6G6T

Crystal structure of human carbonic anhydrase isozyme II with N-butyl-2,4-dichloro-5-sulfamoyl-benzamide


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.12 Å
  • R-Value Free: 0.177 
  • R-Value Work: 0.143 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

Design of two-tail compounds with rotationally fixed benzenesulfonamide ring as inhibitors of carbonic anhydrases.

Zaksauskas, A.Capkauskaite, E.Jezepcikas, L.Linkuviene, V.Kisonaite, M.Smirnov, A.Manakova, E.Grazulis, S.Matulis, D.

(2018) Eur J Med Chem 156: 61-78

  • DOI: 10.1016/j.ejmech.2018.06.059
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Rational design of compounds that would bind specific pockets of the target proteins is a difficult task in drug design. The 12 isoforms of catalytically active human carbonic anhydrases (CAs) have highly similar active sites that make it difficult t ...

    Rational design of compounds that would bind specific pockets of the target proteins is a difficult task in drug design. The 12 isoforms of catalytically active human carbonic anhydrases (CAs) have highly similar active sites that make it difficult to design inhibitors selective for one or several CA isoforms. A series of CA inhibitors based on 2-chloro/bromo-benzenesulfonamide that is largely fixed in the CA active site together with one or two tails yielded compounds that were synthesized and evaluated as inhibitors of CA isoforms. Introduction of a second tail had significant influence on the binding affinity and two-tailed compounds in most cases provided high affinity and selectivity for CA IX and CA XIV. The contacts between several compounds and CA amino acids were determined by X-ray crystallography. Together with the intrinsic enthalpy and entropy of binding they provided the structure-thermodynamics correlations for this series of compounds with the insight how to rationally build compounds with desired CA isoform as a target.


    Organizational Affiliation

    School of Biological Sciences, The University of Auckland, Auckland, New Zealand.,Institute for Integrative Biology of the Cell, CEA, CNRS, Univ Paris-Sud and Université Paris-Saclay, Gif-sur-Yvette, France.,Temasek Life Sciences Laboratory, Department of Biological Sciences, National University of Singapore, Singapore, 117604, Singapore.,Department of Biochemistry & Biophysics, Stockholm University, Stockholm, Sweden.,Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, United States.,Institute for Protein Design, University of Washington, Seattle, WA, USA. emarcos82@gmail.com.,Department of Biophysics, The University of Texas Southwestern Medical Center, Dallas, TX 75390.,From the Laboratório Nacional de Biociências, Centro Nacional de Pesquisa em Energia e Materiais, Campinas, São Paulo 13083-970, Brazil, sandra.dias@lnbio.cnpem.br.,High Pressure and Synchrotron Radiation Physics Division, Bhabha Atomic Research Centre, Mumbai, Maharashtra, India.,California NanoSystems Institute, University of California at Los Angeles, Los Angeles, California.,Department of Life Sciences, National Central University, Taoyuan, 32001, Taiwan. chinyuchen@cc.ncu.edu.tw.,From the Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, Massachusetts 01605 and William.Royer@umassmed.edu.,Food Technology Division, Bhabha Atomic Research Centre, Mumbai, Maharashtra, India.,Department of Neurosurgery, Huashan Hospital, Institutes of Biomedical Sciences, State Key Laboratory of Medical Neurobiology, Department of Systems Biology for Medicine, School of Basic Medical Sciences, Shanghai Medical College of Fudan University, Shanghai, 200032, China. wywen@fudan.edu.cn.,Infinitus (China) Co. Ltd. , Guangzhou 510663 , P. R. China.,State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China.,Department of Experimental Medical Science, Lund University, Lund, Sweden.,Department of Protein - DNA Interactions, Institute of Biotechnology, Vilnius University, Saulėtekio al. 7, Vilnius LT-10257, Lithuania.,State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China. Electronic address: jtzheng@sjtu.edu.cn.,Department of Applied Biology and Chemical Technology, Central Laboratory of Institute of Molecular Technology for Drug Discovery and Synthesis, The Hong Kong Polytechnic University, Hung Hom, Hong Hong, China.,Medical Research Council Centre for Molecular Bacteriology and Infection, Imperial College London, SW7 2AZ London, United Kingdom.,Department of Physiology and Biophysics, Weill Cornell Medical College, New York, New York.,Department of Biochemistry and Molecular Cell Biology, Cornell University, Ithaca, New York. Electronic address: rad82@cornell.edu.,Protein Diffraction Group, Experimental Facility Division, National Synchrotron Radiation Research Center, Hsinchu, 30076, Taiwan.,Cancer Research UK Nucleic Acid Structure Research Group, MSI/WTB Complex, The University of Dundee, Dow Street, Dundee DD1 5EH, UK.,Department of Molecular Biosciences, University of Texas at Austin, Austin, TX 78712, USA.,Bioanalytics, Institute of Biotechnology, Technische Universität Berlin, Berlin, Germany.,From the Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, Massachusetts 01605 and.,the Carlson School of Chemistry and Biochemistry, Clark University, Worcester, Massachusetts 01610.,Institute for Life Sciences, University of Southampton, Southampton SO17 1BJ, United Kingdom, and.,Department of Clinical Microbiology and Immunology, Sackler School of Medicine, Tel Aviv University, 69978 Tel Aviv, Israel.,Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA.,Malopolska Centre of Biotechnology, Jagiellonian University, 30-387 Cracow, Poland.,CNRS, IMoPA, Université de Lorraine, Nancy, F-54000, France. xavier.manival@univ-lorraine.fr.,Institute of Biophysics, Consiglio Nazionale delle Ricerche, Genova, Italy.,Department of Life Sciences, National Central University, Taoyuan, 32001, Taiwan.,Institute of Structural and Molecular Biology, Birkbeck College, University of London, Malet Street, London, United Kingdom.,Equipe labélisée Ligue Nationale Contre le Cancer, 34293, Montpellier, France. edouard.bertrand@igmm.cnrs.fr.,Department of Biochemistry, University of Washington, Seattle, WA, USA. emarcos82@gmail.com.,Faculty of Chemistry and Chemical Technology , University of Ljubljana , Večna pot 113 , SI-1000 Ljubljana , Slovenia.,Department of Herbal Medicine Resources, College of Environmental and Bioresource Sciences, Chonbuk National University, Iksan 54596, Republic of Korea.,Department of Molecular Genetics, German Institute of Human Nutrition, Potsdam-Rehbruecke, Arthur-Scheunert-Allee, Nuthetal, Germany.,Equipe labélisée Ligue Nationale Contre le Cancer, 34293, Montpellier, France.,Faculty of Chemistry, Jagiellonian University, 30-387 Cracow, Poland.,Foundation for Applied Molecular Evolution and the Westheimer Institute of Science & Technology, Alachua, FL 32615, USA.,Ingénierie Moléculaire et Physiopathologie Articulaire, Centre National de la Recherche Scientifique Unité Mixte de Recherche 7365, Université de Lorraine, Biopôle de l'Université de Lorraine, Vandoeuvre-les-Nancy Cedex, France.,Department of Biochemistry, University of Washington, Seattle, WA, USA.,Department of Neurosurgery, Huashan Hospital, Institutes of Biomedical Sciences, State Key Laboratory of Medical Neurobiology, Department of Systems Biology for Medicine, School of Basic Medical Sciences, Shanghai Medical College of Fudan University, Shanghai, 200032, China.,Hybrigenics Services, Paris, 75014, France.,Department of Chemistry, National Tsing Hua University, Hsinchu, 30013, Taiwan.,IGF, CNRS, Université de Montpellier, Montpellier, 34090, France.,INRA, CNRS, Centre des Sciences du Goût et de l'Alimentation, Université de Bourgogne-Franche Comté, Dijon, France.,Janssen Prevention Center, Janssen Pharmaceutical Companies of Johnson & Johnson, Archimedesweg 6, 2333 CN Leiden, the Netherlands.,From the Centre for Biological Sciences, Faculty of Natural & Environmental Sciences, University of Southampton, Southampton SO17 1BJ, United Kingdom.,School of Pharmacy, University of Pittsburgh, Pittsburgh, PA, 15261.,The Medical Research Council Mitochondrial Biology Unit, University of Cambridge, Cambridge Biomedical Campus, CB2 0XY Cambridge, United Kingdom.,Department of Chemical and Biological Engineering; University of Wisconsin-Madison; 1415 Engineering Drive; Madison, WI, 53706.,GM/CA, Advanced Photon Source, Argonne National Laboratory, Argonne, IL 60439.,Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA; Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, CA 92037, USA. Electronic address: wilson@scripps.edu.,Department of Biology, University of Copenhagen, Copenhagen, Denmark.,Department of Biophysics, The University of Texas Southwestern Medical Center, Dallas, TX 75390; dan.rosenbaum@utsouthwestern.edu.,The Medical Research Council Laboratory of Molecular Biology, Cambridge Biomedical Campus, CB2 0QH Cambridge, United Kingdom.,Wellcome Centre for Cell Biology, University of Edinburgh, Edinburgh, UK.,MRC Laboratory of Molecular Biology, Cambridge, UK. jyl@mrc-lmb.cam.ac.,From the Departments of Structural Biology and.,MRC Laboratory of Molecular Biology, Cambridge, UK.,Tri-Institutional PhD Program in Computational Biology and Medicine, Weill Cornell Medical College, New York, New York.,Institute of Biochemistry, Graz University of Technology, Graz, Austria.,Faculty of Biochemistry and Molecular Medicine, University of Oulu, Aapistie 7A, Oulu, Finland.,Temasek Life Sciences Laboratory, Department of Biological Sciences, National University of Singapore, Singapore, 117604, Singapore. caiyu@tll.org.sg.,Janssen Prevention Center, Janssen Pharmaceutical Companies of Johnson & Johnson, Archimedesweg 6, 2333 CN Leiden, the Netherlands; Department of Neurology, Amsterdam Neuroscience, Academic Medical Center, Meidreefberg 9, 1105 AZ Amsterdam, the Netherlands; Department of Epidemiology, Harvard T.H. Chan School of Public Health, 677 Huntington Avenue, Boston, MA 02115, USA.,CNRS, IMoPA, Université de Lorraine, Nancy, F-54000, France.,Institute of Biological Chemistry, Academia Sinica, Taipei, 11529, Taiwan.,Janssen Prevention Center, Janssen Pharmaceutical Companies of Johnson & Johnson, 3210 Merryfield Row, San Diego, CA 92121, USA.,School of Biochemistry, Devi Ahilya University, Indore, India.,Department of Biochemistry, University of Oxford, Oxford, UK.,Infectious Diseases, St. Jude Children's Research Hospital, Memphis, Tennessee 38105.,From the Laboratório Nacional de Biociências, Centro Nacional de Pesquisa em Energia e Materiais, Campinas, São Paulo 13083-970, Brazil.,Section of Structural Biology, Department of Medicine, Imperial College London, London, United Kingdom.,Department of Biological Chemistry, University of California at Los Angeles, Los Angeles, California.,BioBank, First Affiliated Hospital, School of Medicine, Xi'an Jiaotong University, Shaanxi Sheng 710061, China.,From the Laboratório Nacional de Biociências, Centro Nacional de Pesquisa em Energia e Materiais, Campinas, São Paulo 13083-970, Brazil, andre.ambrosio@lnbio.cnpem.br.,CNRS, INSERM, IBSLOR, Université de Lorraine, Nancy, F-54000, France.,Institute for Research in Biomedicine (IRB Barcelona), Barcelona Institute of Science and Technology, Barcelona, Spain. emarcos82@gmail.com.,Institute of Structural and Molecular Biology, Division of Biosciences, University College London, London, United Kingdom.,Cyrus Biotechnology, Seattle, WA, USA.,Department of Biothermodynamics and Drug Design, Institute of Biotechnology, Vilnius University, Saulėtekio al. 7, Vilnius LT-10257, Lithuania. Electronic address: matulis@ibt.lt.,IGMM, CNRS, Université de Montpellier, Montpellier, 34293, France. edouard.bertrand@igmm.cnrs.fr.,Department of Biochemistry; University of Wisconsin-Madison; 440 Henry Mall; Madison, WI, 53706.,Molecular Physiology and Biophysics Section, Porter Neuroscience Research Center, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, United States.,College of Pharmaceutical Sciences , Zhejiang University of Technology , Hangzhou 310014 , P. R. China.,Slovenian NMR Center , National Institute of Chemistry , Hajdrihova 19 , SI-1000 Ljubljana , Slovenia.,Amazon, Seattle, WA, USA.,iBET, Instituto de Biologia Experimental e Tecnológica, Apartado 12, Oeiras, 2781-901, Portugal.,CEITEC-Central European Institute of Technology, Masaryk University, Brno, Czech Republic.,Centre for Cancer Immunology, University of Southampton Faculty of Medicine, University Hospital Southampton, Southampton SO16 6YD, United Kingdom.,The Medical Research Council Mitochondrial Biology Unit, University of Cambridge, Cambridge Biomedical Campus, CB2 0XY Cambridge, United Kingdom; walker@mrc-mbu.cam.ac.uk.,MRC Laboratory of Molecular Biology, Cambridge, United Kingdom.,EN-FIST Center of Excellence , Trg OF 13 , SI-1000 Ljubljana , Slovenia.,Department of Microbiology, Immunology & Molecular Genetics, University of California at Los Angeles, Los Angeles, California.,Department of Biopharmaceutics, Graduate School of Pharmaceutical Sciences, Kumamoto University, Kumamoto 862-0973, Japan.,Department of Chemistry, Umeå University, Umeå, Sweden.,Laboratoire de Spectrométrie de Masse BioOrganique, Université de Strasbourg, CNRS, IPHC UMR 7178, Strasbourg, 67000, France.,Department of Biochemistry & Molecular Biology, Indiana University School of Medicine, Indianapolis, IN 46202, USA.,Department of Biochemistry, University of Washington, Seattle, WA, USA. dabaker@uw.edu.,the Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Menlo Park, California 94025.,Departments of Molecular Biology and Biochemistry, Pharmaceutical Sciences, and Chemistry , University of California, Irvine , Irvine , California 92697-3900 , United States.,Department of Chemistry and Biochemistry, University of California, Santa Cruz, Santa Cruz, CA, USA.,Medical Research Council Centre for Molecular Bacteriology and Infection, Imperial College London, SW7 2AZ London, United Kingdom; s.j.matthews@imperial.ac.uk s.r.wig@imperial.ac.uk.,Center for Molecular Microscopy, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, United States.,Institute for Protein Design, University of Washington, Seattle, WA, USA.,IGMM, CNRS, Université de Montpellier, Montpellier, 34293, France.,Institute for Life Sciences, University of Southampton, Southampton SO17 1BJ, United Kingdom, and eddjames@soton.ac.uk.,Department of Biothermodynamics and Drug Design, Institute of Biotechnology, Vilnius University, Saulėtekio al. 7, Vilnius LT-10257, Lithuania.,Department of Pathology, Amsterdam Neuroscience, VU University Medical Center, de Boelelaan 1117, 1081 HV Amsterdam, the Netherlands.,the Structural Genomics Consortium, University of Oxford, Oxford OX3 7DQ, United Kingdom.,Institute for Protein Design, University of Washington, Seattle, WA, USA. dabaker@uw.edu.,Research Center for Applied Sciences, Academia Sinica, Taipei, 11529, Taiwan.,the Laboratório Nacional de Nanotecnologia, Centro Nacional de Pesquisa em Energia e Materiais, Campinas, São Paulo 13083-970, Brazil.,State Key Laboratory of Medicinal Chemical Biology, College of Life Sciences, Nankai University, Tianjin, 300071, China.,CRBM, University of Montpellier, CNRS, 1919 Route de Mende, Montpellier, 34090, France.,the School of Electrical and Computer Engineering, University of Campinas, São Paulo 13083-852, Brazil, and.,Infectious Diseases, St. Jude Children's Research Hospital, Memphis, Tennessee 38105 charles.rock@stjude.org.,School of Pharmaceutical Sciences , Sun Yat-sen University , Guangzhou 510006 , P. R. China.,Firebird Biomolecular Sciences LLC, Alachua, FL 32615, USA.,Department of Chemical Engineering; Pennsylvania State University; 158 Fenske Laboratory; University Park, PA, 16802.,SOLEIL Synchrotron, L'Orme de Merisiers, Saint-Aubin, Gif-sur-Yvette, France.,Department of Molecular Biology and Biotechnology, University of Sheffield, Sheffield, UK.,Department of Biomedical Sciences, University of Copenhagen, Copenhagen, Denmark.,Department of Veterinary and Animal Sciences, University of Copenhagen, Frederiksberg, Denmark.,Department of Biochemistry and Molecular Cell Biology, Cornell University, Ithaca, New York.,Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA; Beijing Synchrotron Radiation Facility, Institute of High Energy Physics, Chinese Academy of Sciences, Beijing 100049, People's Republic of China.,Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Av. da República, Oeiras, 2780-157, Portugal.,The Bredesen Center for Interdisciplinary Research and Graduate Education, University of Tennessee, Knoxville, Tennessee; Biology and Soft Matter Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee; Department of Physics and Astronomy, University of Tennessee, Knoxville, Tennessee; Shull Wollan Center, Oak Ridge National Laboratory, Oak Ridge, Tennessee.,Laboratory of Cell Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, United States.,Section of Microbiology and MRC Centre for Molecular Bacteriology and Infection, Imperial College London, London, United Kingdom.,The Bredesen Center for Interdisciplinary Research and Graduate Education, University of Tennessee, Knoxville, Tennessee; Joint Institute for Biological Sciences, Oak Ridge National Laboratory, Oak Ridge, Tennessee; Biology and Soft Matter Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee. Electronic address: heberlefa@ornl.gov.,Department of Microbiology and Immunology, University of Otago, 9016 Dunedin, New Zealand.,Division of Life Science, State Key Laboratory of Molecular Neuroscience, Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong, China.,Department of Computer Science, University of California, Santa Cruz, Santa Cruz, CA, USA.




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
BCN
Query on BCN

Download SDF File 
Download CCD File 
A
BICINE
C6 H13 N O4
FSVCELGFZIQNCK-UHFFFAOYSA-N
 Ligand Interaction
ENN
Query on ENN

Download SDF File 
Download CCD File 
A
~{N}-butyl-2,4-bis(chloranyl)-5-sulfamoyl-benzamide
C11 H14 Cl2 N2 O3 S
KRIUYRKSVUBELV-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: 1.12 Å
  • R-Value Free: 0.177 
  • R-Value Work: 0.143 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 42.057α = 90.00
b = 41.196β = 104.19
c = 72.094γ = 90.00
Software Package:
Software NamePurpose
XDSdata reduction
PDB_EXTRACTdata extraction
SCALAdata scaling
REFMACrefinement
Cootmodel building
MOLREPphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2019-03-13
    Type: Initial release