9H96 | pdb_00009h96

STRUCTURE OF PROTEIN KINASE CK2 CATALYTIC SUBUNIT (ISOFORM CK2ALPHA'; CSNK2A2 GENE PRODUCT) IN COMPLEX WITH THE INDENOINDOLE-TYPE INHIBITOR MC11

• PDB DOI: https://doi.org/10.2210/pdb9H96/pdb

• Classification: TRANSFERASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2024-10-30 Released: 2025-08-27 
• Deposition Author(s): Niefind, K., Lindenblatt, D., Werner, C.
• Funding Organization(s): German Research Foundation (DFG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.04 Å
• R-Value Free: 
  0.186 (Depositor), 0.185 (DCC) 
• R-Value Work: 
  0.172 (Depositor), 0.172 (DCC) 
• R-Value Observed: 
  0.173 (Depositor) 

Starting Model: experimental

Literature

Exploring the biological potential of the brominated indenoindole MC11 and its interaction with protein kinase CK2.

Marminon, C., Werner, C., Gast, A., Herfindal, L., Charles, J., Lindenblatt, D., Aichele, D., Mularoni, A., Doskeland, S.O., Jose, J., Niefind, K., Le Borgne, M.

(2025) Biol Chem 406: 125-138

• PubMed: 40116007 
• DOI: https://doi.org/10.1515/hsz-2024-0160
• Primary Citation of Related Structures:  
  9H96, 9H97, 9H9D


• PubMed Abstract: 
  

  Protein kinase CK2 is a promising therapeutic target, especially in oncology. Over the years, various inhibitors have been developed, with polyhalogenated scaffolds emerging as a particularly effective class. Halogens like bromine and chlorine enhance inhibitor stability by forming additional interactions within the ATP pocket. Among halogenated scaffolds, benzotriazole and benzimidazole have led to potent molecules such as 4,5,6,7-tetrabromo-1 H -benzotriazole (IC ₅₀ = 300 nM) and 4,5,6,7-tetrabromo-2-(dimethylamino)benzimidazole (IC ₅₀ = 140 nM). Modifications, including 4,5,6-tribromo-7-ethyl-1 H -benzotriazole (IC ₅₀ = 160 nM), further improved activity. Changing scaffolds while retaining halogens has enabled design of new inhibitors. Flavonols, dibenzofuranones, and the indeno[1,2- b ]indole scaffold are key examples. Halogenation of the reference molecule 5-isopropyl-5,6,7,8-tetrahydroindeno[1,2- b ]indole-9,10-dione ( 4b , IC ₅₀ = 360 nM) significantly boosted potency. The study focused on introducing four halogens, yielding to the compound 1,2,3,4-tetrabromo-5-isopropyl-5,6,7,8-tetrahydroindeno[1,2- b ]indole-9,10-dione ( MC11 ), with an IC ₅₀ of 16 nM. Co-crystallography revealed how bromine atoms enhance binding, and MC11 demonstrated strong in cellulo activity, particularly against leukemic cell lines like IPC-Bcl2.

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Organizational Affiliation: 
• Small Molecules for Biological Targets Team, Centre de Recherche en Cancérologie de Lyon, Centre Léon Bérard, CNRS 5286, INSERM 1052, Université Claude Bernard Lyon 1, University of Lyon, F-69373 Lyon, France.
Department of Chemistry and Biochemistry, Institute of Biochemistry, University of Cologne, Zülpicher Str. 47, D-50674 Köln, Germany.
Institute of Pharmaceutical and Medicinal Chemistry, University of Münster, PharmaCampus, Corrensstraße 48, D-48149 Münster, Germany.
Department of Clinical Science, University of Bergen, N-5009 Bergen, Norway.
Department of Biomedicine, University of Bergen, N-5009 Bergen, Norway.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 43.61 kDa 
• Atom Count: 3,327 
• Modeled Residue Count: 327 
• Deposited Residue Count: 364 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Casein kinase II subunit alpha'	A	364	Homo sapiens	Mutation(s): 1  Gene Names: CSNK2A2, CK2A2 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

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
A1ITG (Subject of Investigation/LOI)	C [auth A]	1,2,3,4-tetrakis(bromanyl)-5-propan-2-yl-7,8-dihydro-6~{H}-indeno[1,2-b]indole-9,10-dione C18 H13 Br4 N O2 HCEYYNWPRCEIOJ-UHFFFAOYSA-N
EDO	B [auth A]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N
CL	D [auth A], E [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.04 Å
• R-Value Free:  0.186 (Depositor), 0.185 (DCC) 
• R-Value Work:  0.172 (Depositor), 0.172 (DCC) 
• R-Value Observed: 0.173 (Depositor) 

Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 46.294	α = 66.37
b = 47.709	β = 89.78
c = 50.359	γ = 89.09

Software Package:

Software Name	Purpose
PHENIX	refinement
autoPROC	data processing
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-08-27 
Deposition Author(s): Niefind, K., Lindenblatt, D., Werner, C.

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

Revision History  

• Version 1.0: 2025-08-27
  Type: Initial release
  
• Version 1.1: 2025-09-03
  Changes: Database references