5N9L

Crystal structure of human Protein kinase CK2 catalytic subunit in complex with the ATP-competitive dibenzofuran inhibitor TF (4b)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.79 Å
  • R-Value Free: 0.199 
  • R-Value Work: 0.164 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

A pi-Halogen Bond of Dibenzofuranones with the Gatekeeper Phe113 in Human Protein Kinase CK2 Leads to Potent Tight Binding Inhibitors.

Schnitzler, A.Gratz, A.Bollacke, A.Weyrich, M.Kucklander, U.Wunsch, B.Gotz, C.Niefind, K.Jose, J.

(2018) Pharmaceuticals 11: --

  • DOI: 10.3390/ph11010023
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Human protein kinase CK2 is an emerging target for neoplastic diseases. Potent lead structures for human CK2 inhibitors are derived from dibenzofuranones. Two new derivatives, 7,9-dichloro-1,2-dihydro-8-hydroxy-4-[(4-methoxyphenylamino)-methylene]dib ...

    Human protein kinase CK2 is an emerging target for neoplastic diseases. Potent lead structures for human CK2 inhibitors are derived from dibenzofuranones. Two new derivatives, 7,9-dichloro-1,2-dihydro-8-hydroxy-4-[(4-methoxyphenylamino)-methylene]dibenzo[ b , d ]furan-3(2 H )-one ( 4a ) and ( E )-1,3-dichloro-6-[(4-methoxyphenylimino)-methyl]dibenzo[ b , d ]furan-2,7-diol ( 5 ) were tested for inhibition of CK2 and induction of apoptosis in LNCaP cells. Both turned out to be tight binding inhibitors, with IC 50 values of 7 nM ( 4a ) and 5 nM ( 5 ) and an apparent K i value of 0.4 nM for both. Compounds 4a and 5 reduced cellular CK2 activity, indicating cell permeability. Cell viability was substantially impaired in LNCaP cells, as well as apoptosis was induced, which was not appearing in non-neoplastic ARPE-19 cells. Co-crystallization of 4a and 5 revealed an unexpected π -halogen bond of the chloro substituent at C9 with the gatekeeper amino acid Phe113, leading to an inverted binding mode in comparison to parent compound 4b , with the Cl at C6 instead, which was co-crystallized as a control. This indicates that the position of the chloro substituent on ring A of the dibenzofuran scaffold is responsible for an inversion of the binding mode that enhances potency.


    Related Citations: 
    • TF--a novel cell-permeable and selective inhibitor of human protein kinase CK2 induces apoptosis in the prostate cancer cell line LNCaP.
      Goetz, C.,Gratz, A.,Kucklaender, U.,Jose, J.
      (2012) Biochim. Biophys. Acta 1820: 970
    • Inclining the purine base binding plane in protein kinase CK2 by exchanging the flanking side-chains generates a preference for ATP as a cosubstrate.
      Yde, C.W.,Ermakova, I.,Issinger, O.G.,Niefind, K.
      (2005) J. Mol. Biol. 347: 399
    • Crystal structure of a C-terminal deletion mutant of human protein kinase CK2 catalytic subunit.
      Ermakova, I.,Boldyreff, B.,Issinger, O.G.,Niefind, K.
      (2003) J. Mol. Biol. 330: 925
    • Structural Hypervariability of the Two Human Protein Kinase CK2 Catalytic Subunit Paralogs Revealed by Complex Structures with a Flavonol- and a Thieno[2,3-d]pyrimidine-Based Inhibitor.
      Niefind, K.,Bischoff, N.,Golub, A.G.,Bdzhola, V.G.,Balanda, A.O.,Prykhod'ko, A.O.,Yarmoluk, S.M.
      (2017) Pharmaceuticals (Basel) 10: --


    Organizational Affiliation

    California Institute for Quantitative Biosciences, University of California, Berkeley, United States.,Institut für Pharmazeutische und Medizinische Chemie, PharmaCampus, Westfälische Wilhelms-Universität Münster, Corrensstraße 48, D-48149 Münster, Germany. gratz.andreas@gmail.com.,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.,College of Life Sciences, Northwest A&F University, Yangling, Shaanxi, 712100, China. Electronic address: weifei_c@nwsuaf.edu.cn.,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.,Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA. laub@mit.edu.,Université Grenoble Alpes, CNRS, CEA, IBS UMR 5075, 38044, Grenoble, France. andre.zapun@ibs.fr.,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.,Mitchell Cancer Institute, The University of South Alabama, Mobile, Alabama.,Experimental Retrovirology Section, HIV and AIDS Malignancy Branch, National Cancer Institute, National Institutes of Health, Bethesda, MD, 20892, USA.,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.,Department of Chemistry and Biochemistry, University of California Los Angeles, Los Angeles, CA 90095, USA.,Howard Hughes Medical Institute, University of California, Berkeley, United States.,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.,Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA.,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.,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.,College of Life Sciences, Northwest A&F University, Yangling, Shaanxi, 712100, China.,the Department of Neuroscience, Mayo Clinic College of Medicine, Jacksonville, Florida 32224.,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.,Heptares Therapeutics Ltd. , BioPark , Welwyn Garden City , Hertfordshire AL7 3AX , U.K.,Molecular Biophysics and Integrative Bio-Imaging Division, Lawrence Berkeley National Laboratory, Berkeley, United States.,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.,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.,Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, MI 48109, USA.,York Structural Biology Laboratory, Department of Chemistry, University of York, Heslington, York YO10 5DD, 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 Clinical Science, Kumamoto University Hospital, Kumamoto, 860-8556, Japan.,Department of Molecular and Cell Biology, University of California, Berkeley, United States.,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.,Biosciences Division, SLAC National Accelerator Laboratory, Stanford University, Stanford, CA, USA.,VIB-VUB Center for Structural Biology, VIB, Brussels, Belgium.,Institut für Pharmazeutische und Medizinische Chemie, PharmaCampus, Westfälische Wilhelms-Universität Münster, Corrensstraße 48, D-48149 Münster, Germany. wuensch@uni-muenster.de.,Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA, USA.,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.,School of Biological Sciences , Nanyang Technological University , 50 Nanyang Drive , Singapore 637551.,DuPont Nutrition and Health, 3329 Agriculture Dr, Madison, WI, 53716, USA.,Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, 37232-2372, USA.,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.,Northeastern Collaborative Access Team, Argonne National Laboratory, Lemont, IL, 60439, USA.,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.,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.,Centre Hospitalier Universitaire de Québec Research Center, Université Laval, Québec City, QC, G1V 4G2, Canada.,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.,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.,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.,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.,CryoEM Shared Resources, Howard Hughes Medical Institute, Janelia Research Campus, Ashburn, VA, USA.,James Cook University, Cairns, Australia.,Membrane Biochemistry and Biophysics, Department of Chemistry, Faculty of Science, Utrecht University, Utrecht, 3584, The Netherlands.,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.,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.,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.,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.,The Sainsbury Laboratory, Norwich Research Park, Norwich, NR4 7UH, UK.,Department of Biological Sciences , National University of Singapore , 14 Science Drive 4 , Singapore 117543.,Université Paris Descartes, Laboratoire de Chimie et Biochimie Pharmacologiques et Toxicologiques UMR 8601 CNRS, Sorbonne Paris Cité (USPC), Paris, 75006, France.,Life Sciences Institute and Department of Biological Chemistry, University of Michigan Medical School, Ann Arbor, MI, USA.,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.,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.,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.,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 Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, CA, USA.,Architecture et Fonction des Macromolécules Biologiques, Centre National de la Recherche Scientifique (CNRS), Campus de Luminy, Case 932, 13288, Marseille Cedex 09, France.,Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Sapporo, 062-8517, Japan. y-yasutake@aist.go.jp.,ConfometRx, Santa Clara, CA, USA.,Center for Environmental Health Sciences MIT, Massachusetts Institute of Technology, Cambridge, MA, USA.,National Center for Global Health and Medicine Research Institute, Tokyo, 162-8655, Japan.,Center for Matrix Biology, Vanderbilt University Medical Center, Nashville, TN, 37232-2372, USA. kyle.l.brown@vanderbilt.edu.,the Department of Medicine, University of California San Diego, La Jolla, California 92037, and.,Medizinische Biochemie und Molekularbiologie, Universität des Saarlandes, Kirrberger Str., Geb. 44, D-66421 Homburg, Germany. michaelweyrich@gmx.de.,Laboratory of Systems Pharmacology, Harvard Medical School, Boston, MA 02115, USA.,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.,Faculdade de Ciências, Departamento de Biologia, Universidade do Porto, Porto, Portugal.,Ipsen Bioscience , 650 East Kendall Street , Cambridge , MA 02142 , 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.,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.,School of Veterinary Sciences, University of Bristol, Bristol, United Kingdom.,Department of Agrifood Production and Environmental Sciences, University of Florence, Florence, Italy.,Institut für Biochemie, Department für Chemie, Universität zu Köln, Zülpicher Straße 47, D-50674 Köln, Germany. kucklaen@uni-duesseldorf.de.,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.,Structural Biology Brussels, Vrije Universiteit Brussel (VUB), Brussels, Belgium.,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.,the Stanford Synchrotron Radiation Light Source, Menlo Park, California 94025.,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 Research Laboratory, Metabolic Regulation Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, South Korea.,Center for Structural Biology, Vanderbilt University Medical Center, Nashville, TN, 37232-2372, USA.,Institute of Biochemistry, Center for Structural and Cell Biology in Medicine, University of Lübeck, Ratzeburger Allee 160, 23562 Lübeck, Germany.,Ipsen Innovation , 5, Avenue du Canada , Les Ulis , France 91940 . Email: sergeauvin@gmail.com ; Tel: +33 160 922481.,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.,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.,Molecular Biophysics Unit, Indian Institute of Science, Bangalore, India.,Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Sapporo, 062-8517, Japan.,Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, CA, USA. kobilka@stanford.edu.,the Department of Cancer Biology, Mayo Clinic Comprehensive Cancer Center, Jacksonville, Florida 32224, radisky.evette@mayo.edu.,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.,Institut für Pharmazeutische und Medizinische Chemie, PharmaCampus, Westfälische Wilhelms-Universität Münster, Corrensstraße 48, D-48149 Münster, Germany. joachim.jose@uni-muenster.de.,RIKEN Program for Drug Discovery and Medical Technology Platforms , 2-1 Hirosawa , Wako , Saitama 351-0198 , Japan.,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.,the Department of Cancer Biology, Mayo Clinic Comprehensive Cancer Center, Jacksonville, Florida 32224.,National Magnetic Resonance Facility at Madison , University of Wisconsin-Madison , 433 Babcock Drive , Madison , Wisconsin 53706 , United States.,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.,the Department of Biology, Technion-Israel Institute of Technology, Haifa 3200003, Israel.,HRMEM Facility, University of British Columbia, Vancouver, BC, Canada.,the National Institute for Biotechnology in the Negev (NIBN), Beer-Sheva 84105, Israel.,Systems Immunity Research Institute, Cardiff University, Cardiff, Wales, United Kingdom.,Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, MI 48109, USA. Electronic address: nkoropat@umich.edu.,the Department of Internal Medicine, Faculty of Medicine and Health Sciences, Ghent University, 9000 Ghent, Belgium.,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.,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.,Broad Institute of Harvard and MIT, Cambridge, MA, USA.,Immunology Division, Garvan Institute of Medical Research, 384 Victoria Road, Darlinghurst, Sydney, NSW, 2010, Australia.,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.,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.,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
Casein kinase II subunit alpha
A
335Homo sapiensMutation(s): 0 
Gene Names: CSNK2A1 (CK2A1)
EC: 2.7.11.1
Find proteins for P68400 (Homo sapiens)
Go to Gene View: CSNK2A1
Go to UniProtKB:  P68400
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
8QH
Query on 8QH

Download SDF File 
Download CCD File 
A
(4~{Z})-6,7-bis(chloranyl)-4-[[(4-methylphenyl)amino]methylidene]-8-oxidanyl-1,2-dihydrodibenzofuran-3-one
C20 H15 Cl2 N O3
ZCTFVCJEVPAGSA-NTEUORMPSA-N
 Ligand Interaction
ACT
Query on ACT

Download SDF File 
Download CCD File 
A
ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
 Ligand Interaction
GOL
Query on GOL

Download SDF File 
Download CCD File 
A
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.79 Å
  • R-Value Free: 0.199 
  • R-Value Work: 0.164 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 57.437α = 90.00
b = 45.706β = 110.94
c = 63.187γ = 90.00
Software Package:
Software NamePurpose
PHASERphasing
PHENIXrefinement
Aimlessdata scaling
XDSdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2018-02-28
    Type: Initial release
  • Version 1.1: 2018-03-07
    Type: Database references
  • Version 1.2: 2018-04-18
    Type: Data collection, Database references
  • Version 1.3: 2018-04-25
    Type: Data collection, Database references