5CQW

Tetragonal Complex Structure of Protein Kinase CK2 Catalytic Subunit with a Benzotriazole-Based Inhibitor Generated by click-chemistry

• PDB DOI: https://doi.org/10.2210/pdb5CQW/pdb
• Entry: 5CQW supersedes: 4BXA

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


• Deposited: 2015-07-22 Released: 2015-09-09 
• Deposition Author(s): Niefind, K., Schnitzler, A., Swider, R., Maslyk, M., Ramos, A.
• Funding Organization(s): German Research Foundation, Spanisch Ministry of Science and Innovation

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.65 Å
• R-Value Free: 0.229 
• R-Value Work: 0.182 
• R-Value Observed: 0.185 

Starting Model: experimental

Literature

Synthesis, Biological Activity and Structural Study of New Benzotriazole-Based Protein Kinase CK2 Inhibitors

Swider, R., Maslyk, M., Zapico, J.M., Coderch, C., Panchuk, R., Skorokhyd, N., Schnitzler, A., Niefind, K., de Pascual-Teresa, B., Ramos, A.

(2015) RSC Adv 5: 72482-72494

• DOI: https://doi.org/10.1039/C5RA12114K

Biological Assembly 1  

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

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

Biological Assembly 2  

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

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 82.83 kDa 
• Atom Count: 5,893 
• Modelled Residue Count: 662 
• Deposited Residue Count: 670 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Casein kinase II subunit alpha	A, B	335	Homo sapiens	Mutation(s): 0  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 GTEx:  ENSG00000101266

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
JRJ	C [auth A], M [auth B]	4-[4-[2-[4,5,6,7-tetrakis(bromanyl)benzotriazol-2-yl]ethyl]-1,2,3-triazol-1-yl]butan-1-amine C14 H15 Br4 N7 KAIWWTMLTRXFON-UHFFFAOYSA-N
SO4	D [auth A], E [auth A], F [auth A], G [auth A], H [auth A], I [auth A], N [auth B], O [auth B], P [auth B], Q [auth B], R [auth B]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
GOL	K [auth A], L [auth A], T [auth B], U [auth B]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
CL	J [auth A], S [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.65 Å
• R-Value Free: 0.229 
• R-Value Work: 0.182 
• R-Value Observed: 0.185 
• Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 127.092	α = 90
b = 127.092	β = 90
c = 126.836	γ = 90

Software Package:

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

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2015-09-09 
Deposition Author(s): Niefind, K., Schnitzler, A., Swider, R., Maslyk, M., Ramos, A.
• This entry supersedes: 4BXA

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Funding Organization	Location	Grant Number
German Research Foundation	Germany	NI 643/4-1
Spanisch Ministry of Science and Innovation	Spain	CTQ2011-24741

Revision History  

• Version 1.0: 2015-09-09
  Type: Initial release
  
• Version 1.1: 2017-09-06
  Changes: Author supporting evidence
• Version 1.2: 2024-01-10
  Changes: Data collection, Database references, Refinement description