Japan.,From the Department of Chemistry and Biochemistry, Montana State University, Bozeman, Montana 59717.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Proteasome subunit alpha type-2
A, O
250Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: PRE8 (PRS4)
EC: 3.4.25.1
Find proteins for P23639 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P23639
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Proteasome subunit alpha type-3
B, P
258Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: PRE9 (PRS5)
EC: 3.4.25.1
Find proteins for P23638 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P23638
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Proteasome subunit alpha type-4
C, Q
254Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: PRE6
EC: 3.4.25.1
Find proteins for P40303 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P40303
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
Proteasome subunit alpha type-5
D, R
260Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: PUP2 (DOA5)
EC: 3.4.25.1
Find proteins for P32379 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P32379
Entity ID: 5
MoleculeChainsSequence LengthOrganismDetails
Proteasome subunit alpha type-6
E, S
234Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: PRE5
EC: 3.4.25.1
Find proteins for P40302 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P40302
Entity ID: 6
MoleculeChainsSequence LengthOrganismDetails
Probable proteasome subunit alpha type-7
F, T
288Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: PRE10 (PRC1, PRS1)
EC: 3.4.25.1
Find proteins for P21242 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P21242
Entity ID: 7
MoleculeChainsSequence LengthOrganismDetails
Proteasome subunit alpha type-1
G, U
252Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: SCL1 (PRC2, PRS2)
EC: 3.4.25.1
Find proteins for P21243 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P21243
Entity ID: 8
MoleculeChainsSequence LengthOrganismDetails
Proteasome subunit beta type-2
H, V
232Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: PUP1
EC: 3.4.25.1
Find proteins for P25043 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P25043
Entity ID: 9
MoleculeChainsSequence LengthOrganismDetails
Proteasome subunit beta type-3
I, W
205Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: PUP3
EC: 3.4.25.1
Find proteins for P25451 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P25451
Entity ID: 10
MoleculeChainsSequence LengthOrganismDetails
Proteasome subunit beta type-4
J, X
198Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: PRE1
EC: 3.4.25.1
Find proteins for P22141 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P22141
Entity ID: 11
MoleculeChainsSequence LengthOrganismDetails
Proteasome subunit beta type-5
K, Y
212Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: PRE2 (DOA3, PRG1)
EC: 3.4.25.1
Find proteins for P30656 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P30656
Entity ID: 12
MoleculeChainsSequence LengthOrganismDetails
Proteasome subunit beta type-6
L, Z
222Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: PRE7 (PRS3, PTS1)
EC: 3.4.25.1
Find proteins for P23724 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P23724
Entity ID: 13
MoleculeChainsSequence LengthOrganismDetails
Proteasome subunit beta type-7
M, a
246Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: PRE4
EC: 3.4.25.1
Find proteins for P30657 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P30657
Entity ID: 14
MoleculeChainsSequence LengthOrganismDetails
Proteasome subunit beta type-1
N, b
196Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: PRE3
EC: 3.4.25.1
Find proteins for P38624 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P38624
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
EQE
Query on EQE

Download SDF File 
Download CCD File 
b, H, K, N, V, Y
(2~{S},3~{R})-4-[[(2~{S})-3-methyl-1-[[(2~{S})-3-methyl-1-oxidanylidene-1-phenylmethoxy-butan-2-yl]amino]-1-oxidanylidene-butan-2-yl]amino]-3-oxidanyl-4-oxidanylidene-2-propan-2-yl-butanoic acid
C24 H36 N2 O7
GGTVHVZKPHXGLU-LWYYNNOASA-N
 Ligand Interaction
CL
Query on CL

Download SDF File 
Download CCD File 
G, U
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
MG
Query on MG

Download SDF File 
Download CCD File 
G, I, K, N, V, W, Y, Z
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.7 Å
  • R-Value Free: 0.214 
  • R-Value Work: 0.179 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 136.750α = 90.00
b = 301.020β = 113.64
c = 145.460γ = 90.00
Software Package:
Software NamePurpose
XSCALEdata scaling
REFMACrefinement
REFMACphasing
XDSdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
German Research FoundationGermanySFB1035/A2

Revision History 

  • Version 1.0: 2018-09-12
    Type: Initial release