4RLL

Crystal structure of human CK2alpha in complex with the ATP-competitive inhibitor 4-[(E)-(fluoren-9-ylidenehydrazinylidene)-methyl] benzoate

• PDB DOI: https://doi.org/10.2210/pdb4RLL/pdb

• Classification: TRANSFERASE/TRANSFERASE INHIBITOR
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2014-10-17 Released: 2014-12-17 
• Deposition Author(s): Guerra, B., Rasmussen, T.D.L., Schnitzler, A., Jensen, H.H., Boldyreff, B.S., Miyata, Y., Marcussen, N., Niefind, K., Issinger, O.G.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.85 Å
• R-Value Free: 0.213 
• R-Value Work: 0.170 
• R-Value Observed: 0.172 

Starting Model: experimental

Literature

Protein kinase CK2 inhibition is associated with the destabilization of HIF-1 alpha in human cancer cells.

Guerra, B., Rasmussen, T.D., Schnitzler, A., Jensen, H.H., Boldyreff, B.S., Miyata, Y., Marcussen, N., Niefind, K., Issinger, O.G.

(2015) Cancer Lett 356: 751-761

• PubMed: 25449433 
• DOI: https://doi.org/10.1016/j.canlet.2014.10.026
• Primary Citation of Related Structures:  
  4RLK, 4RLL


• PubMed Abstract: 
  

  Screening for protein kinase CK2 inhibitors of the structural diversity compound library (DTP NCI/NIH) led to the discovery of 4-[(E)-(fluoren-9-ylidenehydrazinylidene)-methyl]benzoic acid (E9). E9 induces apoptotic cell death in various cancer cell lines and upon hypoxia, the compound suppresses CK2-catalyzed HSP90/Cdc37 phosphorylation and induces HIF-1α degradation. Furthermore, E9 exerts a strong anti-tumour activity by inducing necrosis in murine xenograft models underlining its potential to be used for cancer treatment in future clinical studies. Crystal structure analysis of human and maize CK2α in complex with E9 reveals unique binding properties of the inhibitor to the enzyme, accounting for its affinity and selectivity.

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Organizational Affiliation: 

Biomedical Research Group, BMB, University of Southern Denmark, Odense, Denmark.

Biological Assembly 1  

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

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

Macromolecule Content

• Total Structure Weight: 40.49 kDa 
• Atom Count: 3,080 
• Modelled Residue Count: 329 
• Deposited Residue Count: 335 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Casein kinase II subunit alpha	A	335	Homo sapiens	Mutation(s): 0  Gene Names: CK2A1, 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
E91	C [auth A]	4-[(E)-(9H-fluoren-9-ylidenehydrazinylidene)methyl]benzoic acid C21 H14 N2 O2 UDYNXPSETJWNEU-LPYMAVHISA-N
GOL	B [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.85 Å
• R-Value Free: 0.213 
• R-Value Work: 0.170 
• R-Value Observed: 0.172 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 58.49	α = 90
b = 45.45	β = 111.39
c = 64.01	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2014-12-17 
Deposition Author(s): Guerra, B., Rasmussen, T.D.L., Schnitzler, A., Jensen, H.H., Boldyreff, B.S., Miyata, Y., Marcussen, N., Niefind, K., Issinger, O.G.

Revision History  

• Version 1.0: 2014-12-17
  Type: Initial release
  
• Version 1.1: 2023-09-20
  Changes: Data collection, Database references, Derived calculations, Refinement description