9QRH | pdb_00009qrh

Protein Kinase CK2 and bivalent inhibitors


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.59 Å
  • R-Value Free: 
    0.236 (Depositor), 0.232 (DCC) 
  • R-Value Work: 
    0.193 (Depositor), 0.193 (DCC) 
  • R-Value Observed: 
    0.195 (Depositor) 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.0 of the entry. See complete history


Literature

Picomolar bivalent inhibitors of protein kinase CK2 active against beta-coronavirus replication.

Grenier, D.Lopez Molina, D.S.Gelin, M.Mularoni, A.Guichou, J.F.Delcros, J.G.Martinasso, C.Yang, Y.Ahnou, N.Pawlotsky, J.M.Ahmed-Belkacem, A.Krimm, I.

(2025) Eur J Med Chem 296: 117826-117826

  • DOI: https://doi.org/10.1016/j.ejmech.2025.117826
  • Primary Citation of Related Structures:  
    9QRH, 9QRI, 9QRJ, 9QSR, 9QSS, 9QSU, 9QSV

  • PubMed Abstract: 

    The protein casein kinase 2 (CK2) has been shown to be upregulated in SARS-CoV-2 infections. However, few inhibitors have been tested for antiviral activity against coronaviruses. In this study, highly potent and selective bivalent inhibitors targeting the protein kinase CK2 were developed. The chemical structure of the well-known inhibitor CX-4945 was used as an anchor for the ATP-binding site and was linked by polar and aliphatic linkers to chemical structures that bind the cryptic αD pocket of CK2. The bivalent inhibitor Biv5, which demonstrated a sub-nanomolar kinase inhibition, showed potent antiviral activity against SARS-CoV-2 in HEK-ACE2-TMPRSS2 and Vero cells. In addition, Biv5 significantly reduced viral replication over time in an ex vivo model of primary human nasal epithelial cells. The selectivity of Biv5 was tested against 16 kinases targeted by CX-4945, confirming that targeting the αD pocket confers high selectivity for CK2 to such inhibitors.


  • Organizational Affiliation
    • University Lyon, Université Claude Bernard Lyon 1, INSERM 1052, CNRS 5286, Centre Léon Bérard, Centre de recherche en cancérologie de Lyon, Institut Convergence Plascan, 69373 Lyon, France.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Casein kinase II subunit alpha
A, B
359Homo 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
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
A1I9M (Subject of Investigation/LOI)
Query on A1I9M

Download Ideal Coordinates CCD File 
C [auth A],
J [auth B]
5-[[(3~{E})-3-[4-[2-(3,4-dichlorophenyl)ethylamino]-4-oxidanylidene-butanoyl]iminopropyl]amino]benzo[c][2,6]naphthyridine-8-carboxylic acid
C28 H25 Cl2 N5 O4
MDSSDLXQZDAQAA-INRUPRTJSA-N
SO4
Query on SO4

Download Ideal Coordinates CCD File 
D [auth A]
E [auth A]
F [auth A]
G [auth A]
H [auth B]
D [auth A],
E [auth A],
F [auth A],
G [auth A],
H [auth B],
I [auth B],
K [auth B],
L [auth B],
M [auth B]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.59 Å
  • R-Value Free:  0.236 (Depositor), 0.232 (DCC) 
  • R-Value Work:  0.193 (Depositor), 0.193 (DCC) 
  • R-Value Observed: 0.195 (Depositor) 
Space Group: P 43 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 127.669α = 90
b = 127.669β = 90
c = 124.412γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
Aimlessdata scaling
XDSdata reduction
PHENIXphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Agence Nationale de la Recherche (ANR)FranceANR-21-CE18-0014-01
Agence Nationale de la Recherche (ANR)FranceANR-17-CONV-002

Revision History  (Full details and data files)

  • Version 1.0: 2025-07-30
    Type: Initial release