5YCP

Human PPARgamma ligand binding domain complexed with Rosiglitazone


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.233 
  • R-Value Work: 0.201 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Structural Basis for the Enhanced Anti-Diabetic Efficacy of Lobeglitazone on PPAR gamma.

Jang, J.Y.Bae, H.Lee, Y.J.Choi, Y.I.Kim, H.J.Park, S.B.Suh, S.W.Kim, S.W.Han, B.W.

(2018) Sci Rep 8: 31-31

  • DOI: 10.1038/s41598-017-18274-1
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Peroxisome proliferator-activated receptor γ (PPARγ) is a member of the nuclear receptor superfamily. It functions as a ligand-activated transcription factor and plays important roles in the regulation of adipocyte differentiation, insulin resistance ...

    Peroxisome proliferator-activated receptor γ (PPARγ) is a member of the nuclear receptor superfamily. It functions as a ligand-activated transcription factor and plays important roles in the regulation of adipocyte differentiation, insulin resistance, and inflammation. Here, we report the crystal structures of PPARγ in complex with lobeglitazone, a novel PPARγ agonist, and with rosiglitazone for comparison. The thiazolidinedione (TZD) moiety of lobeglitazone occupies the canonical ligand-binding pocket near the activation function-2 (AF-2) helix (i.e., helix H12) in ligand-binding domain as the TZD moiety of rosiglitazone does. However, the elongated p-methoxyphenol moiety of lobeglitazone interacts with the hydrophobic pocket near the alternate binding site of PPARγ. The extended interaction of lobeglitazone with the hydrophobic pocket enhances its binding affinity and could affect the cyclin-dependent kinase 5 (Cdk5)-mediated phosphorylation of PPARγ at Ser245 (in PPARγ1 numbering; Ser273 in PPARγ2 numbering). Lobeglitazone inhibited the phosphorylation of PPARγ at Ser245 in a dose-dependent manner and exhibited a better inhibitory effect on Ser245 phosphorylation than rosiglitazone did. Our study provides new structural insights into the PPARγ regulation by TZD drugs and could be useful for the discovery of new PPARγ ligands as an anti-diabetic drug, minimizing known side effects.


    Organizational Affiliation

    Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, ON, M5G 1L6, Canada.,Microbiology and Biotechnology, Biocenter Klein Flottbek, Ohnhorststr. 18, 22609 Hamburg, Germany.,a State Key Laboratory of Bioorganic and Natural Products Chemistry , Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences , Shanghai , China.,Department of Chemistry, Grand Valley State University , Allendale, Michigan 49401, United States.,Department of Chemistry, University of Copenhagen, Universitetsparken 5, Copenhagen, DK-2100, Denmark.,Division of Biology and Biological Engineering, California Institute of Technology, 1200 E. California Boulevard, Pasadena, CA 91125, USA. Electronic address: bjorkman@caltech.edu.,University of Florence , Department of Chemistry "Ugo Schiff" , Via della Lastruccia 3 , 50019 Sesto Fiorentino ( Florence ), Italy.,Department of Biochemistry, Schulich School of Medicine and Dentistry, Western University, London, ON, N6A 5C1, Canada.,From the Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai 201800 and hejianhua@sinap.ac.cn.,Department of Drug Design and Pharmacology, University of Copenhagen, 2100 Copenhagen, Denmark.,Howard Hughes Medical Institute, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA.,Department of Chemistry, College of Natural Sciences, Seoul National University, Seoul, 08826, Republic of Korea.,Department of Chemistry and Biochemistry, 103 Chemistry and Biochemistry Building, Montana State University, Bozeman, MT, 59717, USA.,CKD Research Institute, Chong Kun Dang Pharmaceutical Corporation, Yongin, 16995, Republic of Korea.,Shandong Provincial Key Laboratory of Synthetic Biology and CAS Key Laboratory of Biofuels, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Songling Road 189, Qingdao, Shandong 266101, China. cuiqiu@qibebt.ac.cn fengyg@qibebt.ac.cn.,JAN Scientific Inc., Seattle, WA 98105.,Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, Victoria, 3086, Australia.,Department of Pathophysiology, Key Laboratory of Cell Differentiation and Apoptosis of Ministry of Education, Shanghai Jiao-Tong University School of Medicine, Shanghai, China.,Shanghai Key Laboratory of New Drug Design, School of Pharmacy, East China University of Science and Technology, Shanghai, China.,Department of Chemistry and Biochemistry , New Mexico State University , Las Cruces , New Mexico 88003 , United States.,Medicinal Bioinformatics Center, Shanghai Jiao-Tong University School of Medicine, Shanghai, China.,Department of Pharmacology and Chemical Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA 15260.,Beijing Advanced Innovation Center for Structural Biology, Tsinghua-Peking Joint Center for Life Sciences, School of Life Sciences and School of Medicine, Tsinghua University, Beijing 100084, China; Technology Center for Protein Sciences, Ministry of Education Key Laboratory of Protein Sciences, School of Life Sciences, Tsinghua University, Beijing 100084, China.,the Department of Microbiology, University of Washington School of Medicine, Seattle, Washington 98195.,Chan Zuckerberg Biohub, San Francisco, CA, 94158, USA.,Institute of Health Sciences, Shanghai Institutes for Biological Sciences of Chinese Academy of Sciences and Shanghai Jiao-Tong University School of Medicine, Shanghai, China.,Molecular Biology of Microbial Consortia, University of Hamburg, Biocenter Klein Flottbek, Ohnhorststr. 18, 22609, Hamburg, Germany.,Departamento de Microbiología Molecular, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Mexico.,Laboratorio de Estructura Biomolecular, Centro de Investigación en Alimentación y Desarrollo, A.C., Hermosillo, Mexico.,Department of Chemistry and Biochemistry, 3210 N Cramer St, University of Wisconsin-Milwaukee, Milwaukee, WI, 53211, USA.,CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China; Savaid Medical School, University of Chinese Academy of Sciences, Beijing 100049, China. Electronic address: jxqi@im.ac.cn.,From the Department of Biochemistry.,Children's Health Research Institute, Lawson Health Research Institute, 800 Commissioner's Road East, London, ON, N6C 2V5, Canada. sli@uwo.ca.,College of Pharmacy, Chung-Ang University, Seoul, 06974, Republic of Korea.,College of Pharmacy, Pusan National University, Busandaehak-ro, Pusan 46241, Republic of Korea.,Department of Integrative Structural and Computational Biology, Scripps Research Institute, La Jolla, CA, USA. Electronic address: glander@scripps.edu.,State Key Laboratory of High Performance Ceramics and Superfine Microstructure, Shanghai Institute of Ceramics, Chinese Academy of Sciences, Shanghai, China.,CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China.,Department of Chemistry, University of Copenhagen, Universitetsparken 5, Copenhagen, DK-2100, Denmark. Electronic address: leila@chem.ku.dk.,Laboratorio Nacional de Genómica para la Biodiversidad, Centro de Investigación y de Estudios Avanzados del IPN, Guanajuato, Mexico.,Department of Microbiology and Immunology, Montana State University, Bozeman, MT 59717, USA. Electronic address: bwiedenheft@gmail.com.,Department of Pharmacology and Therapeutics, McGill University, Montréal, QC H3G 1Y6, Canada.,CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China; Savaid Medical School, University of Chinese Academy of Sciences, Beijing 100049, China.,the Polymer Chemistry Group, Research Institute for Sustainable Chemistry, AIST, 1-1-1 Higashi, Tsukuba, Ibaraki 305-8565, Japan, and.,Department of Cell and Molecular Biology, Grand Valley State University , Allendale, Michigan 49401, United States.,Department of Biochemistry and Biophysics, Stockholm University, SE-106 91 Stockholm, Sweden. Electronic address: stenmark@dbb.su.se.,Novozymes A/S, Krogshoejvej 36, 2880, Bagsvaerd, Denmark.,Istituto di Biofisica , Consiglio Nazionale delle Ricerche , 56124 Pisa , Italy.,Department of Agricultural Biotechnology, Seoul National University, 1 Gwanak-ro, Seoul 08826, Republic of Korea.,Department of Microbiology, Immunology, and Biochemistry, University of Tennessee Health Science Center, Memphis, TN, United States.,d Department of Cell Biology , Harvard Medical School , Boston , MA , USA.,Center for Biophysics and Computational Biology, University of Illinois at Urbana Champaign, Urbana, Illinois 61801 and.,CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China.,Department of Chemistry and Biochemistry, 1068 W Sheridan Rd, Loyola University Chicago, Chicago, IL, 60660, USA.,Department of Molecular Biosciences, 1200 Sunnyside Ave, University of Kansas, Lawrence, KS, 66045, USA. Electronic address: lamb@ku.edu.,Structural Molecular Biology, Stanford Synchroton Radiation Lightsource, SLAC National Accelerator Laboratory, Stanford University, Menlo Park, CA 94025.,Laboratorio de Investigación Bioquímica, Programa Institucional en Biomedicina Molecular ENMyH-IPN, Ciudad de México, Mexico.,Integrated Program in Neuroscience, McGill University, Montréal, QC H3A 2B4, Canada; Department of Pharmacology and Therapeutics, McGill University, Montréal, QC H3G 1Y6, Canada.,the Bio-based Materials Chemistry Group, Research Institute for Sustainable Chemistry, National Institute of Advanced Industrial Science and Technology (AIST), 3-11-32 Kagamiyama, Higashi-Hiroshima, Hiroshima 739-0046, Japan.,the Graduate School of Advanced Sciences of Matter, Hiroshima University, 1-3-1 Kagamiyama, Higashi-Hiroshima, Hiroshima 739-8530, Japan.,Department of Pharmacology, University of Cambridge, Cambridge CB2 1PD, UK.,Graduate Program in Biophysics, Harvard University, Cambridge, MA, 02138, USA.,Department of Integrative Structural and Computational Biology, Scripps Research Institute, La Jolla, CA, USA.,Department of Structural Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA 15260; acohen@slac.stanford.edu guc9@pitt.edu.,Department of Chemistry, University of California Berkeley, Berkeley, CA, 94720, USA.,Dipartimento di Scienze Chimiche , Università degli Studi di Padova and Istituto di Chimica Biomolecolare, Consiglio Nazionale delle Ricerche , 35131 Padua , Italy.,Istituto Nazionale Biostrutture e Biosistemi , 00136 Rome , Italy.,Beijing Advanced Innovation Center for Structural Biology, Tsinghua-Peking Joint Center for Life Sciences, School of Life Sciences and School of Medicine, Tsinghua University, Beijing 100084, China; Institute of Biology, Westlake Institute for Advanced Study, Westlake University, Shilongshan Road No. 18, Xihu District, Hangzhou 310064, Zhejiang Province, China. Electronic address: shi-lab@tsinghua.edu.cn.,Division of Cardiovascular Medicine, Department of Internal Medicine, Center for Arrhythmia Research, University of Michigan, Ann Arbor, MI, United States.,Department of Pharmacology, University of Cambridge, Cambridge CB2 1PD, UK; Department of Physiology, Pontificia Universidad Católica de Chile, 8331150 Santiago, Chile.,Structural Biology, St. Jude Children's Research Hospital, Memphis, TN, United States.,Department of Bioscience, Tokyo University of Agriculture, Sakuragaoka 1-1-1, Setagaya, Tokyo, 156-8502, Japan.,Centro di Biologia Integrata - CIBIO , Università di Trento , 38123 Povo , Trento , Italy.,Departments of Biochemistry and Molecular Genetics, MaRS Centre, West Tower, Floor 16, Toronto, ON, M5G 1M1, Canada.,Department of Biochemistry and Biophysics, Stockholm University, SE-106 91 Stockholm, Sweden.,Department of Pharmacology and Therapeutics, McGill University, Montréal, QC H3G 1Y6, Canada. Electronic address: derek.bowie@mcgill.ca.,Division of Biology and Biological Engineering, California Institute of Technology, 1200 E. California Boulevard, Pasadena, CA 91125, USA.,CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China; Savaid Medical School, University of Chinese Academy of Sciences, Beijing 100049, China. Electronic address: wenty@im.ac.cn.,Research Institute of Pharmaceutical Sciences, College of Pharmacy, Seoul National University, Seoul, 08826, Republic of Korea.,RIKEN Center for Biosystems Dynamics Research, Suehiro-cho, Tsurumi-ku, Yokohama 230-0045, Japan. takuhiro.ito@riken.jp.,Laboratory of Molecular Immunology and Howard Hughes Medical Institute, The Rockefeller University, New York, NY 10065, USA.,Department of Agricultural Chemistry, Tokyo University of Agriculture, Sakuragaoka 1-1-1, Setagaya, Tokyo, 156-8502, Japan. Electronic address: sue@nodai.ac.jp.,Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA.,Department of Chemistry and Biochemistry, Montana State University, Bozeman, MT 59717, USA.,b Interdisciplinary Research Center on Biology and Chemistry , Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences , Shanghai , China.,Department of Chemical and Biomolecular Engineering, University of California Berkeley, Berkeley, CA, 94720, USA.,Department of Integrative Oncology , BC Cancer Research Centre , V5Z 1L3 Vancouver Vancouver , British Columbia , Canada.,Department of Plant and Microbial Biology, University of California Berkeley, Berkeley, CA, 94720, USA.,Winkle College of Pharmacy, University of Cincinnati, ML 0514, 231 Albert Sabin Way, MSB 3109B, Cincinnati, OH, 45267, USA.,University of Florence , NEUROFARBA Dept., Sezione di Scienze Farmaceutiche , Via Ugo Schiff 6 , 50019 Sesto Fiorentino ( Florence ), Italy.,Burnett School of Biomedical Sciences, College of Medicine , University of Central Florida , Orlando , Florida 32827 , United States.,Department of Pharmaceutical Sciences, University of Connecticut , 69 North Eagleville Road, Storrs, Connecticut 06269, United States.,Department of Microbiology, Immunology and Infectious Diseases, University of Calgary, 2500 University Dr. NW, Calgary, AB, T2N 1N4, Canada.,c Collaborative Innovation Center of Chemistry for Life Sciences , Shanghai Institute of Organic Chemistry, University of Chinese Academy of Sciences, Chinese Academy of Sciences , Shanghai , China.,Department of Physiology, Pontificia Universidad Católica de Chile, 8331150 Santiago, Chile.,Istituto di Chimica del Riconoscimento Molecolare, C.N.R., Milan, Italy.,Swanson School of Engineering, University of Pittsburgh, Pittsburgh, PA 15260.,From the Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai 201800 and yufeng@sinap.ac.cn.,From the Department of Biochemistry, s-nair@life.illinois.edu.,Department of Pharmacology and Physiology , Saint Louis University School of Medicine , M370, Schwitalla Hall, 1402 South Grand Boulevard , Saint Louis , Missouri 63104 , United States.,From the Bioconversion Group and inoue-h@aist.go.jp.,Department of Molecular Biosciences, 1200 Sunnyside Ave, University of Kansas, Lawrence, KS, 66045, USA.,Division of Structural Biology, Medical Institute of Bioregulation, Kyushu University, Fukuoka, Japan.,Department of Biochemistry and Molecular Biology, School of Medicine , Oregon Health & Science University , Portland , Oregon 97239 , United States.,Department of Biochemistry and Biophysics, Stockholm University, SE-106 91 Stockholm, Sweden; Science for Life Laboratory Stockholm University, Box 1031, SE-171 21 Solna, Sweden. Electronic address: gunnar@dbb.su.se.,College of Medicine, Seoul National University, Seoul, 03080, Republic of Korea. swkimmd@snu.ac.kr.,Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Parkville, Australia. mhinds@unimelb.edu.au.,From the Bioconversion Group and.,the University of Chinese Academy of Sciences, Beijing 100049, China.,Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, Victoria, 3086, Australia. m.kvansakul@latrobe.edu.au.,RIKEN Center for Biosystems Dynamics Research, Suehiro-cho, Tsurumi-ku, Yokohama 230-0045, Japan.,Pharmaceutical Sciences, University of Tennessee Health Science Center, Memphis, TN, United States.,Department of Structural Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA 15260.,Department of Chemical Biology & Therapeutics, St. Jude Children's Research Hospital, Memphis, TN, United States.,Department of Microbiology and Immunology, Montana State University, Bozeman, MT 59717, USA.,Department of Biochemistry and Molecular Cell Biology, State Key Laboratory of Oncogenes and Related Genes, Shanghai Key Laboratory of Tumor Microenvironment and Inflammation, Shanghai Jiao-Tong University School of Medicine, Shanghai, China.,Inositol Signaling Group, Signal Transduction Laboratory , National Institute of Environmental Health Sciences , Research Triangle Park , North Carolina 27709 , United States.,Dipartimento di Medicina e Chirurgia , Università di Parma , 43125 Parma , Italy.,Research Institute of Pharmaceutical Sciences, College of Pharmacy, Seoul National University, Seoul, 08826, Republic of Korea. bwhan@snu.ac.kr.,Center for Integrative Chemical Biology and Drug Discovery, Division of Chemical Biology and Medicinal Chemistry, Eshelman School of Pharmacy , University of North Carolina at Chapel Hill , Chapel Hill , North Carolina 27599 , United States.,State Key Laboratory of Microbial Metabolism, Shanghai Jiao-Tong University, Shanghai, China.,Cancer institute, the Affiliated Hospital of Qingdao University, Qingdao Cancer Institute and School of Basic Medicine, Qingdao University, 266021, Qingdao, China.,Institute for Genomic Biology, and.,Infectious Diseases, St. Jude Children's Research Hospital, Memphis, TN, United States.,Department of Biochemistry, Schulich School of Medicine and Dentistry, Western University, London, ON, N6A 5C1, Canada. sli@uwo.ca.,Beijing Advanced Innovation Center for Structural Biology, Tsinghua-Peking Joint Center for Life Sciences, School of Life Sciences and School of Medicine, Tsinghua University, Beijing 100084, China.,The Henry Wellcome Building for Biocatalysis, Biosciences, College of Life and Environmental Sciences, University of Exeter, Exeter, United Kingdom.,Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720.,Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA.,Dipartimento di Scienze degli Alimenti e del Farmaco , Università di Parma , 43124 Parma , Italy.,From the Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai 201800 and.,Structural Molecular Biology, Stanford Synchroton Radiation Lightsource, SLAC National Accelerator Laboratory, Stanford University, Menlo Park, CA 94025; acohen@slac.stanford.edu guc9@pitt.edu.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Peroxisome proliferator-activated receptor gamma
A
283Homo sapiensMutation(s): 0 
Gene Names: PPARG (NR1C3)
Find proteins for P37231 (Homo sapiens)
Go to Gene View: PPARG
Go to UniProtKB:  P37231
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Nuclear receptor coactivator 1
B
16Homo sapiensMutation(s): 0 
Gene Names: NCOA1 (BHLHE74, SRC1)
EC: 2.3.1.48
Find proteins for Q15788 (Homo sapiens)
Go to Gene View: NCOA1
Go to UniProtKB:  Q15788
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
BRL
Query on BRL

Download SDF File 
Download CCD File 
A
2,4-THIAZOLIDIINEDIONE, 5-[[4-[2-(METHYL-2-PYRIDINYLAMINO)ETHOXY]PHENYL]METHYL]-(9CL)
BRL49653; ROSIGLITAZONE
C18 H19 N3 O3 S
YASAKCUCGLMORW-HNNXBMFYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.233 
  • R-Value Work: 0.201 
  • Space Group: P 21 21 2
Unit Cell:
Length (Å)Angle (°)
a = 130.809α = 90.00
b = 53.133β = 90.00
c = 54.570γ = 90.00
Software Package:
Software NamePurpose
MOLREPphasing
REFMACrefinement
HKL-2000data scaling
HKL-2000data reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2017-09-07 
  • Released Date: 2018-09-12 
  • Deposition Author(s): Jang, J.Y., Han, B.W.

Revision History 

  • Version 1.0: 2018-09-12
    Type: Initial release
  • Version 1.1: 2019-03-27
    Type: Data collection, Database references