5JM4

Crystal structure of 14-3-3zeta in complex with a cyclic peptide involving an adamantyl and a dicarboxy side chain


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.34 Å
  • R-Value Free: 0.244 
  • R-Value Work: 0.198 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Structure-Based Design of Non-natural Macrocyclic Peptides That Inhibit Protein-Protein Interactions.

Kruger, D.M.Glas, A.Bier, D.Pospiech, N.Wallraven, K.Dietrich, L.Ottmann, C.Koch, O.Hennig, S.Grossmann, T.N.

(2017) J. Med. Chem. 60: 8982-8988

  • DOI: 10.1021/acs.jmedchem.7b01221

  • PubMed Abstract: 
  • Macrocyclic peptides can interfere with challenging biomolecular targets including protein-protein interactions. Whereas there are various approaches that facilitate the identification of peptide-derived ligands, their evolution into higher affinity ...

    Macrocyclic peptides can interfere with challenging biomolecular targets including protein-protein interactions. Whereas there are various approaches that facilitate the identification of peptide-derived ligands, their evolution into higher affinity binders remains a major hurdle. We report a virtual screen based on molecular docking that allows the affinity maturation of macrocyclic peptides taking non-natural amino acids into consideration. These macrocycles bear large and flexible substituents that usually complicate the use of docking approaches. A virtual library containing more than 1400 structures was screened against the target focusing on docking poses with the core structure resembling a known bioactive conformation. Based on this screen, a macrocyclic peptide 22 involving two non-natural amino acids was evolved showing increased target affinity and biological activity. Predicted binding modes were verified by X-ray crystallography. The presented workflow allows the screening of large macrocyclic peptides with diverse modifications thereby expanding the accessible chemical space and reducing synthetic efforts.


    Organizational Affiliation

    Sunnybrook Research Institute, Toronto, ON, M4N 3M5, Canada. james.carlyle@utoronto.ca.,Institut für Pharmazeutische und Medizinische Chemie, PharmaCampus, Westfälische Wilhelms-Universität Münster, Corrensstraße 48, D-48149 Münster, Germany. gratz.andreas@gmail.com.,Rega Institute for Medical Research and Department of Microbiology and Immunology, KU Leuven, Leuven, 3000, Belgium.,College of Life Sciences, Northwest A&F University, Yangling, Shaanxi, 712100, China. Electronic address: weifei_c@nwsuaf.edu.cn.,Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA. laub@mit.edu.,3Alberta Glycomics Centre and Department of Chemistry, University of Alberta, Edmonton, T6G 2G2 AB Canada.,Université Grenoble Alpes, CNRS, CEA, IBS UMR 5075, 38044, Grenoble, France. andre.zapun@ibs.fr.,Mitchell Cancer Institute, The University of South Alabama, Mobile, Alabama.,Department of Drug Metabolism and Pharmacokinetics, Genentech, South San Francisco, CA, USA.,Structural Studies Division, MRC-LMB, Francis Crick Avenue, Cambridge, CB2 0QH, UK.,Experimental Retrovirology Section, HIV and AIDS Malignancy Branch, National Cancer Institute, National Institutes of Health, Bethesda, MD, 20892, USA.,Department of Chemistry and Biochemistry, University of California Los Angeles, Los Angeles, CA 90095, USA.,Infection and Immunity Program and Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria, 3800, Australia. Richard.berry@monash.edu.,Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, CA, USA. yiorgo@stanford.edu.,Department of Biotechnology , The University of Tokyo , 1-1-1 Yayoi , Bunkyo-ku, Tokyo 113-8657 , Japan.,Macromolecular Crystallography Group, Structural Biology and Biocomputing Program, Spanish National Cancer Research Center (CNIO), c/Melchor Fernández Almagro 3, 28029, Madrid, Spain.,Department of Microchem Proteomics, Genentech, South San Francisco, CA, USA.,David Geffen School of Medicine, University of California Los Angeles and Greater West Los Angeles Health Care System, Los Angeles, CA 90095, USA.,Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02115, USA; Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA.,Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, 37232-2372, USA. kyle.l.brown@vanderbilt.edu.,Department of Infectious Diseases, Genentech, South San Francisco, CA, USA. smith.peter@gene.com.,the Department of Neuroscience, Mayo Clinic College of Medicine, Jacksonville, Florida 32224.,Heptares Therapeutics Ltd. , BioPark , Welwyn Garden City , Hertfordshire AL7 3AX , U.K.,Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China; Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China.,From the Departments of Biological Chemistry and Chemistry and Biochemistry, Howard Hughes Medical Institute, UCLA-DOE Institute, UCLA, Los Angeles, California 90095 and.,Pharmacy & Pharmacology, University of Bath, Claverton Down, Bath, BA2 7AY, United Kingdom.,Department of Immunology, University of Toronto, Toronto, ON, M5S 1A8, Canada.,Department of Applied Life Sciences, Graduate School of Life and Environmental Sciences, Osaka Prefecture University, 1-1 Gakuen-cho, Naka-ku, Sakai, 599-8531, Japan.,Department of Clinical Science, Kumamoto University Hospital, Kumamoto, 860-8556, Japan.,Biosciences Division, SLAC National Accelerator Laboratory, Stanford University, Stanford, CA, USA.,Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720; zhangrui@wustl.edu enogales@lbl.gov.,VIB-VUB Center for Structural Biology, VIB, Brussels, Belgium.,Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA, USA.,Chemical Genomics Centre of the Max Planck Society , Otto-Hahn-Str. 15, 44227 Dortmund, Germany.,National Research Laboratory of Molecular Microbiology and Toxicology, Department of Agricultural Biotechnology, and Center for Food Safety and Toxicology, Seoul National University, Seoul, South Korea mhk8n@kribb.re.kr choish@snu.ac.kr.,Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, United Kingdom.,Institut für Biochemie, Department für Chemie, Universität zu Köln, Zülpicher Straße 47, D-50674 Köln, Germany. Alexander.Schnitzler@posteo.de.,Veterans Affairs Hospital, Nashville, TN, 37232, USA.,Hamburg Centre for Ultrafast Imaging, Institute of Nanostructure and Solid State Physics, Universität Hamburg, CFEL, Luruper Chaussee 149, 22761, Hamburg, Germany. arwen.pearson@cfel.de.,Department of Biomedical Engineering, Institute of Complex Molecular Systems, Eindhoven University of Technology , Den Dolech 2, 5612 AZ Eindhoven, The Netherlands.,School of Biological Sciences , Nanyang Technological University , 50 Nanyang Drive , Singapore 637551.,Structural Molecular Biology Group, Novo Nordisk Foundation Centre for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3B, 2200, Copenhagen, Denmark.,Dipartimento di Bioscienze, Università degli Studi di Milano, 20133, Milano, Italy. carlo.camilloni@unimi.it.,Leadership Alliance, Vanderbilt University Medical Center, Nashville, TN, 37232-2372, USA.,Division of Infection and Immunity, Cardiff University School of Medicine, Cardiff, Wales, United Kingdom.,IAVI Neutralizing Antibody Center and Collaboration of AIDS Vaccine Discovery, The Scripps Research Institute, La Jolla, CA 92037, USA.,Integrative Biomedical Sciences, University of Cape Town, Observatory 7925, Cape Town, 8000, South Africa Edward.Sturrock@uct.ac.za.,Michael Smith Laboratories, University of British Columbia, 2185 East Mall, Vancouver, BC V6T 1Z4, Canada; Department of Chemistry, University of British Columbia, 2036 Main Mall, Vancouver, BC V6T 1Z1, Canada; Department of Biochemistry and Molecular Biology, University of British Columbia, 2350 Health Sciences Mall, Vancouver, BC V6T 1Z3, Canada.,Centre Hospitalier Universitaire de Québec Research Center, Université Laval, Québec City, QC, G1V 4G2, Canada.,Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China; Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China; University of Chinese Academy of Sciences, Beijing, China.,Department of Applied Life Sciences, Graduate School of Life and Environmental Sciences, Osaka Prefecture University, 1-1 Gakuen-cho, Naka-ku, Sakai, 599-8531, Japan. inuit@bioinfo.osakafu-u.ac.jp.,the Molecular Biophysics and Integrated Bioimaging Division, Berkeley Center for Structural Biology, Lawrence Berkeley National Laboratory, Berkeley, California 94720, and.,Koch Institute for Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA.,Department of Chemistry , University of Nevada, Reno , 1664 North Virginia Street , Reno , Nevada 89557 , United States.,University of Cape Town, Anzio Road, Observatory, Cape Town, 7925, South Africa.,CryoEM Shared Resources, Howard Hughes Medical Institute, Janelia Research Campus, Ashburn, VA, USA.,Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology (BIST), C/ Baldiri Reixac, 10, 08028, Barcelona, Spain.,Structural Molecular Biology Group, Novo Nordisk Foundation Centre for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3B, 2200, Copenhagen, Denmark. guillermo.montoya@cpr.ku.dk.,Department of Chemistry, University of Cambridge, Cambridge, CB2 1EW, UK.,James Cook University, Cairns, Australia.,Membrane Biochemistry and Biophysics, Department of Chemistry, Faculty of Science, Utrecht University, Utrecht, 3584, The Netherlands.,Centre de RMN à Très Hauts Champs, Institut des Sciences Analytiques (UMR 5280 CNRS/UCB Lyon 1/ENS Lyon), Université de Lyon, 69100, Villeurbanne, France. guido.pintacuda@ens-lyon.fr.,Infection and Immunity Program and Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria, 3800, Australia.,The University of New South Wales, Faculty of Medicine, St Vincent's Clinical School, Darlinghurst, Sydney, NSW, 2010, Australia.,California NanoSystems Institute, University California Los Angeles, Los Angeles, CA 90095, USA.,HudsonAlpha Institute for Biotechnology, Huntsville, Alabama.,Division of Molecular Biotherapy, Cancer Chemotherapy Center , Japanese Foundation for Cancer Research , 3-8-31 Ariake , Koto-ku, Tokyo 135-8850 , Japan.,Architecture et Fonction des Macromolécules Biologiques, Aix-Marseille Université, Campus de Luminy, Case 932, 13288, Marseille Cedex 09, France.,Departamento de Química, Universidade Nova de Lisboa, Caparica, 2829-516, Portugal.,Department of Structural Biology, Stanford University School of Medicine, Stanford, CA, USA.,i3S - Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal.,The Sainsbury Laboratory, Norwich Research Park, Norwich, NR4 7UH, UK.,Vertex, San Diego, CA, USA.,Department of Biological Sciences , National University of Singapore , 14 Science Drive 4 , Singapore 117543.,State Key Laboratory of Cell Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, Shanghai, China.,Université Paris Descartes, Laboratoire de Chimie et Biochimie Pharmacologiques et Toxicologiques UMR 8601 CNRS, Sorbonne Paris Cité (USPC), Paris, 75006, France.,Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA; IAVI Neutralizing Antibody Center and Collaboration of AIDS Vaccine Discovery, The Scripps Research Institute, La Jolla, CA 92037, USA. Electronic address: andrew@scripps.edu.,Dahlem Centre of Plant Sciences, Department of Plant Physiology and Biochemistry, Freie Universität Berlin, Königin-Luise-Straße 12-16, 14195, Berlin, Germany.,Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China; Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China; Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, China. Electronic address: qma@qdio.ac.cn.,Department of Chemistry & Pharmaceutical Sciences, VU University Amsterdam , De Boelelaan 1083, 1081 HV Amsterdam, The Netherlands.,Chemical Kinomics Research Center, Korea Institute of Science and Technology (KIST), 5 Hwarangro 14-gil, Seongbuk-gu, Seoul 02792, Republic of Korea; KU-KIST Graduate School of Converging Science and Technology, Korea University, 145 Anam-ro, Seongbuk-gu, Seoul 02841, Republic of Korea.,DuPont Nutrition and Health, BP 10, 86220, Dangé-Saint-Romain, France.,Carbapenemase-producing Enterobacteriaceae , Associated French National Reference Center for Antibiotic Resistance , 78 rue du Général Leclerc , 94275 Le Kremlin-Bicêtre , France.,Department of Physiology, Human and Molecular Genetics Center, Medical College of Wisconsin, Milwaukee, Wisconsin.,Institut de Chimie des Substances Naturelles, CNRS UPR 2301, Université Paris-Saclay, LabEx LERMIT , 1 avenue de la Terrasse, Bât. 27 , 91198 Gif-sur-Yvette , France.,Department of Biochemistry and Biophysics, Arrhenius Laboratories for Natural Sciences, Stockholm University, Stockholm, Sweden.,School of Life Science and Technology, ShanghaiTech University, Shanghai, China.,Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, CA, USA.,State Key Laboratory of Molecular Biology, Shanghai Science Research Center, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai, China.,Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Sapporo, 062-8517, Japan. y-yasutake@aist.go.jp.,Center for Environmental Health Sciences MIT, Massachusetts Institute of Technology, Cambridge, MA, USA.,Department of Pathology, Shanghai Tenth People's Hospital, Tongji University School of Medicine, Shanghai, China.,Department of Crystal and Structural Chemistry, Bijvoet Center for Biomolecular Research Utrecht University, Padualaan 8, 3584 CH, Utrecht, The Netherlands.,ARC Centre of Excellence in Advanced Molecular Imaging, Monash University, Clayton, Victoria, 3800, Australia. Jamie.rossjohn@monash.edu.,Center for Matrix Biology, Vanderbilt University Medical Center, Nashville, TN, 37232-2372, USA. kyle.l.brown@vanderbilt.edu.,Department of Biotechnology, Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita, 565-0871, Japan.,Department of Cell Biology, Neurobiology and Anatomy and.,Medizinische Biochemie und Molekularbiologie, Universität des Saarlandes, Kirrberger Str., Geb. 44, D-66421 Homburg, Germany. michaelweyrich@gmx.de.,Institute for Integrative Biology of the Cell (I2BC), CNRS CEA Univ. Paris-Sud, Université Paris-Saclay, Avenue de la Terrasse, 91198 Gif-sur-Yvette, France solange.morera@i2bc.paris-saclay.fr.,Dipartimento di Scienze per gli Alimenti, la Nutrizione e l'Ambiente, Università degli Studi di Milano, 20133, Milano, Italy.,Laboratory of Systems Pharmacology, Harvard Medical School, Boston, MA 02115, USA.,Department of Biochemical and Cellular Pharmacology, Genentech, South San Francisco, CA, USA. heise.christopher@gene.com.,Faculdade de Ciências, Departamento de Biologia, Universidade do Porto, Porto, Portugal.,Département de biochimie, de microbiologie, et de bioinformatique, Faculté des sciences et de génie, Groupe de recherche en écologie buccale, Faculté de médecine dentaire, Université Laval, Québec City, QC, G1V 0A6, Canada.,EA7361 "Structure, dynamic, function and expression of broad spectrum β-lactamases" , Université Paris Sud, Université Paris Saclay, LabEx LERMIT, Faculty of Medicine , 78 rue du Général Leclerc , 94275 Le Kremlin-Bicêtre , France.,Laboratory of Systems Pharmacology, Harvard Medical School, Boston, MA 02115, USA; Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02115, USA; Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA.,RQx Pharmaceuticals, La Jolla, CA, USA.,Department of Agrifood Production and Environmental Sciences, University of Florence, Florence, Italy.,Immunology Division, Garvan Institute of Medical Research, 384 Victoria Road, Darlinghurst, Sydney, NSW, 2010, Australia. d.langley@garvan.org.au.,Institute of Biochemistry, Center for Structural and Cell Biology in Medicine, University of Lübeck, Ratzeburger Allee 160, 23562 Lübeck, Germany; German Center for Infection Research (DZIF), Hamburg - Lübeck - Borstel - Riems Site, University of Lübeck, Germany. Electronic address: hilgenfeld@biochem.uni-luebeck.de.,Department of Biochemistry and Biophysics, Arrhenius Laboratories for Natural Sciences, Stockholm University, Stockholm, Sweden. peterb@dbb.su.se.,Structural Biology and Bioinformatics Division, Council of Scientific and Industrial Research - Indian Institute of Chemical Biology, Kolkata, India.,1Princess Margaret Cancer Centre, Toronto, M5G 1L7 ON Canada.,the Stanford Synchrotron Radiation Light Source, Menlo Park, California 94025.,Infection and Immunity Research Laboratory, Metabolic Regulation Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, South Korea.,Department of Chemistry, Wuxi AppTec, Shanghai, China.,Department of Chemistry & Nano Science, Ewha Womans University, Seoul, 03760, Republic of Korea. Electronic address: chajung@ewha.ac.kr.,Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, VIC 3052, Australia; Department of Medical Biology, The University of Melbourne, Melbourne, VIC 3052, Australia. Electronic address: kluck@wehi.edu.au.,Institute of Biochemistry, Center for Structural and Cell Biology in Medicine, University of Lübeck, Ratzeburger Allee 160, 23562 Lübeck, Germany.,Biochemistry Department, Oxford University, South Parks Road, Oxford, OX1 1HY, UK. ivan.campeotto@leicester.ac.uk.,Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA; IAVI Neutralizing Antibody Center and Collaboration of AIDS Vaccine Discovery, The Scripps Research Institute, La Jolla, CA 92037, USA.,Ipsen Innovation , 5, Avenue du Canada , Les Ulis , France 91940 . Email: sergeauvin@gmail.com ; Tel: +33 160 922481.,Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY, 14853, USA.,Department of Biological Chemistry, John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, UK.,Parker Institute for Cancer Immunotherapy, University of California, San Francisco, CA, 94143, USA.,Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Sapporo, 062-8517, Japan.,Department of Translational Immunology, Genentech, South San Francisco, CA, USA.,the Department of Cancer Biology, Mayo Clinic Comprehensive Cancer Center, Jacksonville, Florida 32224, radisky.evette@mayo.edu.,Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds, LS2 9JT, UK. arwen.pearson@cfel.de.,Department of Infectious Diseases, Genentech, South San Francisco, CA, USA. heise.christopher@gene.com.,RIKEN Program for Drug Discovery and Medical Technology Platforms , 2-1 Hirosawa , Wako , Saitama 351-0198 , Japan.,the Department of Cancer Biology, Mayo Clinic Comprehensive Cancer Center, Jacksonville, Florida 32224.,Protein Production and Characterization Platform, Novo Nordisk Foundation Centre for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3B, 2200, Copenhagen, Denmark.,Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, VIC 3052, Australia.,Department of Immunology, University of Toronto, Toronto, ON, M5S 1A8, Canada. james.carlyle@utoronto.ca.,the Department of Biology, Technion-Israel Institute of Technology, Haifa 3200003, Israel.,Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds, LS2 9JT, UK. ivan.campeotto@leicester.ac.uk.,the National Institute for Biotechnology in the Negev (NIBN), Beer-Sheva 84105, Israel.,Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, MI 48109, USA. Electronic address: nkoropat@umich.edu.,Department of Microbiology and Immunology, University of California, San Francisco, CA, 94143, USA.,CryoEM Shared Resources, Howard Hughes Medical Institute, Janelia Research Campus, Ashburn, VA, USA. yuz@janelia.hhmi.org.,Farncombe Family Digestive Health Research Institute, McMaster University. Department of Medicine, Faculty of Health Sciences, McMaster University, Hamilton, ON, L8S 4K1, Canada.,ARC Centre of Excellence in Advanced Molecular Imaging, Monash University, Clayton, Victoria, 3800, Australia.,Institute of Pharmaceutical Chemistry, Goethe-University Frankfurt, Max von Lauestr. 9, 60438 Frankfurt am Main, Germany; Buchmann Institute for Life Sciences (BMLS) and Structural Genomics Consortium Goethe-University Frankfurt, Max von Lauestr. 9, 60438 Frankfurt am Main, Germany.,Mass Spectrometry for Quantitative Proteomics, Novo Nordisk Foundation Centre for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3B, 2200, Copenhagen, Denmark.,Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada.,Medicinal Chemistry Research Group, Research Centre for Natural Sciences , Hungarian Academy of Sciences , 2 Magyar tudósok körútja , Budapest H-1117 , Hungary.,Institut für Pharmazeutische und Medizinische Chemie, Heinrich-Heine-Universität Düsseldorf, Universitätsstraße 1, D-40225 Düsseldorf, Germany. karsten.niefind@uni-koeln.de.,Hospital for Sick Children, Toronto, Ontario, Canada. john.rubinstein@utoronto.ca.,School of Pharmacy and Pharmaceutical Sciences, Biomedical Sciences Research Institute, Ulster University, Coleraine BT52 1SA, UK.,Department of Biological Sciences, The University of Alabama in Huntsville, Huntsville, Alabama.,Retrovirox, San Diego, CA, USA.,California Institute for Quantitative Biosciences, University of California, Berkeley, United States.,Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02115, USA; Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA. Electronic address: nathanael_gray@dfci.harvard.edu.,Faculty of science and engineering, Kinki University, 3-4-1 Kowakae, Higashi-Osaka, 577-8502, Japan.,National Research Laboratory of Molecular Microbiology and Toxicology, Department of Agricultural Biotechnology, and Center for Food Safety and Toxicology, Seoul National University, Seoul, South Korea.,Biochemistry Department, Oxford University, South Parks Road, Oxford, OX1 1HY, UK.,Hefei National Laboratory for Physical Science at the Microscale, School of Life Sciences, University of Science and Technology of China, 96 Jinzhai Road, Hefei, Anhui 230027, China.,Sunnybrook Research Institute, Toronto, ON, M4N 3M5, Canada.,Faculty of Chemistry and Chemical Biology, TU Dortmund University , Otto-Hahn-Str. 6, 44227 Dortmund, Germany.,From the Avram and Stella Goldstein-Goren Department of Biotechnology Engineering and the National Institute of Biotechnology in the Negev, Ben-Gurion University of the Negev, Beer-Sheva 84105, Israel.,Howard Hughes Medical Institute, University of California, Berkeley, United States.,Institute of Image Processing and Pattern Recognition, Shanghai Jiaotong University, Shanghai, China.,Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA.,Institute for Integrative Biology of the Cell (I2BC), CNRS CEA Univ. Paris-Sud, Université Paris-Saclay, Avenue de la Terrasse, 91198 Gif-sur-Yvette, France.,College of Life Sciences, Northwest A&F University, Yangling, Shaanxi, 712100, China; LBPA, ENS de Cachan, Université Paris-Saclay, Centre National de la Recherche Scientifique, 61 Avenue du Président Wilson, 94235, Cachan, France. Electronic address: xxi01@ens-cachan.fr.,Centre for Bacterial Cell Biology, Institute for Cell and Molecular Bioscience, Newcastle University, Newcastle Upon Tyne, NE2 4AX, United Kingdom.,ARC Centre of Excellence in Advanced Molecular Imaging, Monash University, Clayton, Victoria, 3800, Australia. Richard.berry@monash.edu.,Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720.,4Department of Medical Biophysics, University of Toronto, Toronto, M5G 1L7 ON Canada.,College of Life Sciences, Northwest A&F University, Yangling, Shaanxi, 712100, China.,Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark. jmm@sund.ku.dk.,Research Faculty of Agriculture, Hokkaido University, N-9, W-9, Sapporo 060-8589, Japan.,University of Bath, Building 4 South, Department of Biology and Biochemistry, Claverton Down, Bath, BA2 7AY, United Kingdom.,Dipartimento di Bioscienze, Università degli Studi di Milano, 20133, Milano, Italy. stefano.ricagno@unimi.it.,Molecular Biophysics and Integrative Bio-Imaging Division, Lawrence Berkeley National Laboratory, Berkeley, United States.,Infection and Immunity Research Laboratory, Metabolic Regulation Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, South Korea mhk8n@kribb.re.kr choish@snu.ac.kr.,Center for Advanced Biotechnology and Medicine, and Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, New Jersey, 08854.,Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, MI 48109, USA.,Department of Chemical and Physical Biology, Vanderbilt University, Nashville, Tennessee.,Dipartimento di Bioscienze, Università degli Studi di Milano, 20133, Milano, Italy.,York Structural Biology Laboratory, Department of Chemistry, University of York, Heslington, York YO10 5DD, UK.,Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds, LS2 9JT, UK.,Department of Chemistry, Sejong University, Seoul, South Korea.,IBMC - Instituto de Biologia Molecular e Celular, Universidade do Porto, Porto, Portugal.,ICBAS - Instituto de Ciências Biomédicas Abel Salazar, Porto, Portugal.,Department of Molecular and Cell Biology, University of California, Berkeley, United States.,Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA.,High Magnet Field Laboratory, Chinese Academy of Science, 50 Shushanhu Road, Hefei, Anhui 230031, China.,Laboratory of Systems Pharmacology, Harvard Medical School, Boston, MA 02115, USA. Electronic address: peter_sorger@hms.harvard.edu.,Aspirnaut Summer research program, Vanderbilt University Medical Center, Nashville, TN, 37232-2372, USA.,Department of Structural Biology, Stanford University School of Medicine, Stanford, CA, USA. yiorgo@stanford.edu.,Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, VIC 3052, Australia; Department of Medical Biology, The University of Melbourne, Melbourne, VIC 3052, Australia.,Institut für Pharmazeutische und Medizinische Chemie, PharmaCampus, Westfälische Wilhelms-Universität Münster, Corrensstraße 48, D-48149 Münster, Germany. wuensch@uni-muenster.de.,Department of Biochemical and Cellular Pharmacology, Genentech, South San Francisco, CA, USA.,Department of Biochemistry, University of Toronto, Toronto, Ontario, Canada. john.rubinstein@utoronto.ca.,DuPont Nutrition and Health, 3329 Agriculture Dr, Madison, WI, 53716, USA.,Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, 37232-2372, USA.,Howard Hughes Medical Institute, University of California, Berkeley, CA 94720.,Wolfson Drug Discovery Unit, Centre for Amyloidosis and Acute Phase Proteins, University College London, London, NW3 2PF, UK.,Department of Biochemistry and Biophysics, Arrhenius Laboratories for Natural Sciences, Stockholm University, Stockholm, Sweden. hogbom@dbb.su.se.,Northeastern Collaborative Access Team, Argonne National Laboratory, Lemont, IL, 60439, USA.,Bioinformatics Institute , ASTAR (Agency for Science, Technology and Research) , 30 Biopolis Street, #07-01 Matrix , Singapore 138671 . Email: chandra@bii.a-star.edu.sg ; Tel: +65 6478 8273.,Department of Bioinformatics and Computational Biology, Genentech, South San Francisco, CA, USA.,Félix d'Hérelle Reference Center for Bacterial Viruses, Faculté de médecine dentaire, Université Laval, Québec City, QC, G1V 0A6, Canada. sylvain.moineau@bcm.ulaval.ca.,Structural Biology and Bioinformatics Division, Council of Scientific and Industrial Research - Indian Institute of Chemical Biology, Kolkata, India jayati@iicb.res.in.,From the Departments of Biological Chemistry and Chemistry and Biochemistry, Howard Hughes Medical Institute, UCLA-DOE Institute, UCLA, Los Angeles, California 90095 and david@mbi.ucla.edu.,ConfometRx, Santa Clara, CA, USA. kobilka@stanford.edu.,Department of Biophysics, UT Southwestern Medical Center, Dallas, TX 75390.,Department of Chemistry, University of Duisburg-Essen, Essen, Germany.,Department of Structural Biology, Genentech, South San Francisco, CA, USA.,Department of Biochemistry and Molecular Biology and the Center for Blood Research, University of British Columbia, Vancouver, BC, Canada.,Departments of Biochemistry and Radiation Oncology, The University of Texas Southwestern Medical Center at Dallas, Dallas, TX 75390, USA.,Howard Hughes Medical Institute, Massachusetts Institute of Technology, Cambridge, MA, USA. laub@mit.edu.,Department of Biochemistry and Molecular Biology and the Center for Blood Research, University of British Columbia, Vancouver, BC, Canada. ncjs@mail.ubc.ca.,Merck & Co., Department of Biochemical Engineering and Structure, 2000 Galloping Hill Road, Kenilworth, NJ, 07033, USA.,The Pirbright Institute, Pirbright, Woking, United Kingdom.,Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada. john.rubinstein@utoronto.ca.,Life Sciences Institute and Department of Biological Chemistry, University of Michigan Medical School, Ann Arbor, MI, USA.,p53 Laboratory , ASTAR (Agency for Science, Technology and Research) , 8A Biomedical Grove, #06-04/05, Neuros/Immunos , Singapore 138648 . Email: cjbrown@p53lab.a-star.edu.sg ; Tel: +65 6478 8273.,Institute of Infection and Immunity, Cardiff University School of Medicine, Heath Park, Cardiff, CF14 4XN, UK. Jamie.rossjohn@monash.edu.,ESRF - The European Synchrotron, 38043, Grenoble, France.,Bacteriology-Hygiene Unit , Assistance Publique/Hôpitaux de Paris, Bicêtre Hospital , 78 rue du Général Leclerc , 94275 Le Kremlin-Bicêtre , France.,Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, Ås, 1432, Norway.,Faculty of Pharmaceutical Sciences, Sojo University, Kumamoto, 860-0082, Japan.,Université Grenoble Alpes, CNRS, CEA, IBS UMR 5075, 38044, Grenoble, France.,Department of Genetics, Harvard Medical School, Boston, Massachusetts.,Architecture et Fonction des Macromolécules Biologiques, Centre National de la Recherche Scientifique (CNRS), Campus de Luminy, Case 932, 13288, Marseille Cedex 09, France.,ConfometRx, Santa Clara, CA, USA.,University of Cape Town, Cape Town, South Africa.,Centro di Ricerca Pediatrica Romeo ed Enrica Invernizzi, Università degli Studi di Milano, 20133, Milano, Italy.,National Center for Global Health and Medicine Research Institute, Tokyo, 162-8655, Japan.,the Department of Medicine, University of California San Diego, La Jolla, California 92037, and.,Department of Molecular Medicine, The Scripps Research Institute, La Jolla, CA 92037, USA.,Clinical Research Center for Allergy and Rheumatology, Sagamihara National Hospital, 18-1 Sakuradai, Minami-ku, Sagamihara, 252-0392, Japan.,Division of Biological Chemistry and Drug Discovery, School of Life Sciences, James Black Centre , University of Dundee , Dow Street , DD1 5EH Dundee , Scotland, U.K.,National Center for Global Health and Medicine Research Institute, Tokyo, 162-8655, Japan. kmaeda@ri.ncgm.go.jp.,Research Faculty of Agriculture, Hokkaido University, N-9, W-9, Sapporo 060-8589, Japan. Electronic address: hmori@chem.agr.hokudai.ac.jp.,Ipsen Bioscience , 650 East Kendall Street , Cambridge , MA 02142 , USA.,School of Veterinary Sciences, University of Bristol, Bristol, United Kingdom.,Institut für Biochemie, Department für Chemie, Universität zu Köln, Zülpicher Straße 47, D-50674 Köln, Germany. kucklaen@uni-duesseldorf.de.,Structural Biology Brussels, Vrije Universiteit Brussel (VUB), Brussels, Belgium.,Evolution and Ecology of Resistance to Antibiotics Unit , Institut Pasteur, APHP, Université Paris Sud , 25-28 Rue du Dr Roux , 75015 Paris , France.,Marine Biotechnology Research Center, Korea Institute of Ocean Science and Technology, Ansan 426-744, Republic of Korea.,Division of Plant Biology, Department of Biosciences, University of Helsinki, FIN-00014, Helsinki, Finland.,NDBio Therapeutics Inc., Incheon 21984, Republic of Korea.,Department of Biochemistry, Vanderbilt University, Nashville, TN, 37232-2372, USA.,Department of Pediatrics and Human Development, Michigan State University, Grand Rapids, Michigan.,Molecular and Cell Biology Graduate Program, University of California, Berkeley, CA 94720.,UMR Ecologie Microbienne, CNRS, INRA, VetAgro Sup, UCBL, Université de Lyon, F-69622 Villeurbanne, Lyon, France.,Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02115, USA; Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA; Blais Proteomics Center, Dana-Farber Cancer Institute, Boston, MA 02115, USA.,Infection and Immunity Program and Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria, 3800, Australia. Jamie.rossjohn@monash.edu.,Chemistry Research Laboratory, University of Oxford, Oxford, UK, christopher.schofield@chem.ox.ac.uk.,Department of Chemistry, University of Duisburg-Essen , Universitätstr. 7, 45141 Essen, Germany.,Center for Structural Biology, Vanderbilt University Medical Center, Nashville, TN, 37232-2372, USA.,2Department of Biochemistry, University of Toronto, Toronto, M5S 1A8 ON Canada.,Department of Microbiology, Immunology, & Molecular Genetics, University of California Los Angeles, Los Angeles, CA 90095, USA.,Institute of Pharmaceutical Chemistry, Goethe-University Frankfurt, Max von Lauestr. 9, 60438 Frankfurt am Main, Germany; Buchmann Institute for Life Sciences (BMLS) and Structural Genomics Consortium Goethe-University Frankfurt, Max von Lauestr. 9, 60438 Frankfurt am Main, Germany; German Cancer Network (DKTK), Frankfurt Site, 60438 Frankfurt am Main, Germany.,Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, VIC 3052, Australia; Department of Medical Biology, The University of Melbourne, Melbourne, VIC 3052, Australia. Electronic address: pcolman@wehi.edu.au.,Department of Infectious Diseases, Genentech, South San Francisco, CA, USA.,Hospital for Sick Children, Toronto, Ontario, Canada.,Research Complex at Harwell (RCaH), Rutherford Appleton Laboratory, Harwell Science and Innovation Campus, Didcot, Oxford, OX11 OFA, UK.,Molecular Biophysics Unit, Indian Institute of Science, Bangalore, India.,University of Cape Town, Anzio Road, Observatory, Cape Town, 7945, South Africa.,Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, CA, USA. kobilka@stanford.edu.,Institut de Biologie Structurale, CNRS, CEA, UGA, 30044, Grenoble, France.,Institut de Chimie des Substances Naturelles, CNRS, Avenue de la Terrasse, 91198 Gif-sur-Yvette, France.,From the Division of Immune Regulation, La Jolla Institute for Allergy and Immunology (LJI), La Jolla, California 92037.,Center for Matrix Biology, Vanderbilt University Medical Center, Nashville, TN, 37232-2372, USA.,Département de biochimie, de microbiologie, et de bioinformatique, Faculté des sciences et de génie, Groupe de recherche en écologie buccale, Faculté de médecine dentaire, Université Laval, Québec City, QC, G1V 0A6, Canada. sylvain.moineau@bcm.ulaval.ca.,Univ. Lyon, ENS de Lyon, Univ. Claude Bernard, CNRS UMR 5239, INSERM U1210, LBMC, 46 allée d'Italie Site Jacques Monod, F-69007, Lyon, France.,Department of Microbiology, UT Southwestern Medical Center, Dallas, TX 75390.,Institut für Pharmazeutische und Medizinische Chemie, PharmaCampus, Westfälische Wilhelms-Universität Münster, Corrensstraße 48, D-48149 Münster, Germany. joachim.jose@uni-muenster.de.,Department of Biochemistry, UT Southwestern Medical Center, Dallas, TX 75390.,Leicester Institute of Structural and Chemical Biology, University of Leicester, Lancaster Road, Leicester, LE1 7RH, UK. ivan.campeotto@leicester.ac.uk.,Laboratory of Molecular Modeling and Design, State Key Laboratory of Molecular Reaction Dynamics, Dalian Institute of Chemical Physics, Chinese Academy of Science, Dalian, Liaoning, China.,School of Sports Sciences, Central University of Rajasthan, Rajasthan, India.,HudsonAlpha Institute for Biotechnology, Huntsville, Alabama; jprokop54@gmail.com jlazar@hudsonalpha.org.,From the Avram and Stella Goldstein-Goren Department of Biotechnology Engineering and the National Institute of Biotechnology in the Negev, Ben-Gurion University of the Negev, Beer-Sheva 84105, Israel, papo@bgu.ac.il.,National Magnetic Resonance Facility at Madison , University of Wisconsin-Madison , 433 Babcock Drive , Madison , Wisconsin 53706 , United States.,Department of Biomedical Engineering and Institute for Complex Molecular Systems, Eindhoven University of Technology, Eindhoven, The Netherlands.,Department of Immunology and Microbial Science, The Scripps Research Institute, La Jolla, CA 92037, USA; IAVI Neutralizing Antibody Center and Collaboration of AIDS Vaccine Discovery, The Scripps Research Institute, La Jolla, CA 92037, USA.,Gene Expression & Regulation Program, Wistar Institute, Philadelphia, Pennsylvania.,Medizinische Biochemie und Molekularbiologie, Universität des Saarlandes, Kirrberger Str., Geb. 44, D-66421 Homburg, Germany. claudia.goetz@uks.eu.,Center for Structural Biology, Vanderbilt University Medical Center, Nashville, TN, 37232-2372, USA. kyle.l.brown@vanderbilt.edu.,FLX Bio, South San Francisco, CA, USA.,HRMEM Facility, University of British Columbia, Vancouver, BC, Canada.,Systems Immunity Research Institute, Cardiff University, Cardiff, Wales, United Kingdom.,the Department of Internal Medicine, Faculty of Medicine and Health Sciences, Ghent University, 9000 Ghent, Belgium.,Boehringer Ingelheim RCV GmbH & Co KG , 1221 Vienna , Austria.,Broad Institute of Harvard and MIT, Cambridge, MA, USA.,Centre de RMN à Très Hauts Champs, Institut des Sciences Analytiques (UMR 5280 CNRS/UCB Lyon 1/ENS Lyon), Université de Lyon, 69100, Villeurbanne, France.,Department of Discovery Chemistry, Genentech, South San Francisco, CA, USA.,Section on Nephrology, Department of Internal Medicine, Wake Forest School of Medicine, Winston-Salem, North Carolina; and.,Immunology Division, Garvan Institute of Medical Research, 384 Victoria Road, Darlinghurst, Sydney, NSW, 2010, Australia.,Faculty of Advanced Life Science, Hokkaido University, N-10, W-8, Sapporo 060-0810, Japan.,Michael Smith Laboratories, University of British Columbia, 2185 East Mall, Vancouver, BC V6T 1Z4, Canada.,Aduro Biotech, Berkeley, CA, USA.,School of Biochemistry, University of Bristol, Bristol, United Kingdom.,Institut für Pharmazeutische und Medizinische Chemie, PharmaCampus, Westfälische Wilhelms-Universität Münster, Corrensstraße 48, D-48149 Münster, Germany. andre.bo@web.de.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
14-3-3 protein zeta/delta
A, B
230Homo sapiensMutation(s): 0 
Gene Names: YWHAZ
Find proteins for P63104 (Homo sapiens)
Go to Gene View: YWHAZ
Go to UniProtKB:  P63104
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
GLN-GLY-MKD-ANG-ASP-MKD-LEU-ASP-LEU-ALA-CLU
D, E
11N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
BEZ
Query on BEZ

Download SDF File 
Download CCD File 
A, B
BENZOIC ACID
C7 H6 O2
WPYMKLBDIGXBTP-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  3 Unique
IDChainsTypeFormula2D DiagramParent
6L9
Query on 6L9
D, E
NON-POLYMERC6 H10 N2 O5

--

A1G
Query on A1G
D, E
NON-POLYMERC12 H19 N O2

--

MKD
Query on MKD
D, E
L-PEPTIDE LINKINGC9 H19 N O2

--

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.34 Å
  • R-Value Free: 0.244 
  • R-Value Work: 0.198 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 84.920α = 90.00
b = 105.740β = 90.00
c = 113.930γ = 90.00
Software Package:
Software NamePurpose
XDSdata reduction
PHASERphasing
XSCALEdata scaling
PDB_EXTRACTdata extraction
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Emmy Noether programGermanyGR3592/2-1
German Research FoundationGermanySFB1093

Revision History 

  • Version 1.0: 2017-05-10
    Type: Initial release
  • Version 1.1: 2018-10-24
    Type: Author supporting evidence, Data collection, Database references
  • Version 1.2: 2018-12-19
    Type: Data collection, Derived calculations