6GUC

CDK2/CyclinA in complex with SU9516


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.223 
  • R-Value Work: 0.192 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Differences in the Conformational Energy Landscape of CDK1 and CDK2 Suggest a Mechanism for Achieving Selective CDK Inhibition.

Wood, D.J.Korolchuk, S.Tatum, N.J.Wang, L.Z.Endicott, J.A.Noble, M.E.M.Martin, M.P.

(2019) Cell Chem Biol 26: 121-130.e5

  • DOI: 10.1016/j.chembiol.2018.10.015
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Dysregulation of the cell cycle characterizes many cancer subtypes, providing a rationale for developing cyclin-dependent kinase (CDK) inhibitors. Potent CDK2 inhibitors might target certain cancers in which CCNE1 is amplified. However, current CDK2 ...

    Dysregulation of the cell cycle characterizes many cancer subtypes, providing a rationale for developing cyclin-dependent kinase (CDK) inhibitors. Potent CDK2 inhibitors might target certain cancers in which CCNE1 is amplified. However, current CDK2 inhibitors also inhibit CDK1, generating a toxicity liability. We have used biophysical measurements and X-ray crystallography to investigate the ATP-competitive inhibitor binding properties of cyclin-free and cyclin-bound CDK1 and CDK2. We show that these kinases can readily be distinguished by such inhibitors when cyclin-free, but not when cyclin-bound. The basis for this discrimination is unclear from either inspection or molecular dynamics simulation of ligand-bound CDKs, but is reflected in the contacts made between the kinase N- and C-lobes. We conclude that there is a subtle but profound difference between the conformational energy landscapes of cyclin-free CDK1 and CDK2. The unusual properties of CDK1 might be exploited to differentiate CDK1 from other CDKs in future cancer therapeutic design.


    Organizational Affiliation

    Department of Chemistry, King's College London, Britannia House, 7 Trinity Street, London SE1 1DB, UK; Structural Biology and Biophysics Unit, Fondazione Ri.MED, Via Bandiera, 11, 90133 Palermo, Italy.,NMR Research Center, Indian Institute of Science , Bangalore, Karnataka 560012, India.,Department of Biochemistry and Biophysics, University of California, San Francisco, CA 94143.,Newcastle Cancer Centre, Northern Institute for Cancer Research, Medical School, Newcastle University, Paul O'Gorman Building, Framlington Place, Newcastle upon Tyne NE2 4HH, UK. Electronic address: mathew.martin@ncl.ac.uk.,Department of Chemistry, University of Illinois at Urbana-Champaign, Champaign, IL, USA.,Department of Analytical Biochemistry, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Gronostajowa 7, 30-387 Kraków, Poland. Electronic address: benedykt.wladyka@uj.edu.pl.,Griffith Institute for Drug Discovery, Griffith University, Don Young Road, Nathan, Brisbane, Queensland 4111, Australia.,Beijing Advanced Innovation Center for Food Nutrition and Human Health, State Key Laboratory of Agrobiotechnology, China Agricultural University, Beijing 100193, China. Electronic address: chenzhongzhou@cau.edu.cn.,Center of Biomedical Analysis, Tsinghua University, 100084, Beijing, China.,Newcastle Cancer Centre, Northern Institute for Cancer Research, Medical School, Newcastle University, Paul O'Gorman Building, Framlington Place, Newcastle upon Tyne NE2 4HH, UK.,Industrial Enzymes National Engineering Laboratory, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China.,Centre de Biologie Cellulaire de Montpellier, CNRS, University Montpellier, UMR5237, 34090 Montpellier, France.,Faculty of Chemistry, Biological and Chemical Research Centre, University of Warsaw, Żwirki i Wigury 101, 02-089 Warszawa, Poland. Electronic address: lyam@chem.uw.edu.pl.,School of Food Science and Technology, National Engineering Research Center of Seafood, Dalian Polytechnic University, 116034, Dalian, China. duming@dlpu.edu.cn.,School of Life and Environmental Sciences, Deakin University, Melbourne, Victoria, Australia.,Beijing Advanced Innovation Center for Food Nutrition and Human Health, College of Food Science & Nutritional Engineering, China Agricultural University, Key Laboratory of Functional Dairy, Ministry of Education, 100083, Beijing, China. gzhao@cau.edu.cn.,Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720.,School of Life Sciences, University of Science and Technology of China, Anhui, 230026, China.,Department of Microbiology and Immunology, University of Michigan Medical School, 5641 Medical Science Building II, 1150 West Medical Center Drive, Ann Arbor, MI 48109-0620, USA.,NEUROFARBA Dept., Sezione di Scienze Farmaceutiche, Università degli Studi di Firenze, Via Ugo Schiff 6, 50019 Sesto Fiorentino, Florence, Italy.,Amgen Research, Department of Therapeutic Discovery, Amgen Inc., 7990 Enterprise Street, Burnaby, BC V5A 1V7, Canada.,Department of Pharmaceutical Sciences, College of Pharmacy , University of Kentucky , 789 South Limestone Street , Lexington , Kentucky 40536 , United States.,Department of Biochemistry, University of Illinois at Urbana-Champaign, Champaign, IL, USA. vddonk@illinois.edu.,Newcastle Cancer Centre, Northern Institute for Cancer Research, Medical School, Newcastle University, Paul O'Gorman Building, Framlington Place, Newcastle upon Tyne NE2 4HH, UK. Electronic address: martin.noble@ncl.ac.uk.,Department of Biochemistry, University of Illinois at Urbana-Champaign, Champaign, IL, USA.,Beijing Advanced Innovation Center for Food Nutrition and Human Health, State Key Laboratory of Agrobiotechnology, China Agricultural University, Beijing 100193, China.,Department of Molecular and Cell Biology, University of Connecticut, Storrs, United States.,Institute of Biochemistry and Biophysiscs, Polish Academy of Science, Laboratory of Biological NMR, Pawińskiego 5A, 02-106 Warszawa, Poland. Electronic address: aejchart@ibb.waw.pl.,Howard Hughes Medical Institute, Oregon Health & Science University, Portland, Oregon, United States of America.,School of Pharmaceutical Sciences , Sun Yat-Sen University , Guangzhou 510006 , P.R. China.,School of Biotechnology and Biomolecular Sciences, the University of New South Wales, Sydney, NSW, 2052, Australia. h.rob.yang@unsw.edu.au.,Amgen Research, Department of Cardiometabolic Disorders, Amgen Inc., 1120 Veterans Blvd., South San Francisco, CA 94080, USA.,Biogen, 225 Binney Street, Cambridge, MA 02142, USA. Electronic address: paul.weinreb@biogen.com.,Department of Biological Sciences, Mount Holyoke College, 50 College Street, South Hadley, MA 01075, USA.,Amgen Research, Department of Cardiometabolic Disorders, Amgen Inc., One Amgen Center Dr., Thousand Oaks, CA 91320, USA.,School of Biotechnology and Biomolecular Sciences, the University of New South Wales, Sydney, NSW, 2052, Australia.,Instituto de Biociências, Letras e Ciências Exatas , Universidade Estadual Paulista , Rua Cristóvão Colombo , 2265 São José do Rio Preto , Brazil.,Division of Biological and Environmental Sciences and Engineering, King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Saudi Arabia. Electronic address: jaremko@gmail.com.,Photon Science, SLAC National Accelerator Laboratory, Menlo Park, CA, 94025-7015, USA.,Department of Chemistry, University of Cambridge, CB2 1EW Cambridge, United Kingdom.,Griffith Institute for Drug Discovery, Griffith University, Don Young Road, Nathan, Brisbane, Queensland 4111, Australia. Electronic address: s.poulsen@griffith.edu.au.,Beijing Advanced Innovation Center for Structural Biology, MOE Key Laboratory for Protein Science, Tsinghua-Peking Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing, 100084, China. jiaweiwu@suda.edu.cn.,Department of Chemistry, King's College London, Britannia House, 7 Trinity Street, London SE1 1DB, UK.,Diagnostics and Therapeutics, Georgia State University, Atlanta, Georgia, 30302-3965.,Howard Hughes Medical Institute, University of California, Berkeley, CA 94720.,School of Pharmaceutical Sciences; MOE Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology, Tsinghua University, Beijing, 100084, China.,The Ohio State University College of Medicine, 473 W 12th Ave, Columbus, OH, 43210, USA.,Howard Hughes Medical Institute, University of California, San Francisco, CA 94143.,Department of Structural Biology, Stanford University School of Medicine, Stanford, CA, 94305, USA.,Drug Design Laboratory, Graduate School of Medical Life Science, Yokohama City University, Tsurumi, Yokohama 230-0045, Japan.,Department of Developmental Biology, Stanford University School of Medicine, Stanford, CA, 94305, USA.,Department of Physiology, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, 6525 GA Nijmegen, The Netherlands.,Department of Analytical Biochemistry, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Gronostajowa 7, 30-387 Kraków, Poland. Electronic address: pawel.mak@uj.edu.pl.,Sorbonne Universités, Université Pierre et Marie Curie, 75006 Paris, France.,From the Department of Biochemistry, College of Life Science & Biotechnology, Yonsei University, Seoul 03722, South Korea, wlee@spin.yonsei.ac.kr.,Institute of Molecular Enzymology, Soochow University, Suzhou, Jiangsu, 215123, China.,Complex Systems Division, Beijing Computational Science Research Center, 10 East Xibeiwang Road, Haidian District, Beijing 100193, China, hgliu@csrc.ac.cn.,Beijing Advanced Innovation Center for Structural Biology, MOE Key Laboratory for Protein Science, Tsinghua-Peking Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing, 100084, China.,Amgen Research, Department of Therapeutic Discovery, Amgen Inc., 1120 Veterans Blvd., South San Francisco, CA 94080, USA.,Institute of Biological Chemistry, Academia Sinica, Taipei, 11529, Taiwan.,Vollum Institute, Oregon Health & Science University, Portland, Oregon, United States of America.,Department of Microbiology, Immunology and Tropical Medicine and Research Center for Neglected Diseases of Poverty, School of Medicine and Health Sciences, George Washington University , Washington D.C. 20037, United States.,Department of Chemistry , The University of Texas at Austin , Austin , Texas 78712 , United States.,Department of Chemistry and Chemical Biology, Cornell University, NE-CAT, Advanced Photon Source, Argonne, Illinois, USA.,Beijing Advanced Innovation Center for Food Nutrition and Human Health, College of Food Science & Nutritional Engineering, China Agricultural University, Key Laboratory of Functional Dairy, Ministry of Education, 100083, Beijing, China.,Departamento de Bioquímica e Imunologia, Instituto de Ciências Biológicas , Universidade Federal de Minas Gerais , Av. Antônio Carlos , 6627 Belo Horizonte , Brazil.,Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, Victoria, Australia.,School of Biology, Centers for Georgia State University, Atlanta, Georgia, 30302-3965.,University of Wyoming School of Pharmacy, 1000 E. University Ave., HS 596, Laramie, WY, 82071, USA.,Department of Biochemistry, University of Illinois at Urbana-Champaign, Champaign, IL, USA. s-nair@life.uiuc.edu.,Division of Biomedical Sciences, School of Medicine , University of California Riverside , 900 University Avenue , Riverside , California 92521 , United States.,Center for Biophysics and Computational Biology, University of Illinois at Urbana-Champaign, Champaign, IL, USA. s-nair@life.uiuc.edu.,Department of Ophthalmology, University of California, San Francisco, CA 94158.,CSIRO, 343 Royal Parade, Parkville, Melbourne, Victoria 3052, Australia.,Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720; jfraser@fraserlab.com enogales@lbl.gov.,Department of Biochemistry and Molecular Genetics, University of Alabama at Birmingham, Birmingham, Alabama, USA.,Department of Biochemistry and Biophysics, University of California, San Francisco, CA 94143; david.julius@ucsf.edu yifan.cheng@ucsf.edu jenny.vanderwijst@radboudumc.nl.,Unité Récepteurs-canaux, Institut Pasteur, UMR 3571, CNRS, 75015 Paris, France.,Department of Molecular Biosciences , The University of Texas at Austin , Austin , Texas 78712 , United States.,Picobiology Institute, Graduate School of Life Science, University of Hyogo, 3-2-1 Kouto, Kamigori-cho, Ako-gun, Hyogo 678-1297, Japan.,Howard Hughes Medical Institute, University of Illinois at Urbana-Champaign, Champaign, IL, USA. vddonk@illinois.edu.,Department of Chemistry, Georgia State University, Atlanta, Georgia, 30302-3965.,Amgen Research, Department of Cardiometabolic Disorders, Amgen Inc., One Amgen Center Dr., Thousand Oaks, CA 91320, USA. dlloyd@amgen.com.,Departamento de Química, Centro de Investigación en Síntesis Química, Universidad de La Rioja, La Rioja, Spain.,Amgen Research, Department of Pharmacokinetics and Drug Metabolism, Amgen Inc., One Amgen Center Dr., Thousand Oaks, CA 91320, USA.,Department of Physiology, University of California, San Francisco, CA 94143 david.julius@ucsf.edu yifan.cheng@ucsf.edu jenny.vanderwijst@radboudumc.nl.,Unité Dynamique Structurale des Macromolécules, Institut Pasteur, UMR 3528, CNRS, 75015 Paris, France; marc.delarue@pasteur.fr.,National Leading Research Laboratory of Drug Resistance Proteomics, Department of Biological Sciences, Myongji University, 116 Myongjiro, Yongin, Gyeonggido 17058, Republic of Korea.,Molecular Biophysics Unit, Indian Institute of Science , Bangalore, Karnataka 560012, India.,Centre for Biodiscovery and Molecular Development of Therapeutics, Australian Institute of Tropical Health and Medicine, James Cook University , Cairns 4870, Queensland Australia.,Amgen Research, Department of Therapeutic Discovery, Amgen Inc., One Amgen Center Dr., Thousand Oaks, CA 91320, USA.,California Institute for Quantitative Biology (QB3), University of California, Berkeley, CA 94720.,Department of Chemical and Systems Biology, Stanford University School of Medicine, Stanford, CA, 94305, USA. mochly@stanford.edu.,Department of Cell and Molecular Biology, Uppsala University, Biomedical Center, PO Box 596, SE-751 24 Uppsala, Sweden.,Department of Microbiology, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Gronostajowa 7, 30-387 Kraków, Poland; Małopolska Centre of Biotechnology, Jagiellonian University, Gronostajowa 7a, 30-387 Kraków, Poland. Electronic address: grzegorz.dubin@uj.edu.pl.,Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, CA 94158.,National Leading Research Laboratory of Drug Resistance Proteomics, Department of Biological Sciences, Myongji University, 116 Myongjiro, Yongin, Gyeonggido 17058, Republic of Korea. Electronic address: sangheelee@mju.ac.kr.,Chapman University School of Pharmacy (CUSP), Harry and Diane Rinker Health Science Campus, Chapman University, Irvine, CA, 92618, USA.,Physics Department, and Biodesign Center for Applied Structural Discovery, Arizona State University, Tempe, Arizona 85287.,Departamento de Microbiología, Facultad de Salud , Universidad del Valle , Calle 4B No. 36-00 Cali , Colombia.,Biogen, 225 Binney Street, Cambridge, MA 02142, USA.,Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720; jfraser@fraserlab.com enogales@lbl.gov.,Department of Chemical and Systems Biology, Stanford University School of Medicine, Stanford, CA, 94305, USA.,Department of Engineering Physics, Tsinghua University, Beijing 100086, China.,Unité Dynamique Structurale des Macromolécules, Institut Pasteur, UMR 3528, CNRS, 75015 Paris, France.,Neurimmune AG, Wagistrasse 13, 8952 Schlieren, Switzerland; Institute for Regenerative Medicine, University of Zurich, Wagistrasse 12, 8952 Schlieren, Switzerland.,Institute of Molecular Enzymology, Soochow University, Suzhou, Jiangsu, 215123, China. jiaweiwu@suda.edu.cn.,Expression Génétique Microbienne , UMR 8261, CNRS, Université Paris, Institut de Biologie Physico-Chimique , 13 rue Pierre et Marie Curie , 75005 Paris , France.,Department of Chemistry, King's College London, Britannia House, 7 Trinity Street, London SE1 1DB, UK. Electronic address: rivka.isaacson@kcl.ac.uk.,Pediatric Dentistry and Microbiology, University of Alabama at Birmingham, Birmingham, Alabama, USA.,Department of Chemistry, University of Illinois at Urbana-Champaign, Champaign, IL, USA. vddonk@illinois.edu.,Biogen, 225 Binney Street, Cambridge, MA 02142, USA; Neurimmune AG, Wagistrasse 13, 8952 Schlieren, Switzerland. Electronic address: andreas.weihofen@biogen.com.,Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, United States.,Complex Systems Division, Beijing Computational Science Research Center, 10 East Xibeiwang Road, Haidian District, Beijing 100193, China.,Centre for Biomolecular Spectroscopy and Randall Division of Cell and Molecular Biophysics, King's College London, New Hunt's House, Guy's Campus, London SE1 1UL, UK.,State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei Collaborative Innovation Center for Green Transformation of Bio-resources, Environmental Microbial Technology Center of Hubei Province, Hubei Key Laboratory of Industrial Biotechnology, College of Life Sciences, Hubei University, Wuhan, 430062, China.,Department of Biochemistry, College of Natural and Agricultural Sciences , University of California Riverside , 900 University Avenue , Riverside , California 92521 , United States.,Laboratoire de Chimie des Processus Biologiques, CNRS-UMR 8229, Collège De France , Université Pierre et Marie Curie , 11 place Marcelin Berthelot , 75231 Paris Cedex 05 , France.,Departamento de Microbiologia, Instituto de Ciências Biomédicas , Universidade de São Paulo , Avenida Prof. Lineu Prestes , 1374 São Paulo , Brazil.,Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720.,Department of Systems Biology and Division of Life Sciences, Yonsei University, Seoul 03722, South Korea.,Amgen Research, Comparative Biology and Safety Sciences, Amgen Inc., 360 Binney St., Cambridge, MA 02141, USA.,Department of Biochemistry and Molecular Genetics, University of Alabama at Birmingham, Birmingham, Alabama, USA champy@uab.edu.,Department of Chemistry, Stanford University, Stanford, CA, 94305-5080, USA.,From the Department of Biochemistry, College of Life Science & Biotechnology, Yonsei University, Seoul 03722, South Korea.,Biotechnology and Drug Design, Georgia State University, Atlanta, Georgia, 30302-3965.,Division of Microbiology and Immunology, Department of Pathology, University of Utah School of Medicine, Salt Lake City, United States.,Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, California 94025, and.,Laboratoire de Biochimie Théorique, CNRS UPR9080 , Institut de Biologie Physico-Chimique , 13 rue Pierre et Marie Curie , 75005 Paris , France.,Neurimmune AG, Wagistrasse 13, 8952 Schlieren, Switzerland.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Cyclin-dependent kinase 2
A, C
302Homo sapiensMutation(s): 0 
Gene Names: CDK2 (CDKN2)
EC: 2.7.11.22
Find proteins for P24941 (Homo sapiens)
Go to Gene View: CDK2
Go to UniProtKB:  P24941
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Cyclin-A2
B, D
268Bos taurusMutation(s): 0 
Gene Names: CCNA2
Find proteins for P30274 (Bos taurus)
Go to Gene View: CCNA2
Go to UniProtKB:  P30274
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SU9
Query on SU9

Download SDF File 
Download CCD File 
A, C
(3Z)-3-(1H-IMIDAZOL-5-YLMETHYLENE)-5-METHOXY-1H-INDOL-2(3H)-ONE
SU9516
C13 H11 N3 O2
QNUKRWAIZMBVCU-WCIBSUBMSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
TPO
Query on TPO
A, C
L-PEPTIDE LINKINGC4 H10 N O6 PTHR
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.223 
  • R-Value Work: 0.192 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 75.353α = 90.00
b = 135.825β = 90.00
c = 149.625γ = 90.00
Software Package:
Software NamePurpose
PHASERphasing
xia2data reduction
REFMACrefinement
Aimlessdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Medical Research Council (United Kingdom)United KingdomMR/N009738/1
Cancer Research UKUnited KingdomC2115/A21421

Revision History 

  • Version 1.0: 2018-12-05
    Type: Initial release
  • Version 1.1: 2019-01-30
    Type: Data collection, Database references