6E7J

HIV-1 wild type protease with GRL-042-17A, 3-phenylhexahydro-2h-cyclopenta[d]oxazol-2-one with a bicyclic oxazolidinone scaffold as the P2 ligand


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.3 Å
  • R-Value Free: 0.182 
  • R-Value Work: 0.148 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Design and Synthesis of Potent HIV-1 Protease Inhibitors Containing Bicyclic Oxazolidinone Scaffold as the P2 Ligands: Structure-Activity Studies and Biological and X-ray Structural Studies.

Ghosh, A.K.Williams, J.N.Ho, R.Y.Simpson, H.M.Hattori, S.I.Hayashi, H.Agniswamy, J.Wang, Y.F.Weber, I.T.Mitsuya, H.

(2018) J. Med. Chem. 61: 9722-9737

  • DOI: 10.1021/acs.jmedchem.8b01227
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • We have designed, synthesized, and evaluated a new class of potent HIV-1 protease inhibitors with novel bicyclic oxazolidinone derivatives as the P2 ligand. We have developed an enantioselective synthesis of these bicyclic oxazolidinones utilizing a ...

    We have designed, synthesized, and evaluated a new class of potent HIV-1 protease inhibitors with novel bicyclic oxazolidinone derivatives as the P2 ligand. We have developed an enantioselective synthesis of these bicyclic oxazolidinones utilizing a key o-iodoxybenzoic acid mediated cyclization. Several inhibitors displayed good to excellent activity toward HIV-1 protease and significant antiviral activity in MT-4 cells. Compound 4k has shown an enzyme K i of 40 pM and antiviral IC 50 of 31 nM. Inhibitors 4k and 4l were evaluated against a panel of highly resistant multidrug-resistant HIV-1 variants, and their fold-changes in antiviral activity were similar to those observed with darunavir. Additionally, two X-ray crystal structures of the related inhibitors 4a and 4e bound to HIV-1 protease were determined at 1.22 and 1.30 Å resolution, respectively, and revealed important interactions in the active site that have not yet been explored.


    Organizational Affiliation

    Center for Women's Infectious Disease Research, Washington University in St Louis, St Louis, MO, USA. Hultgren@wustl.edu.,Henry Wellcome Building for Biocatalysis, Biosciences, University of Exeter, UK.,Center for Drug Discovery, Department of Chemistry and Chemical Biology, Northeastern University, Boston, MA 02115, USA; Department of Pharmaceutical Sciences, Northeastern University, Boston, MA 02115, USA.,Institute of Biochemistry, ETH Zurich, Zurich, Switzerland. volodymyr.korkhov@psi.ch.,Department of Crystallography and Structural Biology, Instituto Química-Física Rocasolano, Consejo Superior de Investigaciones Científicas, Madrid, Spain.,Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford OX1 3RE, UK. Electronic address: ervin.fodor@path.ox.ac.uk.,School of Biochemistry and Immunology, Trinity College Dublin, Dublin, 2, Ireland.,Laboratory of Biomolecular Research, Division of Biology and Chemistry, Paul Scherrer Institute, Villigen, Switzerland.,Synchrotron Radiation Research Section of MCL, National Cancer Institute, S Cass Ave 9700, Argonne, IL, U.S.A. milosz.ruszkowski@nih.gov.,Vector-Borne Diseases Laboratories, Department of Pathobiological Sciences, School of Veterinary Medicine, Louisiana State University, Baton Rouge, LA 70803, USA.,Shanghai Institute of Applied Physics, Chinese Academy of Sciences, No. 239 Zhangheng Road, Shanghai 201204, China.,X-Lab for Transmembrane Signaling Research, Department of Biomedical Engineering and McGovern Institute for Brain Research, Tsinghua University, Beijing, 100084, China.,School of Biological Science and Medical Engineering, Beihang University, Beijing, 100083, China. liu-lab@vip.163.com.,Science for Life Laboratory, Stockholm University, Solna, Sweden.,Experimental Retrovirology Section, HIV and AIDS Malignancy Branch , National Cancer Institute, National Institutes of Health , Bethesda , Maryland 20892 , United States.,Department of Microbiology, Immunology and Molecular Genetics, University of California, Los Angeles, Los Angeles, California, USA.,Division of Infectious Diseases and International Medicine, Department of Medicine, University of Minnesota, Minneapolis, MN, 55455, USA.,Department of Chemistry - BMC, Uppsala University, Box 576, Uppsala, S-751 23, Sweden. lynn.kamerlin@kemi.uu.se.,From the Institute for Cell and Molecular Biosciences, Newcastle University, Newcastle upon Tyne NE2 4HH, United Kingdom and alan.cartmell2@newcastle.ac.uk.,School of Chemistry, National University of Ireland Galway, University Road, Galway, Ireland.,Department of Chemical Sciences, University of Naples Federico II, Complesso Universitario di Monte Sant'Angelo, via Cintia, I-80126 Napoli, Italy.,JEM Utilization Center, Human Spaceflight Technology Directorate , Japan Aerospace Exploration Agency (JAXA) , 2-1-1 Sengen , Tsukuba-shi , Ibaraki 305-8505 , Japan.,Department of Structural Biology, Max Planck Institute of Biophysics, Frankfurt, Germany.,Department of Chemistry, Indiana University Bloomington, Bloomington, Indiana, USA.,School of Medicine, Tsinghua University, Beijing, 100084, China.,Faculty of Agriculture, Ehime University, Matsuyama, Japan.,Department of Applied Chemistry, Faculty of Science and Engineering , Chuo University , 1-13-27 Kasuga , Bunkyo-ku , Tokyo 112-8551 , Japan.,IAdChem (Institute for Advanced Research in Chemical Science) and Department of Inorganic Chemistry, Universidad Autónoma de Madrid, 28049, Spain.,IAdChem (Institute for Advanced Research in Chemical Science) and Department of Inorganic Chemistry, Universidad Autónoma de Madrid, 28049, Spain. Electronic address: adoracion.gomez@uam.es.,Center for Structural Biology, and.,Center for Chemical Biology and Drug Discovery, Departments of Pharmacological Sciences and Oncological Sciences, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai , New York, New York 10029, United States.,Faculty of Biological and Environmental Sciences, Molecular and Integrative Bioscience Research Programme, University of Helsinki, Helsinki, Finland ausra.domanska@helsinki.fi sarah.butcher@helsinki.fi.,iHuman Institute, ShanghaiTech University, Shanghai 201210, China.,Living Systems Institute, University of Exeter, Exeter, UK.,Medical School, Institute of Biochemistry II, Goethe University Frankfurt, Frankfurt, Germany.,Department of Chemistry, Indiana University Bloomington, Bloomington, Indiana, USA xjuan@iqfr.csic.es winklerm@indiana.edu giedroc@indiana.edu.,Horticultural Sciences Department, University of Florida, Gainesville, FL, U.S.A. adha@ufl.edu.,School of Biological Sciences, Faculty of Biology Medicine and Health, University of Manchester, Manchester Academic Health Science Centre, Manchester, UK.,Science for Life Laboratory, Department of Medicine Solna, Karolinska Institutet, 17165 Stockholm, Sweden; adnane.achour@ki.se T.van_Hall@lumc.nl.,Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama University, 1-1-1, Tsushima-naka, Kita-ku, Okayama, 700-8530, Japan. nyasui@okayama-u.ac.jp.,State Key Laboratory of Applied Organic Chemistry, Key Laboratory of Nonferrous Metal Chemistry and Resources Utilization of Gansu Province, College of Chemistry and Chemical Engineering, Lanzhou University , Lanzhou 730000, China.,Center for Molecular Biology of RNA, Department of Molecular, Cell and Developmental Biology, University of California, Santa Cruz, CA 95064 harry@nuvolari.ucsc.edu.,Laboratory of Physiologic Studies, National Institute on Alcohol Abuse and Alcoholism, NIH, Bethesda, MD 20892, USA.,Laboratory of Membrane Biophysics and Biology, The Rockefeller University, New York, United States.,Faculty of Biological and Environmental Sciences, Molecular and Integrative Bioscience Research Programme, University of Helsinki, Helsinki, Finland.,Department of Pharmacology and Toxicology, University of Toronto , Toronto, ON M5S 1A8, Canada.,Laboratory of Metals in Medicine (MetMed), Department of Chemistry "U. Schiff", University of Florence, Via della Lastruccia 3, 50019 Sesto Fiorentino, Italy.,New York Structural Biology Center, New York, NY, USA.,Genetics and Biochemistry Branch, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, United States.,iHuman Institute, ShanghaiTech University, Shanghai 201210, China; School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China. Electronic address: liuzhj@shanghaitech.edu.cn.,Max Planck Institute for Developmental Biology, Tübingen, Germany.,CNC - Center for Neuroscience and Cell Biology, University of Coimbra, 3004-517 Coimbra, Portugal.,Viral Special Pathogens Branch, Centers for Disease Control and Prevention, Atlanta, GA 30329, USA. Electronic address: mko2@cdc.gov.,California NanoSystems Institute, University of California, Los Angeles, Los Angeles, California, USA.,Department of Physics, University of Wisconsin, Milwaukee, WI, USA.,Tsinghua-Peking Center for Life Sciences, Tsinghua University, Beijing, 100084, China. zhangyanqing15@mail.tsinghua.edu.cn.,Department of Biology, Northeastern Illinois University, Chicago, IL, USA.,Department of Infectious Diseases, Karolinska University Hospital, Solna, 17176 Stockholm, Sweden.,Department of Biology, Johns Hopkins University, Baltimore, MD, 21218, USA.,a Molecular Cancer Research Group, Department of Medical Biology , University of Tromsø -The Arctic University of Norway , Tromsø , Norway.,Department of Pharmacy, Dongguk University, Goyang 10326, Korea.,Department of Chemistry, College of Natural Sciences, Seoul National University, Seoul 08826, Korea.,Department of Medicine, Harvard Medical School, Boston, MA 02115, USA.,Center for Molecular Biology of RNA, Department of Molecular, Cell and Developmental Biology, University of California, Santa Cruz, CA 95064.,School of Biological Sciences, University of Essex, Colchester CO4 3SQ, United Kingdom.,Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai, PRC.,Department of Pharmacology, University of Colorado School of Medicine, Aurora, CO 80045.,Protein Structure Section, Macromolecular Crystallography Laboratory, National Cancer Institute, Frederick, MD 21702, USA.,Institute of Life Science and Natural Resources, Korea University, Seoul, 02841, Republic of Korea.,Departments of Infectious Diseases and Hematology , Kumamoto University Graduate School of Biomedical Sciences , Kumamoto 860-8556 , Japan.,From the Department of Physiology, University of Tennessee Health Science Center, Memphis, Tennessee 38163 and jcordero@uthsc.edu.,Howard Hughes Medical Institute, Chevy Chase, United States.,State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing, PRC.,MTA-SE Ion Channel Research Group, Semmelweis University, Budapest, Hungary.,State Key Laboratory of Membrane Biology, Peking-Tsinghua Center for Life Sciences, School of Life Sciences, Peking University, Beijing, PRC.,Department of Biological Sciences, Bridge Institute, University of Southern California, Los Angeles, CA 90089, USA; Moscow Institute of Physics and Technology, Dolgoprudny, Russia.,State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, National Institute of Diagnostics and Vaccine Development in Infectious Diseases, School of Life Science, School of Public Health, Xiamen University, Xiamen 361102, P.R. China.,Provincial University Key Laboratory of Cellular Stress Response and Metabolic Regulation, College of Life Science, Fujian Normal University, Fuzhou, China.,Medical Oncology, Leiden University Medical Center, 2333 ZA Leiden, the Netherlands; adnane.achour@ki.se T.van_Hall@lumc.nl.,Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, USA.,National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Center for Plant Stress Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 201204, China. Electronic address: wmxing@sibs.ac.cn.,Department of Chemistry - BMC, Uppsala University, Box 576, Uppsala, S-751 23, Sweden.,Center for the Investigation of Membrane Excitability Diseases, Washington University in St Louis, St Louis, MO, USA. yuanp@wustl.edu.,Protein Analysis Group, Department of Pharmacy, University of Copenhagen, Copenhagen 2100, Denmark. Electronic address: kasper.rand@sund.ku.dk.,State Key Laboratory of Membrane Biology, Peking-Tsinghua Center for Life Sciences, School of Life Sciences, Peking University, Beijing, PRC; Tsinghua-Peking Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing, PRC.,Center for Biomolecular Structure and Dynamics, The University of Montana, Missoula, United States.,From the Institute for Organic Chemistry and Chemical Biology, Centre for Biomolecular Magnetic Resonance (BMRZ), Goethe-University Frankfurt am Main, Max-von-Laue-Strasse 7, D-60438 Frankfurt am Main, Germany.,Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, USA. mvandon@its.jnj.com wilson@scripps.edu.,Department of Nephrology, Changzheng Hospital, Second Military Medical University, Shanghai, 200433, China.,iHuman Institute, ShanghaiTech University, Shanghai 201210, China; School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China.,Department of Chemistry, University of Copenhagen, Copenhagen 2100, Denmark.,Department of Plant & Microbial Biology, University of California, Berkeley, CA 94720; view@berkeley.edu monica.balsera@csic.es.,Key Laboratory of Chemical Biology and Molecular Engineering of Education Ministry, Institute of Molecular Science, Shanxi University, Taiyuan, 030006, China.,Beijing Advanced Innovation Center for Biomedical Engineering, Beihang University, Beijing, China, 102402.,Department of Biological Chemistry and Pharmacology , The Ohio State University , Columbus , Ohio 43210 , United States.,d Peptide Chemistry Science Technology Platform , The Francis Crick Institute , London , UK.,Department of Biomolecular Mechanisms, Max Planck Institute for Medical Research, Jahnstrasse 29, 69120 Heidelberg, Germany.,Tsinghua-Peking Center for Life Sciences, Tsinghua University, Beijing, 100084, China. wangtingliang@mail.tsinghua.edu.cn.,The Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, CA, USA.,Russian Research Center of Molecular Diagnostics and Therapy, Simpheropolsky Blvd. 8, 113149, Moscow, Russia.,Science for Life Laboratory, Department of Medicine Solna, Karolinska Institutet, 17165 Stockholm, Sweden.,Discovery Sciences, Janssen Research & Development, 1400 McKean Rd., Spring House, PA, USA.,Department of Chemistry, University of Florida, Gainesville, FL, U.S.A.,Center for Women's Infectious Disease Research, Washington University in St Louis, St Louis, MO, USA.,Department of Molecular Medicine, Scripps Research, Jupiter, FL 33458, USA.,Department of Life Sciences and the National Institute for Biotechnology in the Negev, Ben Gurion University of the Negev, Beer-Sheva, Israel.,Vaccine Research Center, NIAID, National Institutes of Health, Bethesda, MD, 20892, USA. pdkwong@nih.gov.,Janssen Infectious Diseases and Vaccines, Janssen Research & Development, Archimedesweg 4-6, Leiden, Netherlands.,Department of Biology, Indiana University Bloomington, Bloomington, Indiana, USA xjuan@iqfr.csic.es winklerm@indiana.edu giedroc@indiana.edu.,Department of Chemistry, Umeå University, Umeå, Sweden.,Department of Picobiology, University of Hyogo, 3-2-1 Koto, Kamigori-cho, Ako-gun, Hyogo 678-1297, Japan.,Department of Bioengineering, University of California, Los Angeles, Los Angeles, California, USA.,Department of Physics, Ohio State University, Columbus, OH 43210.,Department of Plant Pathology, Nanjing Agricultural University, Nanjing 210095, China; Key Laboratory of Integrated Management of Crop Diseases and Pests (Ministry of Education), Nanjing 210095, China. Electronic address: wangyc@njau.edu.cn.,Novozymes A/S, Krogshøjvej 36, Bagsværd 2880, Denmark.,Department of Molecular Physiology and Biophysics.,Department of Chemistry, School of Physical Sciences, University of Liverpool, UK.,Laboratoire de Biologie Moléculaire et Cellulaire, Université de Neuchâtel, 2000 Neuchâtel, Switzerland.,State Key Laboratory of Membrane Biology, Peking-Tsinghua Center for Life Sciences, School of Life Sciences, Peking University, Beijing, PRC. Electronic address: gaon@pku.edu.cn.,Department of Biology, Technische Universität Darmstadt, D64287 Darmstadt, Germany.,Faculty of Medicine, Anatomy, University of Helsinki, 00014 Helsinki, Finland.,Department of Microbiology, Radboud University, Heyendaalseweg 135, 6525 AJ Nijmegen, The Netherlands.,School of Life Sciences, Tsinghua University, Beijing, 100084, China. zhangyanqing15@mail.tsinghua.edu.cn.,Department of Cell Biology and Physiology, Washington University in St Louis, St Louis, MO, USA.,Department of Biochemistry and Molecular Biology and ‡Department of Immunology, Mayo Clinic , Rochester, Minnesota 55905, United States.,Department of Biomedical Laboratory Science, College of Health Science, Eulji University, Daejeon, South Korea.,Vaccine Research Center, NIAID, National Institutes of Health, Bethesda, MD, 20892, USA.,Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA.,Department of Crystallography and Structural Biology, Instituto Química-Física Rocasolano, Consejo Superior de Investigaciones Científicas, Madrid, Spain xjuan@iqfr.csic.es winklerm@indiana.edu giedroc@indiana.edu.,Department of Pharmaceutical Chemistry and Macromolecule and Vaccine Stabilization Center, University of Kansas, Lawrence, KS, USA.,Helsinki Institute of Life Sciences, Institute of Biotechnology, University of Helsinki, Helsinki, Finland.,Center for Applied Structural Discovery, Arizona State University, 85287 Tempe, AZ, USA.,Laboratory of Metals in Medicine (MetMed), Department of Chemistry "U. Schiff", University of Florence, Via della Lastruccia 3, 50019 Sesto Fiorentino, Italy. Electronic address: luigi.messori@unifi.it.,Department of Chemistry and Biochemistry, Southern Illinois University, Carbondale, United States.,Jiangsu Key Laboratory of Translational Research and Therapy for Neuro-Psycho-Diseases and Department of Medicinal Chemistry, College of Pharmaceutical Sciences, Soochow University , Suzhou, Jiangsu 215123, China.,Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, The Netherlands.,Department of Biochemistry and Molecular Biophysics Graduate Group, University of Pennsylvania, Philadelphia, PA, USA.,Metabolomics Unit, CIC bioGUNE, CIBERehd, Parque Tecnologico de Bizkaia, Derio, Spain.,School of Biological Science and Medical Engineering, Beihang University, Beijing, 100083, China.,Departments of Discovery Chemistry and Molecular Technologies, Bristol-Myers Squibb Research and Development, Cambridge, MA, 02142, USA.,Viral Special Pathogens Branch, Centers for Disease Control and Prevention, Atlanta, GA 30329, USA.,Centre for Biomolecular Magnetic Resonance, Institute for Biophysical Chemistry, Goethe University Frankfurt, Frankfurt, Germany.,Instituto de Biología Molecular y Celular del Cáncer, Consejo Superior de Investigaciones Científicas - University of Salamanca, Campus Unamuno, 37007 Salamanca, Spain.,NHC Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, PRC. Electronic address: jinqi@ipbcams.ac.cn.,Department of Biotechnology & Bioinformatics, Korea University, Sejong, South Korea.,Department of Structural Biology, Stanford University, Stanford, United States.,Department of Chemistry and Department of Medicinal Chemistry , Purdue University , 560 Oval Drive , West Lafayette , Indiana 47907 , United States.,Department of Biochemistry and Biophysics, Stockholm University, Stockholm, Sweden.,Department of Bioengineering, University of California, Los Angeles, Los Angeles, California, USA Hong.Zhou@UCLA.edu.,Discovery Sciences, Janssen Research & Development, Turnhoutseweg 30, Beerse, Belgium.,Department of Medical Biochemistry, Semmelweis University, Budapest, Hungary.,Department of Integrative Structural and Computational Biology, The Scripps Research Institute, Jupiter, United States.,Department of Medical Biochemistry and Biophysics, Umeå University, Umeå, SE-90187, Sweden. erik.tm.johansson@umu.se.,NHC Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, PRC.,Department of Chemistry, University of Copenhagen, Copenhagen 2100, Denmark. Electronic address: leila@chem.ku.dk.,Mycology Reference Laboratory, National Centre for Microbiology, Instituto de Salud Carlos III, Majadahonda, Madrid, Spain.,Department of Plant Pathology, Nanjing Agricultural University, Nanjing 210095, China; Key Laboratory of Integrated Management of Crop Diseases and Pests (Ministry of Education), Nanjing 210095, China.,Beijing Advanced Innovation Center for Structural Biology, Tsinghua University, Beijing, 100084, China.,Chromatin Structure and Mobile DNA, The Francis Crick Institute, London, NW1 1AT, UK.,Department of Applied Chemistry, Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita, Osaka 565-0871, Japan.,Dipartimento di Scienze Chimiche della Vita e della Sostenibilità Ambientale, Università di Parma and INSTM UdR Parma, Parco Area delle Scienze 17/A, 43124, Parma, Italy.,Department of Biomedical and Pharmaceutical Sciences, The University of Montana, Missoula, United States.,Graduate School of Medical Science and Engineering, College of Life Science and Bioengineering, Korea Advanced Institute of Science and Technology, Daejeon, South Korea.,c Molecular Cell Biology of Autophagy Laboratory , The Francis Crick Institute , London , UK.,School of Life Sciences, University of Science and Technology of China , Hefei 230026, China.,Department of Picobiology, University of Hyogo, 3-2-1 Koto, Kamigori-cho, Ako-gun, Hyogo 678-1297, Japan; Core Research for Evolutional Science and Technology(CREST), Japan Science and Technology Agency, 4-1-8 Honcho, Kawaguchi, Saitama 332-0012, Japan; SPring-8 Center, RIKEN, 1-1-1 Koto, Sayo-cho, Sayo-gun, Hyogo 679-5148, Japan. Electronic address: hig@sci.u-hyogo.ac.jp.,Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota Twin Cities, Minneapolis, MN, 55455, USA. Electronic address: aihar001@umn.edu.,Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Boston, MA 02215, USA.,Max Planck Institute of Biochemistry, Martinsried, Germany.,Protein Analysis Group, Department of Pharmacy, University of Copenhagen, Copenhagen 2100, Denmark.,Metabolic Engineering Group, Departamento de Microbiología y Genética, Universidad de Salamanca, 37007 Salamanca, Spain.,Department of Pharmaceutical Science, General and Organic Chemistry Section, University of Milan, 20133 Milan, Italy.,Janssen Prevention Center, Janssen Pharmaceutical Companies of Johnson & Johnson, Archimedesweg 6, Leiden, Netherlands. mvandon@its.jnj.com wilson@scripps.edu.,Department of Molecular Microbiology, Washington University in St Louis, St Louis, MO, USA.,Guangdong Provincial Key Laboratory of Biocomputing, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences , Guangzhou 510530, China.,Nanoscience Center, Department of Biological and Environmental Sciences, University of Jyvaskyla, 40014 Jyvaskyla, Finland.,From the Institute for Cell and Molecular Biosciences, Newcastle University, Newcastle upon Tyne NE2 4HH, United Kingdom and.,Department of Molecular Medicine, The Scripps Research Institute, La Jolla, CA, USA.,Department of Chemistry , East Carolina University , Greenville , North Carolina 27858 , United States.,Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford OX1 3RE, UK; Division of Structural Biology, Henry Wellcome Building for Genomic Medicine, University of Oxford, Oxford OX3 7BN, UK.,College of Pharmacy, Chung-Ang University, Seoul, 06974, Republic of Korea.,Skaggs Graduate School of Chemical and Biological Sciences, The Scripps Research Institute, Jupiter, United States.,Department of Chemistry and Molecular Biology, University of Gothenburg, 40530 Gothenburg, Sweden.,National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Center for Plant Stress Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 201204, China.,Ministry of Education Key Laboratory of Protein Science, Tsinghua University, Beijing, 100084, China. zhangyanqing15@mail.tsinghua.edu.cn.,From the Institute for Organic Chemistry and Chemical Biology, Centre for Biomolecular Magnetic Resonance (BMRZ), Goethe-University Frankfurt am Main, Max-von-Laue-Strasse 7, D-60438 Frankfurt am Main, Germany schwalbe@nmr.uni-frankfurt.de.,Instituto de Recursos Naturales y Agrobiología de Salamanca, Consejo Superior de Investigaciones Científicas, 37008 Salamanca, Spain view@berkeley.edu monica.balsera@csic.es.,Institute for Cancer Research, Fox Chase Cancer Center, Philadelphia, PA, USA.,b Structural Biology , The Francis Crick Institute , London , UK.,Department of Bioscience, Graduate School of Agriculture, Ehime University, Matsuyama, Japan.,Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, USA.,Ministry of Education Key Laboratory of Protein Science, Tsinghua University, Beijing, 100084, China.,Computer Assisted Drug Design, Bristol-Myers Squibb Research and Development, Wallingford, CT, 06492, USA.,Division of Biotechnology, College of Life Sciences and Biotechnology, Korea University, Seoul, 02841, Republic of Korea.,Department of Medicine, Imperial College London, St-Mary's Campus, Norfolk Place, London, W2 1PG, UK.,Novartis Institutes for Biomedical Research (China), Zhangjiang Hi-Tech Park , Pudong New Area, Shanghai 201203, China.,Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford OX1 3RE, UK.,Division of Structural Biology, Henry Wellcome Building for Genomic Medicine, University of Oxford, Oxford OX3 7BN, UK; Diamond Light Source, Harwell Science and Innovation Campus, Didcot OX11 0DE, UK. Electronic address: jonathan@strubi.ox.ac.uk.,Institute of Biochemistry, ETH Zurich, Zurich, Switzerland.,Department of Chemistry and Biochemistry , The Ohio State University , Columbus , Ohio 43210 , United States.,Bach Institute of Biochemistry, Research Center of Biotechnology of the Russian Academy of Sciences, Leninsky Ave. 33, 119071, Moscow, Russia.,Molecular Biophysics Group, Institute of Integrative Biology, Faculty of Health and Life Sciences, University of Liverpool, UK.,Department of Biological Chemistry, John Innes Centre, Norwich Research Park, Norwich NR4 7UH, United Kingdom.,California NanoSystems Institute, University of California, Los Angeles, Los Angeles, CA 90095, USA.,Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA; The Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, CA 92037, USA. Electronic address: erica@scripps.edu.,School of Biological Sciences, University of East Anglia, Norwich NR4 7TJ, United Kingdom.,Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, IL, USA.,iHuman Institute, ShanghaiTech University, Shanghai 201210, China; School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China; University of the Chinese Academy of Sciences, Beijing 100049, China.,School of Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, 214122, Jiangsu, China; The Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, Jiangnan University, 1800 Lihu Road, Wuxi, 214122, Jiangsu, China. Electronic address: gcdu@jiangnan.edu.cn.,Centro Universitario de la Defensa, Ctra. Huesca s/n, 50090 Zaragoza, Spain.,Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, 214122, Jiangsu, China; School of Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, 214122, Jiangsu, China.,Department of Pathology, The University of Chicago, Chicago, IL, United States.,Department of Cell Biology, Graduate School of Medicine, Kyoto University, Yoshidakonoe-cho, Sakyo-ku, Kyoto 606-8501, Japan.,Structural Genomics Consortium, University of Toronto , Toronto, ON M5G 1L7, Canada.,Ministry of Education Key Laboratory of Protein Science, Tsinghua University, Beijing, 100084, China. wangtingliang@mail.tsinghua.edu.cn.,Department of Chemistry and Industrial Chemistry (DCCI), University of Pisa, Via Moruzzi, 13, 56124 Pisa, Italy; Laboratory of Metals in Medicine (MetMed), Department of Chemistry "U. Schiff", University of Florence, Via della Lastruccia 3, 50019 Sesto Fiorentino, Italy.,Cell Therapy Institute, Nova Southeastern University, Fort Lauderdale, FL 33314; and.,Department of Molecular Medicine, The Scripps Research Institute, Jupiter, United States.,X-Lab for Transmembrane Signaling Research, Department of Biomedical Engineering and McGovern Institute for Brain Research, Tsinghua University, Beijing, 100084, China. liu-lab@vip.163.com.,School of Life Sciences, Tsinghua University, Beijing, 100084, China.,Vanderbilt Brain Institute, Vanderbilt University School of Medicine, Nashville, Tennessee 37232.,Department of Molecular Microbiology, Washington University in St Louis, St Louis, MO, USA. Hultgren@wustl.edu.,Department of Biology, Indiana University Bloomington, Bloomington, Indiana, USA.,Department of Bioengineering and Therapeutic Science , University of California, San Francisco , San Francisco , California 94158 , United States.,Department of Pharmacology, University of Colorado School of Medicine, Aurora, CO 80045; tatiana.kutateladze@ucdenver.edu.,Japan Synchrotron Radiation Research Institute, 1-1-1 Kouto, Sayo-cho, Sayo-gun, Hyogo 679-5198, Japan.,iHuman Institute, ShanghaiTech University, Shanghai 201210, China; School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China; Department of Biological Sciences, Bridge Institute, University of Southern California, Los Angeles, CA 90089, USA.,School of Energy and Chemical Engineering, Ulsan National Institute of Science and Technology (UNIST), Ulsan 44919, Korea.,Department of Molecular Physiology and Biophysics, terunaga.nakagawa@vanderbilt.edu.,Division of Structural Biology, Henry Wellcome Building for Genomic Medicine, University of Oxford, Oxford OX3 7BN, UK.,Medical Oncology, Leiden University Medical Center, 2333 ZA Leiden, the Netherlands.,Center for the Investigation of Membrane Excitability Diseases, Washington University in St Louis, St Louis, MO, USA.,Instituto de Biología Molecular y Celular del Cáncer, Consejo Superior de Investigaciones Científicas and Universidad de Salamanca, 37007 Salamanca, Spain.,Centre for Molecular and Structural Biochemistry, School of Chemistry, University of East Anglia, Norwich NR4 7TJ, United Kingdom.,Department of Biological Sciences, Graduate School of Science, University of Tokyo, 2-11-16 Yayoi, Bunkyo-ku, Tokyo, 113-0032, Japan.,Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota Twin Cities, Minneapolis, MN, 55455, USA.,Janssen Infectious Diseases and Vaccines, Janssen Research & Discovery, Turnhoutseweg 30, Beerse, Belgium.,Campus Chemical Instrument Center , The Ohio State University , Columbus , Ohio 43210 , United States.,Institute of Biochemistry, University of Zurich, Zurich, Switzerland.,Beijing Advanced Innovation Center for Structural Biology, Tsinghua University, Beijing, 100084, China. zhangyanqing15@mail.tsinghua.edu.cn.,Beijing Advanced Innovation Center for Structural Biology, Tsinghua University, Beijing, 100084, China. wangtingliang@mail.tsinghua.edu.cn.,Committee on Microbiology, The University of Chicago, Chicago, IL, United States.,Scripps Institution of Oceanography, University of California, San Diego, La Jolla, CA 92093.,Centre for Molecular and Structural Biochemistry, School of Chemistry, University of East Anglia, Norwich NR4 7TJ, United Kingdom; n.le-brun@uea.ac.uk.,College of Allopathic Medicine, Nova Southeastern University, Fort Lauderdale, FL 33328.,Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama University, 1-1-1, Tsushima-naka, Kita-ku, Okayama, 700-8530, Japan.,Department of Molecular Membrane Biology, Max Planck Institute of Biophysics, Frankfurt, Germany.,Division of Infectious Diseases, Wadsworth Center, New York State Department of Health, Albany, NY, USA.,University of Chinese Academy of Sciences, Beijing, China.,From the Department of Physiology, University of Tennessee Health Science Center, Memphis, Tennessee 38163 and.,Department of Food and Nutrition, Duksung Women's University, Seoul, South Korea.,RIKEN SPring-8 Center, 1-1-1 Kouto, Sayo-cho, Sayo-gun, 679-5148 Hyogo, Japan.,Department of Biological Sciences, Bridge Institute, University of Southern California, Los Angeles, CA 90089, USA.,Umeå Center for Microbial Research, Umeå University, Umeå, Sweden.,Department of Chemistry , University of California, Davis , Davis , California 95695 , United States.,Radboud Institute for Molecular Life Sciences, Department of Pediatrics, Radboud University Medical Centre, Nijmegen, The Netherlands.,Eppley Institute for Research in Cancer and Allied Diseases, Fred & Pamela Buffett Cancer Center, University of Nebraska Medical Center, Omaha, NE, 68198, USA.,Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, 02215, USA.,Departament de Bioquímica i Biologia Molecular and Institut de Biotecnologia i Biomedicina, Universitat Autònoma de Barcelona, Bellaterra, Barcelona, Spain.,iHuman Institute, ShanghaiTech University, Shanghai 201210, China; School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China; Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Science, Chinese Academy of Sciences, Shanghai, China; University of the Chinese Academy of Sciences, Beijing 100049, China.,Department of Chemistry and Ralph Adams Institute for Bioanalytical Chemistry, University of Kansas, Lawrence, KS, USA.,Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA.,DiscoveRx Corporation , Fremont, California 94538, United States.,Janssen Prevention Center, Janssen Pharmaceutical Companies of Johnson & Johnson, Archimedesweg 6, Leiden, Netherlands.,School of Life Sciences, Tsinghua University, Beijing, 100084, China. liu-lab@vip.163.com.,Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, United States.,Instituto de Biología Molecular y Celular del Cáncer, Consejo Superior de Investigaciones Científicas - University of Salamanca, Campus Unamuno, 37007 Salamanca, Spain. Electronic address: pereda@usal.es.,Department of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, Ås, Norway.,Department of Biology, Molecular Basis of Disease , Georgia State University , Atlanta , Georgia 30303 , United States.,Department of Cell Biology and Physiology, Washington University in St Louis, St Louis, MO, USA. yuanp@wustl.edu.,Department of Refractory Viral Infections , National Center for Global Health and Medicine Research Institute , Tokyo 162-8655 , Japan.,School of Medicine, Tsinghua University, Beijing, 100084, China. liu-lab@vip.163.com.,School of Medicine, Tsinghua University, Beijing, 100084, China. wangtingliang@mail.tsinghua.edu.cn.,Department of Microbiology, Immunology, and Molecular Genetics, University of California, Los Angeles, Los Angeles, CA 90095, USA.,State Key Laboratory of Respiratory Disease, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences , Guangzhou 510530, China.,Summer Undergraduate Research Fellows (SURF) program, The Scripps Research Institute, Jupiter, United States.,Department of Medical Biophysics, University of Toronto and Princess Margaret Cancer Centre , 101 College Street, MaRS South Tower, Suite 707, Toronto, ON M5G 1L7, Canada.,Department of Chemistry and Biochemistry and Division of Biological Sciences, University of California, San Diego, San Diego, CA 92093-0378, USA.,Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama University, 1-1-1, Tsushima-naka, Kita-ku, Okayama, 700-8530, Japan. a_yama@cc.okayama-u.ac.jp.,Beijing Advanced Innovation Center for Biomedical Engineering, Beihang University, Beijing, China, 102402. liu-lab@vip.163.com.,Center for Marine Environmental Studies (CMES), Ehime University, Matsuyama, Japan.,Cluster of Excellence Macromolecular Complexes, Goethe University Frankfurt, Frankfurt, Germany.,Horticultural Sciences Department, University of Florida, Gainesville, FL, U.S.A.,State Key Laboratory of Structural Chemistry, Fujian Institute of Research on the Structure of Matter, Chinese Academy of Sciences, Fuzhou, China.,Tsinghua-Peking Center for Life Sciences, Tsinghua University, Beijing, 100084, China.,Department of Medical Biochemistry and Biophysics, Umeå University, Umeå, SE-90187, Sweden.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Protease
A, B
99Human immunodeficiency virus type 1 group M subtype B (isolate HXB2)Mutation(s): 0 
Gene Names: gag-pol
Find proteins for P04585 (Human immunodeficiency virus type 1 group M subtype B (isolate HXB2))
Go to UniProtKB:  P04585
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NA
Query on NA

Download SDF File 
Download CCD File 
A, B
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
CL
Query on CL

Download SDF File 
Download CCD File 
A, B
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
HWY
Query on HWY

Download SDF File 
Download CCD File 
A
(3aS,5R,6aR)-2-oxo-3-phenylhexahydro-2H-cyclopenta[d][1,3]oxazol-5-yl [(2S,3R)-3-hydroxy-4-{[(4-methoxyphenyl)sulfonyl](2-methylpropyl)amino}-1-phenylbutan-2-yl]carbamate
C34 H41 N3 O8 S
MCFYAJCOYWLLEO-YGMVDIOKSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
HWYIC50: 436 nM BINDINGMOAD
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.3 Å
  • R-Value Free: 0.182 
  • R-Value Work: 0.148 
  • Space Group: P 21 21 2
Unit Cell:
Length (Å)Angle (°)
a = 59.793α = 90.00
b = 86.043β = 90.00
c = 45.875γ = 90.00
Software Package:
Software NamePurpose
HKL-2000data reduction
SHELXLrefinement
HKL-2000data scaling
PHASERphasing
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)United StatesGM53386
National Institutes of Health/National Cancer Institute (NIH/NCI)United StatesGM62920
National Institutes of Health/National Cancer Institute (NIH/NCI)United Statesthe Intramural Research Program of the Center for Cancer Research
Department of Energy (DOE, United States)United StatesW-31-109-Eng-38
National Institutes of Health/National Cancer Institute (NIH/NCI)United Statesthe Intramural Research Program of the Center for Cancer Research
Ministry of Education, Culture, Sports, Science and Technology (Japan)Japana Grant-in-Aid for Scientific Research (Priority Areas)
Ministry of Education, Culture, Sports, Science and Technology (Japan)Japanthe Grant to the Cooperative Research Project on Clinical and Epidemiological Studies of Emerging and Reemerging Infectious Diseases (Renkei Jigyo)

Revision History 

  • Version 1.0: 2018-11-07
    Type: Initial release
  • Version 1.1: 2018-11-21
    Type: Data collection, Database references
  • Version 1.2: 2019-07-17
    Type: Data collection, Refinement description
  • Version 1.3: 2019-12-04
    Type: Author supporting evidence