6MX3

Crystal structure of human STING (G230A, H232R, R293Q) in complex with Compound 1


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.362 Å
  • R-Value Free: 0.202 
  • R-Value Work: 0.188 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Discovery of a Novel cGAMP Competitive Ligand of the Inactive Form of STING.

Siu, T.Altman, M.D.Baltus, G.A.Childers, M.Ellis, J.M.Gunaydin, H.Hatch, H.Ho, T.Jewell, J.Lacey, B.M.Lesburg, C.A.Pan, B.S.Sauvagnat, B.Schroeder, G.K.Xu, S.

(2019) ACS Med Chem Lett 10: 92-97

  • DOI: 10.1021/acsmedchemlett.8b00466
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Drugging large protein pockets is a challenge due to the need for higher molecular weight ligands, which generally possess undesirable physicochemical properties. In this communication, we highlight a strategy leveraging small molecule active site di ...

    Drugging large protein pockets is a challenge due to the need for higher molecular weight ligands, which generally possess undesirable physicochemical properties. In this communication, we highlight a strategy leveraging small molecule active site dimers to inhibit the large symmetric binding pocket in the STING protein. By taking advantage of the 2:1 binding stoichiometry, maximal buried interaction with STING protein can be achieved while maintaining the ligand physicochemical properties necessary for oral exposure. This mode of binding requires unique considerations for potency optimization including simultaneous optimization of protein-ligand as well as ligand-ligand interactions. Successful implementation of this strategy led to the identification of 18 , which exhibits good oral exposure, slow binding kinetics, and functional inhibition of STING-mediated cytokine release.


    Organizational Affiliation

    Institut für Medizinische und Pharmazeutische Chemie, Technische Universität Braunschweig, Braunschweig, Germany.,Division of Life Science, State Key Laboratory of Molecular Neuroscience, Hong Kong University of Science and Technology, Hong Kong, China.,the Norwegian College of Fisheries Science, Arctic University of Norway, N-9037 Tromsø, Norway, and.,Department of Microbiology and Immunology, College of Veterinary Medicine, China Agricultural University, Beijing, China.,Department of Structural Biochemistry, Max Planck Institute of Molecular Physiology, Dortmund, Germany.,Shenzhen Key Laboratory for Neuronal Structural Biology, Biomedical Research Institute, Shenzhen Peking University-The Hong Kong University of Science and Technology Medical Center, Shenzhen, China.,Department of Biophysics, School of Basic Medical Sciences, Peking University Health Science Center, Beijing 100191, China; Institute of Systems Biomedicine, School of Basic Medical Sciences, Peking University Health Science Center, Beijing 100191, China; Beijing Key Laboratory of Tumor Systems Biology, Peking University Health Science Center, Beijing 100191, China.,Key Laboratory of Animal Epidemiology of the Ministry of Agriculture, Haidian District, Beijing, China.,Laboratório de Espectrometria de Massa, Embrapa Recursos Genéticos e Biotecnologia, Brasília, Distrito Federal, Brazil. Electronic address: carlos.bloch@embrapa.br.,Institut de Recherches Microbiologiques Jean-Marie Wiame - Labiris, 1070 Brussels, Belgium.,Gorlaeus Laboratories , Leiden Institute of Chemistry and Netherlands Proteomics Centre , Einsteinweg 55 , 2333 CC Leiden , Netherlands.,Department of Molecular and Systems Biology and Norris Cotton Cancer Center , Geisel School of Medicine at Dartmouth , 1 Medical Centre Drive HB7936 , Lebanon , New Hampshire 03756 , United States.,Center of Pharmaceutical Engeneering (PVZ), Technische Universität Braunschweig, Braunschweig, Germany.,Department of Biochemistry, School of Medicine, Case Western Reserve University, Cleveland, OH, 44106, USA.,Institute of Molecular Biology & Biophysics, ETH Zurich, 8093, Zurich, Switzerland. allain@mol.biol.ethz.ch.,Collaborative Innovation Center of New Drug Research and Safety Evaluation, Zhengzhou University, Zhengzhou 450001, China.,Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York 14853, USA.,Center for Plant Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China.,Biomedical Research Institute, Korea Institute of Science and Technology, Seoul, 02792, Republic of Korea. Electronic address: eunice@kist.re.kr.,College of Life Sciences, Peking University, Beijing 100871, China.,Department of Biochemistry and Molecular Medicine, Université de Montréal, Montréal, QC, H3C 3J7, Canada.,School of Biological Sciences, Seoul National University, Seoul, Republic of Korea.,RIKEN Center for Biosystems Dynamics Research, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama 230-0045, Japan.,VIB-VUB Center For Structural Biology, 1050 Brussels, Belgium.,College of Chemistry and Molecular Engineering, Zhengzhou University, Zhengzhou 450001, China.,Department of Biochemistry and the Emory Comprehensive Glycomics Core, Emory University School of Medicine, Atlanta, GA, 30322, USA.,Institute of Biochemistry, University of Cologne, 50674 Koeln, Germany.,Center for RNA Research, Institute for Basic Science, Seoul, Republic of Korea.,ManRos Therapeutics, Hôtel de Recherche, Centre de Perharidy, Roscoff, France.,Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario, Canada.,Olema Pharmaceuticals, San Francisco, CA, 94107, USA. leslie@olemapharma.com.,Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX, 77030, USA.,RIKEN Center for Biosystems Dynamics Research, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama 230-0045, Japan. kurumizaka@iam.u-tokyo.ac.jp shunichi.sekine@riken.jp.,Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104-6059, USA. blackbe@pennmedicine.upenn.edu.,Center for Integrated Protein Science at the Department Chemie, Lehrstuhl für Biochemie , Technische Universität München , 85748 Garching , Germany.,Hefei National Laboratory for Physical Sciences at the Microscale and School of Life Sciences, University of Science and Technology of China, Hefei Anhui, China.,Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario, Canada. jwhitney@mcmaster.ca.,Tetramer Core, BRI at Virginia Mason, Seattle, WA, USA.,Translational Research Program, BRI at Virginia Mason, Seattle, WA, USA.,Department of Pharmacology, Baylor College of Medicine, Houston, TX, 77030, USA.,Department of Chemistry , University of Florence , Via della Lastruccia 3 , 50019 Sesto Fiorentino, Florence , Italy.,Photosynthesis Research Center, Key Laboratory of Photobiology, Institute of Botany, Chinese Academy of Sciences, Beijing, China. kuangty@ibcas.ac.cn.,Molecular Biophysics and Integrated Bioimaging, Berkeley Center for Structural Biology, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA.,Structural Biology Group, European Synchrotron Radiation Facility, CS 40220, F-38043, Grenoble, France. christoph.mueller_dieckmann@esrf.fr.,Laboratoire de Microbiologie, Université libre de Bruxelles (ULB), 6041 Gosselies, Belgium.,Departamento de Química, Universidade Federal de São Carlos (UFSCar), São Carlos, São Paulo, Brazil.,Instituto de Química, Universidade de Brasília (UnB), Brasília, Distrito Federal, Brazil; Instituto de Biociências, Universidade Federal do Estado do Rio de Janeiro (UNIRIO), Rio de Janeiro, Rio de Janeiro, Brazil.,Institute of Molecular Biology & Biophysics, ETH Zurich, 8093, Zurich, Switzerland.,Division of Structural Biology, Department of Pharmaceutical Sciences, School of Pharmacy, Iwate Medical University, Yahaba, Japan.,Ben May Department for Cancer Research, University of Chicago, Chicago, IL, 60637, USA. sfanning@uchicago.edu.,Department of Structural Biochemistry, Max Planck Institute of Molecular Physiology, Dortmund, Germany. stefan.raunser@mpi-dortmund.mpg.de.,Faculty of Science, University of Zurich, Zurich, 8057, Switzerland.,Department of Plant Science, Rothamsted Research, Harpenden, Herts AL5 2JQ, United Kingdom.,Department of Chemical Biology and Therapeutics, St. Jude Children's Research Hospital, Memphis, Tennessee, USA.,Olema Pharmaceuticals, San Francisco, CA, 94107, USA.,Key Laboratory for Insect-Pollinator Biology of the Ministry of Agriculture, Institute of Apiculture, Chinese Academy of Agricultural Sciences, Beijing, China.,Astex Pharmaceuticals , 436 Cambridge Science Park , Cambridge , CB4 0QA , UK . Email: honorine.lebraud@astx.com ; Email: tom.heightman@astx.com.,Pohang Accelerator Laboratory, Pohang University of Science and Technology, Pohang, Republic of Korea ygkim76@postech.ac.kr.,Innovation Center for Structural Biology, Tsinghua-Peking Joint Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing 100084, China.,Hefei National Laboratory for Physical Sciences at Microscale,CAS Key Laboratory of Brain Function and Disease, Neurodegenerative Disorder Research Center, School of Life Sciences, University of Science and Technology of China, Hefei, China.,Structural Biology Group, European Synchrotron Radiation Facility, CS 40220, F-38043, Grenoble, France.,Department of Structural Biology, Weizmann Institute of Science, Rehovot, 7610001, Israel.,Pohang Accelerator Laboratory, Pohang University of Science and Technology, Pohang, Kyungbuk, 37673, Republic of Korea.,Takeda California, Inc. , 10410 Science Center Drive , San Diego , California 92121 , United States.,Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, 77030, USA. vprasad@bcm.edu.,Biomedical Research Institute, Korea Institute of Science and Technology, Seoul, 02792, Republic of Korea.,Howard Hughes Medical Institute, Seattle, WA, USA.,Université de Lorraine, INRA, IAM, Nancy, France. eric.gelhaye@univ-lorraine.fr.,Department of Chemistry, University of Duisburg-Essen, Universitätsstr. 7, 45117, Essen, Germany.,Department of Physiology and Biophysics, School of Medicine, Case Western Reserve University, Cleveland, OH, 44106, USA.,Ben May Department for Cancer Research, University of Chicago, Chicago, IL, 60637, USA.,Department of Biochemistry, School of Medicine, Case Western Reserve University, Cleveland, OH, 44106, USA. qinj@ccf.org.,Department of Oncology-Pathology , Karolinska Institute , CCK R8:01 , Karolinska Hospital , 171 76 Stockholm , Sweden.,Department of Biochemistry and Molecular Medicine, Université de Montréal, Montréal, QC, H3C 3J7, Canada. john.pascal@umontreal.ca.,High Pressure and Synchrotron Radiation Physics Division, Bhabha Atomic Research Center, Mumbai 400 085, India.,International Institute of Molecular and Cell Biology in Warsaw, Warsaw, Poland.,Departments of Chemistry, Immunology, Chemistry Modeling and Informatics, In Vitro Pharmacology, Target Protein Design and Structural Chemistry, Merck & Co., Inc., 33 Avenue Louis Pasteur, Boston, Massachusetts 02115, United States.,Department of Molecular Cardiology, Lerner Research Institute, Cleveland Clinic, 9500 Euclid Avenue, Cleveland, OH, 44195, USA. qinj@ccf.org.,Graduate School of Innovative Life Science , University of Toyama , 2630 Sugitani , Toyama 930-0194 , Japan.,Institute for Interdisciplinary Science, Okayama University, Okayama, Japan.,Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University, Poznan, Poland.,Department of Biophysics, School of Basic Medical Sciences, Peking University Health Science Center, Beijing 100191, China; Institute of Systems Biomedicine, School of Basic Medical Sciences, Peking University Health Science Center, Beijing 100191, China; Beijing Key Laboratory of Tumor Systems Biology, Peking University Health Science Center, Beijing 100191, China. Electronic address: yunch@hsc.pku.edu.cn.,Department of Neuroscience, College of Veterinary Medicine, Research Institute for Veterinary Science, and BK21 PLUS Program for Creative Veterinary Science Research, Seoul National University, Seoul, 08826, Republic of Korea. Electronic address: ehur1@snu.ac.kr.,Arietis Pharma, Boston, Massachusetts, USA m.lafleur@arietiscorp.com.,Department of Molecular Cardiology, Lerner Research Institute, Cleveland Clinic, 9500 Euclid Avenue, Cleveland, OH, 44195, USA.,the Department of Biosciences, University of Oslo, P.O. Box 1066, Blindern, N-0316 Oslo, Norway.,Rheumatology Unit, Department of Medicine Solna, Center for Molecular Medicine, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden.,Laboratory of Chromatin Structure and Function, Institute for Quantitative Biosciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-0032, Japan.,Laboratory of Chromatin Structure and Function, Institute for Quantitative Biosciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-0032, Japan. kurumizaka@iam.u-tokyo.ac.jp shunichi.sekine@riken.jp.,Department of Chemistry, Université de Montréal, Montréal, QC, H3C 3J7, Canada.,Department of Biology, York University, Toronto, Ontario M3J 1P3, Canada.,Computational Biochemistry, Zentrum für Medizinische Biotechnologie, Fakultät für Biologie, Universität Duisburg-Essen, Universitätsstr. 2, 45117, Essen, Germany.,Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104-6059, USA.,Université de Lorraine, CNRS, CRM2, Nancy, France. claude.didierjean@univ-lorraine.fr.,Science for Life Laboratory, Department of Medicine Solna, Karolinska Institutet, Sweden; Department of Infectious Diseases, Karolinska University Hospital, Stockholm, Sweden.,Department of Cell Biochemistry, University of Groningen, Groningen 9747 AG, Netherlands.,DISFARM, Dipartimento di Scienze Farmaceutiche, Sezione Chimica Generale e Organica, Università degli Studi, Milano, Italy.,Université de Lorraine, INRA, IAM, Nancy, France.,Department of Microbiology, School of Dentistry, Aichi Gakuin University, Nagoya, Japan.,Michael DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, Ontario, Canada. jwhitney@mcmaster.ca.,Photosynthesis Research Center, Key Laboratory of Photobiology, Institute of Botany, Chinese Academy of Sciences, Beijing, China.,State Key Laboratory of Membrane Biology, Beijing Advanced Innovation Center for Structural Biology, School of Life Sciences, Tsinghua University, Beijing, China. suisf@mail.tsinghua.edu.cn.,Institute of Medical Microbiology, University of Zurich, 8006, Zurich, Switzerland.,Structural Biology Brussels, Vrije Universiteit Brussel, 1050 Brussels, Belgium.,Institute of Biochemistry, ETH Zurich, 8093, Zurich, Switzerland.,Max-Planck Institute for Plant Breeding Research, 50829 Cologne, Germany.,Biochemistry, Cellular, and Molecular Biology, University of Tennessee, Knoxville, Tennessee 37996, USA.,Institute for Pharmaceutical Chemistry, Structural Genomics Consortium and Buchmann Institute for Molecular Life Sciences, Johann Wolfgang Goethe-University, Frankfurt am Main, Germany.,State Key Laboratory of Membrane Biology, Beijing Advanced Innovation Center for Structural Biology, School of Life Sciences, Tsinghua University, Beijing, China.,Pfizer Worldwide Research & Development , 610 Main Street, Cambridge, Massachusetts 02139, United States.,Abteilung Physikalische Biochemie, Max-Planck-Institut für molekulare Physiologie, Dortmund, Germany.,Institute of Molecular Systems Biology, ETH Zurich, 8093, Zurich, Switzerland.,Institute for Advanced Study, Hong Kong University of Science and Technology, Hong Kong, China.,Instituto de Química, Universidade de Brasília (UnB), Brasília, Distrito Federal, Brazil; Departamento de Áreas Acadêmicas, Instituto Federal de Educação, Ciência e Tecnologia e Goiás (IFG), Luziânia, Goiás, Brazil.,Rheumatology Unit, Department of Medicine Solna, Center for Molecular Medicine, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden. Electronic address: Vivianne.malmstrom@ki.se.,Department of Biochemistry, University of Zurich, 8057, Zurich, Switzerland.,Department of Microbiology and Immunology, College of Veterinary Medicine, China Agricultural University, Beijing, China zhangnianzhi@cau.edu.cn xiachun@cau.edu.cn.,Chemical Biology, Zentrum für Medizinische Biotechnologie, Fakultät für Biologie, Universität Duisburg-Essen, Universitätsstr. 2, 45117, Essen, Germany.,Graduate School of Advanced Science and Engineering, Waseda University, 2-2 Wakamatsu-cho, Shinjuku-ku, Tokyo 162-8480, Japan.,State Key Laboratory of Bioorganic and Natural Products Chemistry, Center for Excellence in Molecular Synthesis, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, 345 Lingling Road, Shanghai, 200032, China.,Convergence Research Center for Diagnosis, Treatment and Care System of Dementia, Korea Institute of Science and Technology, Seoul, Republic of Korea.,From the Department of Cell and Molecular Biology, Uppsala University, Box 596, S-751 24 Uppsala, Sweden, inger.andersson@icm.uu.se.,From the Department of Cell and Molecular Biology, Uppsala University, Box 596, S-751 24 Uppsala, Sweden.,Max Planck Institute for Evolutionary Anthropology, D-04103, Leipzig, Germany.,Brain Science Institute, Korea Institute of Science and Technology, Seoul, 02792, Republic of Korea; Department of Neuroscience, Korea University of Science and Technology, Daejeon, Republic of Korea; Department of Neuroscience, College of Veterinary Medicine, Research Institute for Veterinary Science, and BK21 PLUS Program for Creative Veterinary Science Research, Seoul National University, Seoul, 08826, Republic of Korea.,Pohang Accelerator Laboratory, Pohang University of Science and Technology, Pohang, Republic of Korea.,Laboratory of Chemical Biology and Institute of, Complex Molecular Systems, Department of Biomedical Engineering, Eindhoven University of Technology, Den Dolech 2, 5612, AZ, Eindhoven, The Netherlands.,Department of Microbiology, University of Washington, Seattle, WA, USA.,Neuroscience Drug Discovery Unit, Research , Takeda Pharmaceutical Company Limited , 26-1, Muraoka-Higashi 2-chome, Fujisawa , Kanagawa 251-8555 , Japan.,Université de Lorraine, LERMAB, Nancy, France.,Michael DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, Ontario, Canada.,Magnetic Resonance Center CERM , University of Florence , Via Luigi Sacconi 6 , 50019 Sesto Fiorentino, Florence , Italy.,Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX, 77030, USA. vprasad@bcm.edu.,Discipline of Biosciences and Biomedical Engineering, Indian Institute of Technology Indore, Indore 453 552, India.,Structural Genomics Consortium, Nuffield Department of Medicine, Oxford University, Oxford, United Kingdom.,Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw, Poland.,The Francis Crick Institute, London, NW1 1AT, United Kingdom.,Arietis Pharma, Boston, Massachusetts, USA.,Rheumatology Unit, Department of Medicine Solna, Center for Molecular Medicine, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden; Science for Life Laboratory, Department of Medicine Solna, Karolinska Institutet, Sweden; Department of Infectious Diseases, Karolinska University Hospital, Stockholm, Sweden.,Department of Hematology and Oncology , Kantonsspital St. Gallen , 9007 St. Gallen , Switzerland.,Department of Biochemical Sciences A.Rossi-Fanelli, University of Rome La Sapienza, Rome, Italy.,Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, 77030, USA.,Department of Medical Sciences, Rheumatology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden.,Université de Lorraine, CNRS, CRM2, Nancy, France.,Department of Medicine, Baylor College of Medicine, Houston, TX, 77030, USA.,Faculty of Pharmaceutical Sciences , University of Toyama , 2630 Sugitani , Toyama 930-0914 , Japan.,Department of Systems Biology, Harvard Medical School, Boston, MA, 02115, USA.,Laboratório de Espectrometria de Massa, Embrapa Recursos Genéticos e Biotecnologia, Brasília, Distrito Federal, Brazil.,Institute of Medical Microbiology, University of Zurich, 8006, Zurich, Switzerland. vpanse@imm.uzh.ch.,School of Biological Science and Technology, University of Jinan, Jinan, China.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Stimulator of interferon genes protein
A, B
188Homo sapiensMutation(s): 3 
Gene Names: TMEM173 (ERIS, MITA, STING)
Find proteins for Q86WV6 (Homo sapiens)
Go to Gene View: TMEM173
Go to UniProtKB:  Q86WV6
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CA
Query on CA

Download SDF File 
Download CCD File 
B
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
K5P
Query on K5P

Download SDF File 
Download CCD File 
A, B
(3S,4S)-2-(4-tert-butylphenyl)-3-(4-methoxyphenyl)-1-oxo-1,2,3,4-tetrahydroisoquinoline-4-carboxylic acid
C27 H27 N O4
VLZBEPGIJKIYGT-BJKOFHAPSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.362 Å
  • R-Value Free: 0.202 
  • R-Value Work: 0.188 
  • Space Group: C 2 2 21
Unit Cell:
Length (Å)Angle (°)
a = 70.200α = 90.00
b = 77.710β = 90.00
c = 125.410γ = 90.00
Software Package:
Software NamePurpose
Aimlessdata scaling
BUSTERrefinement
BUSTERphasing
PDB_EXTRACTdata extraction
XDSdata processing
AutoPROCdata processing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2018-12-19
    Type: Initial release
  • Version 1.1: 2019-01-30
    Type: Data collection, Database references