6A1C

Crystal structure of the CK2a1-go289 complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.68 Å
  • R-Value Free: 0.196 
  • R-Value Work: 0.138 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

Cell-based screen identifies a new potent and highly selective CK2 inhibitor for modulation of circadian rhythms and cancer cell growth.

Oshima, T.Niwa, Y.Kuwata, K.Srivastava, A.Hyoda, T.Tsuchiya, Y.Kumagai, M.Tsuyuguchi, M.Tamaru, T.Sugiyama, A.Ono, N.Zolboot, N.Aikawa, Y.Oishi, S.Nonami, A.Arai, F.Hagihara, S.Yamaguchi, J.Tama, F.Kunisaki, Y.Yagita, K.Ikeda, M.Kinoshita, T.Kay, S.A.Itami, K.Hirota, T.

(2019) Sci Adv 5: eaau9060-eaau9060

  • DOI: 10.1126/sciadv.aau9060

  • PubMed Abstract: 
  • Compounds targeting the circadian clock have been identified as potential treatments for clock-related diseases, including cancer. Our cell-based phenotypic screen revealed uncharacterized clock-modulating compounds. Through affinity-based target dec ...

    Compounds targeting the circadian clock have been identified as potential treatments for clock-related diseases, including cancer. Our cell-based phenotypic screen revealed uncharacterized clock-modulating compounds. Through affinity-based target deconvolution, we identified GO289, which strongly lengthened circadian period, as a potent and selective inhibitor of CK2. Phosphoproteomics identified multiple phosphorylation sites inhibited by GO289 on clock proteins, including PER2 S693. Furthermore, GO289 exhibited cell type-dependent inhibition of cancer cell growth that correlated with cellular clock function. The x-ray crystal structure of the CK2α-GO289 complex revealed critical interactions between GO289 and CK2-specific residues and no direct interaction of GO289 with the hinge region that is highly conserved among kinases. The discovery of GO289 provides a direct link between the circadian clock and cancer regulation and reveals unique design principles underlying kinase selectivity.


    Organizational Affiliation

    National Key Laboratory of Crop Genetic Improvement, Huazhong Agriculture University, 430072, Wuhan, China.,PRESTO, JST, Nagoya 464-8601, Japan.,ERATO Itami Molecular Nanocarbon Project, JST, Nagoya 464-8601, Japan.,RIKEN SPring-8 Center, 1-1-1 Kouto, Sayo-cho, Sayo-gun, Hyogo 679-5148, Japan.,Institute of Biology, Westlake Institute for Advanced Study, Hangzhou, China.,Shanghai Institute of Precision Medicine, 200125, Shanghai, China. huangchh@shsmu.edu.cn.,Department of Health Sciences, Graduate School of Medical Sciences, Kyushu University, Fukuoka 812-8582, Japan.,Key laboratory of Cell Differentiation and Apoptosis of Chinese Ministry of Education, Shanghai Jiao Tong University School of Medicine, 200025, Shanghai, China. leim@shsmu.edu.cn.,Department of Physiology and Systems Bioscience, Kyoto Prefectural University of Medicine, Kyoto 602-8566, Japan.,Institute of Transformative Bio-Molecules, Nagoya University, Nagoya 464-8601, Japan.,Department of Physics, Graduate School of Science, Nagoya University, Nagoya 464-8601, Japan, and RIKEN Center for Computational Science, Kobe 650-0047, Japan.,Department of Stem Cell Biology and Medicine/Cancer Stem Cell Research, Kyushu University Graduate School of Medical Sciences, Fukuoka 812-8582, Japan.,Department of Physiology, Faculty of Medicine, Saitama Medical University, Saitama 350-0495, Japan.,Beijing Advanced Innovation Center for Structural Biology, Tsinghua-Peking Joint Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing, China. shi-lab@tsinghua.edu.cn.,Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, 200011, Shanghai, China. huangchh@shsmu.edu.cn.,Graduate School of Science, Osaka Prefecture University, Osaka 599-8531, Japan.,Applied Biotechnology Group, Biomedical Science School, Universidad Europea de Madrid, Urbanización El Bosque, Calle Tajo, s/n, 28670, Villaviciosa de Odón, Spain; Grupo de Investigación en Desarrollo Agroindustrial Sostenible, Universidad de la Costa, CUC, Calle 58 # 55 - 66, Barranquilla, Colombia. Electronic address: jesus.fernandez2@universidadeuropea.es.,Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, 200011, Shanghai, China.,Department of Physiology and Advanced Research Center for Medical Science, Toho University School of Medicine, Tokyo 143-8540, Japan.,Center for Advanced Medical Innovation, Kyushu University, Fukuoka 812-8582, Japan.,Division of Agronomy and Horticultural Science, Graduate School of Agriculture, Kyoto University, Uji-shi, Japan.,Shanghai Institute of Precision Medicine, 200125, Shanghai, China.,Beijing Advanced Innovation Center for Structural Biology, Tsinghua-Peking Joint Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing, China.,Institute of Biology, Westlake Institute for Advanced Study, Hangzhou, China. shi-lab@tsinghua.edu.cn.,Department of Applied Chemistry and Biotechnology, Graduate School of Engineering, University of Fukui, Fukui-shi, Japan.,Technology Center for Protein Sciences, Ministry of Education Key Laboratory of Protein Sciences, School of Life Sciences, Tsinghua University, Beijing, China.,Shanghai Institute of Precision Medicine, 200125, Shanghai, China. leim@shsmu.edu.cn.,Department of Chemistry, Graduate School of Science, Nagoya University, Nagoya 464-8601, Japan.,National Center for Protein Science Shanghai, State Key Laboratory of Molecular Biology, CAS Center for Excellence on Molecular Cell Science, Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, University of Chinese Academy of Sciences, 200031, Shanghai, China.,Department of Applied Chemistry, Waseda University, Tokyo 169-8555, Japan.,Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, 200011, Shanghai, China. leim@shsmu.edu.cn.,Applied Biotechnology Group, Biomedical Science School, Universidad Europea de Madrid, Urbanización El Bosque, Calle Tajo, s/n, 28670, Villaviciosa de Odón, Spain.,Keck School of Medicine, University of Southern California, Los Angeles, CA 90089, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Casein kinase II subunit alpha
A
340Homo 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
NA
Query on NA

Download SDF File 
Download CCD File 
A
SODIUM ION
Na
FKNQFGJONOIPTF-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
9NX
Query on 9NX

Download SDF File 
Download CCD File 
A
5-bromanyl-2-methoxy-4-[(E)-(3-methylsulfanyl-5-phenyl-1,2,4-triazol-4-yl)iminomethyl]phenol
C17 H15 Br N4 O2 S
DARDDBZKGVEVKB-VXLYETTFSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.68 Å
  • R-Value Free: 0.196 
  • R-Value Work: 0.138 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 51.657α = 90.00
b = 78.831β = 90.00
c = 79.403γ = 90.00
Software Package:
Software NamePurpose
MOLREPphasing
HKL-2000data reduction
HKL-2000data scaling
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2019-03-06
    Type: Initial release