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 
  • R-Value Observed: 0.140 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.1 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: https://doi.org/10.1126/sciadv.aau9060
  • Primary Citation of Related Structures:  
    6A1C

  • 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 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

    Institute of Transformative Bio-Molecules, Nagoya University, Nagoya 464-8601, Japan.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Casein kinase II subunit alpha340Homo sapiensMutation(s): 0 
Gene Names: CSNK2A1CK2A1
EC: 2.7.11.1
UniProt & NIH Common Fund Data Resources
Find proteins for P68400 (Homo sapiens)
Explore P68400 
Go to UniProtKB:  P68400
PHAROS:  P68400
GTEx:  ENSG00000101266 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP68400
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
9NX
Query on 9NX

Download Ideal Coordinates CCD File 
B [auth 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
EDO
Query on EDO

Download Ideal Coordinates CCD File 
AA [auth A]
BA [auth A]
CA [auth A]
D [auth A]
E [auth A]
AA [auth A],
BA [auth A],
CA [auth A],
D [auth A],
E [auth A],
F [auth A],
G [auth A],
H [auth A],
I [auth A],
J [auth A],
K [auth A],
L [auth A],
M [auth A],
N [auth A],
O [auth A],
P [auth A],
Q [auth A],
R [auth A],
S [auth A],
T [auth A],
U [auth A],
V [auth A],
W [auth A],
X [auth A],
Y [auth A],
Z [auth A]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
NA
Query on NA

Download Ideal Coordinates CCD File 
C [auth A]SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.68 Å
  • R-Value Free: 0.196 
  • R-Value Work: 0.138 
  • R-Value Observed: 0.140 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 51.657α = 90
b = 78.831β = 90
c = 79.403γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2019-03-06
    Type: Initial release
  • Version 1.1: 2023-11-22
    Changes: Data collection, Database references, Refinement description