9GCW | pdb_00009gcw

Crystal structure of protein kinase CK2 catalytic subunit (csnk2a1 gene product) in complex with the dual CK2/HDAC inhibitor IOR-160

• PDB DOI: https://doi.org/10.2210/pdb9GCW/pdb

• Classification: TRANSFERASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2024-08-02 Released: 2025-07-30 
• Deposition Author(s): Niefind, K., Werner, C., Lindenblatt, D.
• Funding Organization(s): German Research Foundation (DFG)

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.86 Å
• R-Value Free: 
  0.233 (Depositor), 0.235 (DCC) 
• R-Value Work: 
  0.188 (Depositor), 0.189 (DCC) 
• R-Value Observed: 
  0.190 (Depositor) 

Starting Model: experimental

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

• PubMed: 40672667 
• DOI: https://doi.org/10.1021/acsptsci.5c00192
• Primary Citation 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.
Angiogenesis Group, Oncology Area, Center for Biomedical Research of La Rioja (CIBIR), Logroño 26006, Spain.
Department of Nursing, University of La Rioja, Logroño 26004, Spain.
Institute of Biochemistry, Department of Chemistry and Biochemistry, University of Cologne, Cologne D 50674, Germany.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 42.15 kDa 
• Atom Count: 3,013 
• Modeled Residue Count: 330 
• Deposited Residue Count: 349 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Casein kinase II subunit alpha	A	349	Homo sapiens	Mutation(s): 0  Gene Names: CSNK2A1 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

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
A1IKB (Subject of Investigation/LOI)	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
CL	C [auth A], D [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.86 Å
• R-Value Free:  0.233 (Depositor), 0.235 (DCC) 
• R-Value Work:  0.188 (Depositor), 0.189 (DCC) 
• R-Value Observed: 0.190 (Depositor) 

Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 73.617	α = 90
b = 73.617	β = 90
c = 131.415	γ = 90

Software Package:

Software Name	Purpose
autoPROC	data reduction
autoPROC	data scaling
PHASER	phasing
PHENIX	refinement

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2025-07-30 
Deposition Author(s): Niefind, K., Werner, C., Lindenblatt, D.

---

Funding Organization	Location	Grant Number
German Research Foundation (DFG)	Germany	NI 643/4-2
German Research Foundation (DFG)	Germany	NI 643/11-1

Revision History  

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