Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

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

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

Macromolecule Content

• Total Structure Weight: 39.98 kDa 
• Atom Count: 3061 
• Modelled Residue Count: 327 
• Deposited Residue Count: 328 
• Unique protein chains: 1

6FVG

The Structure of CK2alpha with CCh507 bound

• PDB DOI: 10.2210/pdb6FVG/pdb

• Classification: TRANSFERASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2018-03-02 Released: 2019-06-19 
• Deposition Author(s): Brear, P., Prudent, R., Laudet, B., Filhol, O., Cochet, C., Sautel, C., Moucadel, V., Bestgen, B., Engel, M., Ettaoussi, M., Lomberget, T., Le Borgne, M., Kufareva, I., Abagyan, R., Hyvonen, M.
• Funding Organization(s): Wellcome Trust

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.60 Å
• R-Value Free: 0.229 
• R-Value Work: 0.206 
• R-Value Observed: 0.208 

Literature

Discovery of holoenzyme-disrupting chemicals as substrate-selective CK2 inhibitors.

Kufareva, I., Bestgen, B., Brear, P., Prudent, R., Laudet, B., Moucadel, V., Ettaoussi, M., Sautel, C.F., Krimm, I., Engel, M., Filhol, O., Borgne, M.L., Lomberget, T., Cochet, C., Abagyan, R.

(2019) Sci Rep 9: 15893-15893

• PubMed: 31685885 
• DOI: 10.1038/s41598-019-52141-5
• Primary Citation of Related Structures:  
  6FVF, 6FVG


• PubMed Abstract: 
  

CK2 is a constitutively active protein kinase overexpressed in numerous malignancies. Interaction between CK2α and CK2β subunits is essential for substrate selectivity. The CK2α/CK2β interface has been previously targeted by peptides to achieve functional effects; however, no small molecules modulators were identified due to pocket flexibility and open shape. Here we generated numerous plausible conformations of the interface using the fumigation modeling protocol, and virtually screened a compound library to discover compound 1 that suppressed CK2α/CK2β interaction in vitro and inhibited CK2 in a substrate-selective manner. Orthogonal SPR, crystallography, and NMR experiments demonstrated that 4 and 6, improved analogs of 1, bind to CK2α as predicted. Both inhibitors alter CK2 activity in cells through inhibition of CK2 holoenzyme formation. Treatment with 6 suppressed MDA-MB231 triple negative breast cancer cell growth and induced apoptosis. Altogether, our findings exemplify an innovative computational-experimental approach and identify novel non-peptidic inhibitors of CK2 subunit interface disclosing substrate-selective functional effects.

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Organizational Affiliation: 

University of California, San Diego, Skaggs School of Pharmacy and Pharmaceutical Sciences, La Jolla, CA, 92093, USA. [e-mail].

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Casein kinase II subunit alpha	A	328	Homo sapiens	Mutation(s): 4  Gene Names: CSNK2A1, CK2A1 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

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ATP	C [auth A]	ADENOSINE-5'-TRIPHOSPHATE C10 H16 N5 O13 P3 ZKHQWZAMYRWXGA-KQYNXXCUSA-N
E8K	B [auth A]	[1-[2-(phenylsulfonylamino)ethyl]piperidin-4-yl]methyl 1~{H}-indole-3-carboxylate C23 H27 N3 O4 S IAUOQYCDFSEWNE-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.60 Å
• R-Value Free: 0.229 
• R-Value Work: 0.206 
• R-Value Observed: 0.208 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 60.183	α = 90
b = 45.931	β = 111.22
c = 63.706	γ = 90

Software Package:

Software Name	Purpose
Aimless	data scaling
BUSTER	refinement
PDB_EXTRACT	data extraction
DIALS	data reduction
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Deposited Date: 2018-03-02 
• Released Date: 2019-06-19 
Deposition Author(s): Brear, P., Prudent, R., Laudet, B., Filhol, O., Cochet, C., Sautel, C., Moucadel, V., Bestgen, B., Engel, M., Ettaoussi, M., Lomberget, T., Le Borgne, M., Kufareva, I., Abagyan, R., Hyvonen, M.

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Funding Organization	Location	Grant Number
Wellcome Trust	United Kingdom	107714/Z/15/Z

Revision History  

• Version 1.0: 2019-06-19
  Type: Initial release
  
• Version 1.1: 2020-07-01
  Changes: Database references