9GXY | pdb_00009gxy

Crystal structure of protein kinase CK2 catalytic subunit (CSNK2A2 gene product) in complex with the dual CK2/HDAC inhibitor IOR-160


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.16 Å
  • R-Value Free: 
    0.178 (Depositor), 0.178 (DCC) 
  • R-Value Work: 
    0.160 (Depositor), 0.161 (DCC) 
  • R-Value Observed: 
    0.161 (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

Targeting Casein Kinase 2 and Histone Deacetylase with a Dual Inhibitor Effectively Reduces Tumor Growth in a Triple-Negative Breast Cancer Xenograft Model.

Ortin, I.Ochoa-Callejero, L.Werner, C.Lindenblatt, D.Niefind, K.Martinez, A.de Pascual-Teresa, B.Ramos, A.

(2025) Acs Pharmacol Transl Sci 8: 2093-2105

  • DOI: https://doi.org/10.1021/acsptsci.5c00192
  • Primary Citation of Related Structures:  
    9GCW, 9GXY

  • PubMed Abstract: 

    In a previous study, IOR-160 was identified as a potent dual inhibitor of CK2 and HDAC enzymes. In this study, we evaluated its selectivity and therapeutic potential. IOR-160 exhibited high selectivity for CK2 within a panel of 21 kinases and more widespread inhibitory activity against histone deacetylases (HDAC 1, 2, 3, and 6, low activity for HDAC8). Using a mouse model of triple-negative breast cancer (MDA-MB-231), we further explored its effects on disease progression. Notably, animals treated with IOR-160 exhibited no detectable signs of toxicity or behavioral side effects relative to untreated mice. In a xenograft study, IOR-160 significantly reduced tumor growth ( p = 0.0336) and decreased tumor burden ( p = 0.0454) compared to the vehicle (DMSO)-treated group. In addition, IOR-160 modulated critical cellular signaling pathways, demonstrated by the inhibition of AKT phosphorylation ( p = 0.0175) and a significant increase in acetylated α-tubulin ( p = 0.0023), confirming the dual action of IOR-160 in vivo . Furthermore, X-ray crystallography revealed the binding mode of IOR-160 to CK2, showing high conservation compared to that of the known CK2 inhibitor CX-4945. These results suggest that IOR-160 has significant potential as an antitumor agent. Nonclinical and clinical studies become now necessary to validate the efficacy of this new chemical entity as a potential drug.


  • Organizational Affiliation
    • Departamento de Química y Bioquímica, Facultad de Farmacia, Universidad San Pablo-CEU, CEU Universities, Urbanización Montepríncipe, Boadilla del Monte 28668, Spain.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Casein kinase II subunit alpha'364Homo sapiensMutation(s): 1 
Gene Names: CSNK2A2CK2A2
EC: 2.7.11.1
UniProt & NIH Common Fund Data Resources
Find proteins for P19784 (Homo sapiens)
Explore P19784 
Go to UniProtKB:  P19784
PHAROS:  P19784
GTEx:  ENSG00000070770 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP19784
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
A1IKB (Subject of Investigation/LOI)
Query on A1IKB

Download Ideal Coordinates CCD File 
B [auth A]5-[[8-(oxidanylamino)-8-oxidanylidene-octyl]amino]benzo[c][2,6]naphthyridine-8-carboxylic acid
C21 H24 N4 O4
RLZROBMWZRHTER-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.16 Å
  • R-Value Free:  0.178 (Depositor), 0.178 (DCC) 
  • R-Value Work:  0.160 (Depositor), 0.161 (DCC) 
  • R-Value Observed: 0.161 (Depositor) 
Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 46.343α = 66.58
b = 47.734β = 89.78
c = 50.706γ = 88.99
Software Package:
Software NamePurpose
PHENIXrefinement
autoPROCdata reduction
autoPROCdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
German Research Foundation (DFG)GermanyNI 643/11-1

Revision History  (Full details and data files)

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