5LLC

Crystal structure of human carbonic anhydrase isozyme II with 3-(Methylamino)-2,5,6-trifluoro-4-[(2-phenylethyl)sulfonyl]benzenesulfonamide


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.1 Å
  • R-Value Free: 0.161 
  • R-Value Work: 0.138 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Crystal structure correlations with the intrinsic thermodynamics of human carbonic anhydrase inhibitor binding.

Smirnov, A.Zubriene, A.Manakova, E.Grazulis, S.Matulis, D.

(2018) PeerJ 6: e4412-e4412

  • DOI: 10.7717/peerj.4412
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The structure-thermodynamics correlation analysis was performed for a series of fluorine- and chlorine-substituted benzenesulfonamide inhibitors binding to several human carbonic anhydrase (CA) isoforms. The total of 24 crystal structures of 16 inhib ...

    The structure-thermodynamics correlation analysis was performed for a series of fluorine- and chlorine-substituted benzenesulfonamide inhibitors binding to several human carbonic anhydrase (CA) isoforms. The total of 24 crystal structures of 16 inhibitors bound to isoforms CA I, CA II, CA XII, and CA XIII provided the structural information of selective recognition between a compound and CA isoform. The binding thermodynamics of all structures was determined by the analysis of binding-linked protonation events, yielding the intrinsic parameters, i.e., the enthalpy, entropy, and Gibbs energy of binding. Inhibitor binding was compared within structurally similar pairs that differ by para- or meta -substituents enabling to obtain the contributing energies of ligand fragments. The pairs were divided into two groups. First, similar binders-the pairs that keep the same orientation of the benzene ring exhibited classical hydrophobic effect, a less exothermic enthalpy and a more favorable entropy upon addition of the hydrophobic fragments. Second, dissimilar binders-the pairs of binders that demonstrated altered positions of the benzene rings exhibited the non-classical hydrophobic effect, a more favorable enthalpy and variable entropy contribution. A deeper understanding of the energies contributing to the protein-ligand recognition should lead toward the eventual goal of rational drug design where chemical structures of ligands could be designed based on the target protein structure.


    Organizational Affiliation

    Institute for Molecular Bioscience, The University of Queensland, Brisbane 4072, Australia. Dorien.VanLysebetten@UGent.be.,RIKEN SPring-8 Center, 1-1-1 Kouto, Sayo, Hyogo 679-5148, Japan.,The RIKEN SPring-8 Center, 1-1-1 Koto, Sayo-cho, Sato-gun, Hyogo, 678-5248, Japan.,Centre for Plant Sciences, Faculty of Biological Sciences, University of Leeds, Leeds, United Kingdom.,College of Life Science and Technology, Huazhong Agricultural University, Wuhan, Hubei 430070, China; State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, Hubei 430070, China. Electronic address: hejin@mail.hzau.edu.cn.,Department of Biochemistry and Molecular Biology, University of Oklahoma Health Sciences Center, Oklahoma City, Oklahoma (J.M.B., M.L.W., A.M.R., A.A.P.) and School of Biological Sciences, University of Auckland, Auckland, New Zealand (D.L.H.).,Departamento de Química, Universidad de La Rioja, Centro de Investigación en Síntesis Química, E-26006, Logroño, Spain.,Ikerbasque, Basque Foundation for Science, Maria Diaz de Haro 13, 48009, Bilbao, Spain.,Illawarra Health and Medical Research Institute, University of Wollongong, Wollongong 2522, Australia. jeffreym@uow.edu.au.,Cambridge Graphene Centre, University of Cambridge, 9 JJ Thomson Avenue, Cambridge, CB3 OFA, UK.,Infection and Immunity Program, Department of Microbiology, Monash University, Clayton, 3800, Australia.,Cardiovascular Research Institute, University of California at San Francisco, San Francisco, CA, USA. lijunliuks@gmail.com.,Department of Chemical Sciences, University of Padova, via Marzolo 1, 35131, Padova, Italy. massimo.bellanda@unipd.it.,Human Health Therapeutics Portfolio , National Research Council Canada , 100 Sussex Drive , Ottawa , Ontario , Canada K1A 0R6.,IGF, Univ Montpellier, CNRS, INSERM, 34090 Montpellier, France.,DLX Scientific, Lawrence, KS, USA. lijunliuks@gmail.com.,Institute for Molecular Bioscience, The University of Queensland, Brisbane 4072, Australia. t.durek@uq.edu.au.,Howard Hughes Medical Institute, and Departments of Molecular and Cellular Physiology, and Structural Biology, Program in Immunology, Stanford University School of Medicine, Stanford, California, USA.,College of Life Science and Technology, Huazhong Agricultural University, Wuhan, Hubei 430070, China. Electronic address: zoutingting@mail.hzau.edu.cn.,Department of Pharmaceutical Chemistry, University of Debrecen, 4032, Debrecen, Hungary.,Dept. of Biological Chemistry, John Innes Centre, Norwich Research Park, Norwich, United Kingdom.,Dipartimento di Scienze degli Alimenti e del Farmaco, Università degli Studi di Parma, Parco Area delle Scienze 27/A, 43124, Parma, Italy.,Department of Pharmacy and Biotechnology, University of Bologna, Viale Giuseppe Fanin 40, 40127, Bologna, Italy.,Institute for Molecular Bioscience, The University of Queensland, Brisbane 4072, Australia. d.craik@imb.uq.edu.au.,Dipartimento di Scienze Matematiche, Fisiche e Informatiche, Università degli Studi di Parma, Parco Area delle Scienze 7/A, 43124, Parma, Italy.,NTU Institute of Structural Biology, Nanyang Technological University, Singapore, Singapore. sbhushan@ntu.edu.sg.,Banting and Best Department of Medical Research and Department of Molecular Genetics, University of Toronto, Terrence Donnelly Centre for Cellular &Biomolecular Research, Toronto, Ontario, Canada.,Department of Organic Chemistry, Faculty of Chemistry, University of Łódź, Tamka 12, PL-91403 Łódź, Poland.,Department of Pharmaceutical Chemistry, University of California at San Francisco, San Francisco, CA, USA. xiaokun.shu@ucsf.edu.,Research Center Borstel , Leibniz Lung Center , Parkallee 22 , Borstel D-23845 , Germany.,Department of Biology and Konstanz Research School Chemical Biology, University of Konstanz, Universitätsstrasse 10, 78457, Konstanz, Germany.,IFN-CNR, Dipartimento di Fisica, Politecnico di Milano, Piazza Leonardo da Vinci 32, 20133, Milano, Italy.,Biostructural Mechanism Laboratory, RIKEN, SPring-8 Center, 1-1-1 Kouto, Sayo, Hyogo 679-5148, Japan.,Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory , Stanford University , Menlo Park , California 94025 , United States.,Biological Pharmacological Research Laboratories, Central Pharmaceutical Research Institute, Japan Tobacco Inc., 1-1, Murasaki-cho, Takatsuki, Osaka, 569-1125, Japan.,the Department of Agronomy and Horticulture, University of Nebraska, Lincoln, Nebraska 68588.,Department of Organic Chemistry II, Faculty of Science & Technology, University of the Basque Country, 48940, Leioa, Bizkaia, Spain.,Center for Computational Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki, 305-8577, Japan.,From the Institute for Protein Design.,Department of Pharmaceutical Chemistry , University of California San Francisco , San Francisco , California 94158 , United States.,College of Life Science and Technology, Huazhong Agricultural University, Wuhan, Hubei 430070, China.,School of Biological Sciences, Nanyang Technological University, Singapore, Singapore. sbhushan@ntu.edu.sg.,Laboratorio de Fisicoquímica Biológica, Instituto de Química Biológica, Facultad de Ciencias, Universidad de la República, Igua 4425, 11400, Montevideo, Uruguay.,Dipartimento di Scienze Matematiche, Fisiche e Informatiche, Università degli Studi di Parma, Parco Area delle Scienze 7/A, 43124, Parma, Italy. stefania.abbruzzetti@unipr.it.,Institute for Glycomics, Gold Coast Campus, Griffith University, Queensland, 4222, Australia.,Department of Molecular Medicine, University of South Florida Morsani College of Medicine, 12901 Bruce B. Downs Blvd., Tampa, Florida 33612, United States.,IHAP, Université de Toulouse, INRA, ENVT, Toulouse, France.,Cardiovascular Research Institute, University of California at San Francisco, San Francisco, CA, USA. xiaokun.shu@ucsf.edu.,Pharmaceutical Frontier Research Laboratories, Central Pharmaceutical Research Institute, Japan Tobacco Inc., 1-13-2, Fukuura, Kanazawa-Ku, Yokohama, Kanagawa, 236-0004, Japan.,Department of Chemistry, University of Pennsylvania, Philadelphia, PA, USA.,Department of Chemistry "Ugo Schiff", University of Florence, Via della Lastruccia 3, 50019, Sesto Fiorentino (FI), Italy.,Pharmaceutical Frontier Research Laboratories, Central Pharmaceutical Research Institute, Japan Tobacco Inc., 1-13-2, Fukuura, Kanazawa-Ku, Yokohama, Kanagawa, 236-0004, Japan. masato.noguchi@jt.com.,Department of Chemistry, Graduate School of Science, Tohoku University, Aramaki, Aoba-ku, Sendai, Miyagi, 980-8578, Japan.,Institut de Biologie Structurale (IBS), Univ. Grenoble Alpes, CEA, CNRS, 38044, Grenoble, France.,Department of Biochemistry and Biophysics, University of California at San Francisco, San Francisco, CA, USA.,Illawarra Health and Medical Research Institute, University of Wollongong, Wollongong 2522, Australia. djadams@uow.edu.au.,From the Institute for Protein Design, chris.bahl@proteininnovation.org.,the Institute for Protein Innovation, Boston, Massachusetts 02115.,Institute for Molecular Bioscience, The University of Queensland, Brisbane 4072, Australia. thomas.dash@imb.uq.edu.au.,CBS, Univ Montpellier, CNRS, INSERM, 34090 Montpellier, France. Electronic address: gilles.labesse@cbs.cnrs.fr.,Department of Chemical Sciences, University of Padova, via Marzolo 1, 35131, Padova, Italy.,Center for BioImaging Sciences, National University of Singapore, Singapore, Singapore.,Illawarra Health and Medical Research Institute, University of Wollongong, Wollongong 2522, Australia. rfinolu@uow.edu.au.,Biostructural Mechanism Laboratory, RIKEN, SPring-8 Center, 1-1-1 Kouto, Sayo, Hyogo 679-5148, Japan; Advanced Electron Microscope Development Unit, RIKEN-JEOL Collaboration Center, RIKEN Baton Zone Program, 1-1-1 Kouto, Sayo, Hyogo 679-5148, Japan. Electronic address: yone@spring8.or.jp.,Department of Chemistry , Fresno State University , 2555 East San Ramon Avenue, MS SB70 , Fresno , California 93740 , United States.,Department of Chemistry , University of California, Irvine , Irvine , California 92697-2025 , United States.,Cell and Molecular Sciences Group, Dundee Effector Consortium, James Hutton Institute, Invergowrie, Dundee, United Kingdom.,Institute for Molecular Bioscience, The University of Queensland, Brisbane 4072, Australia. peta.harvey@imb.uq.edu.au.,Graduate School of Natural Science and Technology, Kanazawa University, Kakuma, Kanazawa, Ishikawa, 920-1192, Japan.,Department of Chemistry , Box H, Brown University , Providence , Rhode Island 02912-9108 , United States.,CRBM, "Equipe Labellisée Ligue Contre le Cancer", Univ Montpellier, CNRS, 34000 Montpellier, France.,Howard Hughes Medical Institute, University of Washington, Seattle, Washington 98195.,Molecular Physiology and Biological Physics, University of Virginia School of Medicine, Charlottesville, VA, 22908, USA.,Department of Nutrition, Food Sciences and Gastronomy, Faculty of Pharmacy and Food Sciences and Institute of Biomedicine (IBUB), University of Barcelona, Avda. Prat de la Riba 171, Santa Coloma de Gramenet, Spain. fjluque@ub.edu.,Instituto de Biocomputación y Fisica de Sistemas Complejos (BIFI), BIFI-IQFR (CSIC) Joint Unit, Universidad de Zaragoza, 50018, Zaragoza, Spain.,National Institute of Public Health-National Institute of Hygiene, Chocimska 24, PL-00791, Warsaw, Poland.,Department of Biochemistry and Molecular Biology, University of Oklahoma Health Sciences Center, Oklahoma City, Oklahoma (J.M.B., M.L.W., A.M.R., A.A.P.) and School of Biological Sciences, University of Auckland, Auckland, New Zealand (D.L.H.) augen-pioszak@ouhsc.edu.,School of Biology, Faculty of Biology Medicine and Health, Michael Smith Building, The University of Manchester, Oxford Road, Manchester, M13 9PL, UK. robert.ford@manchester.ac.uk.,Department of Pharmaceutical Chemistry, University of California at San Francisco, San Francisco, CA, USA.,From the Department of Biology, Washington University, St. Louis, Missouri 63130 and.,Department of Chemistry and Konstanz Research School Chemical Biology, University of Konstanz, Universitätsstrasse 10, 7857, Konstanz, Germany.,Department of Biothermodynamics and Drug Design, Institute of Biotechnology, Vilnius University, Vilnius, Lithuania.,Institute of Low Temperature Science, Hokkaido University Kita19-Nishi8, Kita-ku, 060-0819, Sapporo, Japan.,CRBM, "Equipe Labellisée Ligue Contre le Cancer", Univ Montpellier, CNRS, 34000 Montpellier, France. Electronic address: serge.roche@crbm.cnrs.fr.,School of Life Sciences, University of Dundee, Dundee, United Kingdom.,Institute for Molecular Bioscience, The University of Queensland, Brisbane 4072, Australia. nyoman.kurniawan@cai.uq.edu.au.,Howard Hughes Medical Institute, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, New York 10065, and.,Dipartimento di Scienze Matematiche, Fisiche e Informatiche, Università degli Studi di Parma, Parco Area delle Scienze 7/A, 43124, Parma, Italy. cristiano.viappiani@unipr.it.,Institut Pasteur de Montevideo, Mataojo 2020, 11400, Montevideo, Uruguay.,School of Biology, Faculty of Biology Medicine and Health, Michael Smith Building, The University of Manchester, Oxford Road, Manchester, M13 9PL, UK.,CBS, Univ Montpellier, CNRS, INSERM, 34090 Montpellier, France.,Savaid Medical School, University of Chinese Academy of Sciences, Beijing, 101408, China.,Institute for Molecular Bioscience, The University of Queensland, Brisbane 4072, Australia. justine.hill1@gmail.com.,Fundación ARAID, 50018, Zaragoza, Spain.,Institut de Biologie Structurale (IBS), Univ. Grenoble Alpes, CEA, CNRS, 38044, Grenoble, France. thibaut.crepin@ibs.fr.,Department of Chemistry , University of Natural Resources and Life Sciences , A-1190 Vienna , Austria.,Department of Biochemistry, and.,Department of Pharmaceutical Chemistry, University of California at San Francisco, San Francisco, CA, USA. william.degrado@ucsf.edu.,eBIC, Diamond Light Source Ltd, Diamond House, Harwell Science & Innovation Campus, Oxfordshire, Didcot, OX11 0DE, UK.,Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA.,Magnetic Resonance Center (CERM), University of Florence, Via L. Sacconi 6, 50019, Sesto Fiorentino (FI), Italy.,University of Chinese Academy of Sciences, Beijing, 101408, China.,Chemical Research Laboratories, Central Pharmaceutical Research Institute, Japan Tobacco Inc., 1-1, Murasaki-cho, Takatsuki, Osaka, 569-1125, Japan.,Integrated Structural Biology Grenoble (ISBG) - UMS 3518 (CNRS-CEA-UJF-EMBL), 38044, Grenoble, France.,Pharmaceutical Frontier Research Laboratories, Central Pharmaceutical Research Institute, Japan Tobacco Inc., 1-13-2, Fukuura, Kanazawa-Ku, Yokohama, Kanagawa, 236-0004, Japan. tsuyoshi.adachi@jt.com.,Cardiovascular Research Institute, University of California at San Francisco, San Francisco, CA, USA.,New England Biolabs, 240 County Road, Ipswich, MA, 01938, USA.,Department of Nutrition, Food Sciences and Gastronomy, Faculty of Pharmacy and Food Sciences and Institute of Biomedicine (IBUB), University of Barcelona, Avda. Prat de la Riba 171, Santa Coloma de Gramenet, Spain.,Copenhagen Center for Glycomics, Department of Cellular and Molecular Medicine, School of Dentistry, University of Copenhagen, Copenhagen, Denmark.,Faculty of Pharmacy and Biochemistry, University of Zagreb, Ante Kovačića 1, Zagreb, Croatia.,Department of Protein-DNA Interactions, Institute of Biotechnology, Vilnius University, Vilnius, Lithuania.,Department of Chemistry and Biochemistry , University of Wisconsin-Milwaukee , Milwaukee , Wisconsin 53201 , United States.,Molecular Modeling Section (MMS), Department of Pharmaceutical and Pharmacological Sciences, University of Padova, via Marzolo 5, Padova, Italy.,the Structural Biology Program and.,Department of Biochemistry and Microbiology , University of Victoria , P.O. Box 3055 STN CSC, Victoria , British Columbia , Canada V8P 3P6.,Orphagen Pharmaceuticals, 11558 Sorrento Valley Road, Suite 4, San Diego, California, 92121, USA.,Molecular Physiology and Biological Physics, University of Virginia School of Medicine, Charlottesville, VA, 22908, USA. jochen_zimmer@virginia.edu.,Department of Chemistry &Biochemistry and the Harper Cancer Research Institute, University of Notre Dame, Notre Dame, Indiana, USA.,Ramaciotti Centre for Electron Microscopy, Monash University, Clayton, 3800, Australia.,UCIBIO, REQUIMTE, Departamento de Química, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, 2829-516, Caparica, Portugal.,Institute for Neurodegenerative Diseases, University of California at San Francisco, San Francisco, CA, USA. william.degrado@ucsf.edu.,Max-Planck Institute for Chemical Energy Conversion, Stiftstrasse 34-36, D-45470, Mülheim an der Ruhr, Germany.,Centre de RMN à Très Hauts Champs, Institut des Sciences Analytiques (UMR 5280 - CNRS, ENS Lyon, UCB Lyon 1), Université de Lyon, 5 rue de la Doua, 69100, Villeurbanne, France.,Department of Biochemistry, University of Oxford, Oxford, OX1 3QU, UK.,From the Department of Biology, Washington University, St. Louis, Missouri 63130 and jjez@wustl.edu.,Cardiovascular Research Institute, University of California at San Francisco, San Francisco, CA, USA. william.degrado@ucsf.edu.,School of Biological Sciences, Nanyang Technological University, Singapore, Singapore.,College of Life Science and Technology, Huazhong Agricultural University, Wuhan, Hubei 430070, China; State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, Hubei 430070, China.,CIC bioGUNE, Bizkaia Technology Park, Building 801A, 48170, Derio, Spain.,Department of Picobiology, Graduate School of Life Science, University of Hyogo, 3-2-1 Koto, Kamigori-cho, Ako-gun, Hyogo, 678-1297, Japan.,School of Chemistry, Monash University, Clayton, 3800, Australia.,College of Life Science and Technology, Huazhong Agricultural University, Wuhan, Hubei 430070, China; National Key Laboratory of Crop Genetic Improvement and National Centre of Plant Gene Research, Huazhong Agricultural University, Wuhan, Hubei 430070, China.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Carbonic anhydrase 2
A
260Homo sapiensMutation(s): 0 
Gene Names: CA2
EC: 4.2.1.1
Find proteins for P00918 (Homo sapiens)
Go to Gene View: CA2
Go to UniProtKB:  P00918
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download SDF File 
Download CCD File 
A
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
V26
Query on V26

Download SDF File 
Download CCD File 
A
2,3,6-tris(fluoranyl)-5-(methylamino)-4-(2-phenylethylsulfonyl)benzenesulfonamide
C15 H15 F3 N2 O4 S2
WQFYXDRMKJAGFX-UHFFFAOYSA-N
 Ligand Interaction
EDO
Query on EDO

Download SDF File 
Download CCD File 
A
1,2-ETHANEDIOL
ETHYLENE GLYCOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
DMS
Query on DMS

Download SDF File 
Download CCD File 
A
DIMETHYL SULFOXIDE
C2 H6 O S
IAZDPXIOMUYVGZ-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.1 Å
  • R-Value Free: 0.161 
  • R-Value Work: 0.138 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 42.209α = 90.00
b = 41.078β = 104.11
c = 71.968γ = 90.00
Software Package:
Software NamePurpose
REFMACrefinement
SCALAdata scaling
MOLREPphasing
PDB_EXTRACTdata extraction
XDSdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2017-08-16
    Type: Initial release
  • Version 1.1: 2018-05-16
    Type: Data collection, Database references