7A1B

Crystal structure of human protein kinase CK2alpha' (CSNK2A2 gene product) in complex with the ATP-competitive inhibitor 5,6-dibromo-1H-triazolo[4,5-b]pyridine

• PDB DOI:  https://doi.org/10.2210/pdb7A1B/pdb

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


• Deposited: 2020-08-12 Released: 2020-12-09 
• Deposition Author(s): Niefind, K., Lindenblatt, D., Toelzer, C., Bretner, M., Chojnacki, K., Wielechowska, M., Winska, P.
• Funding Organization(s): German Research Foundation (DFG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.29 Å
• R-Value Free: 0.193 
• R-Value Work: 0.157 
• R-Value Observed: 0.158 

Literature

Synthesis, biological properties and structural study of new halogenated azolo[4,5-b]pyridines as inhibitors of CK2 kinase.

Chojnacki, K., Lindenblatt, D., Winska, P., Wielechowska, M., Toelzer, C., Niefind, K., Bretner, M.

(2021) Bioorg Chem 106: 104502-104502

• PubMed: 33317841 
• DOI: https://doi.org/10.1016/j.bioorg.2020.104502
• Primary Citation of Related Structures:  
  7A1B, 7A1Z, 7A22, 7A2H, 7A49, 7A4B, 7A4C


• PubMed Abstract: 
  

The new halogenated 1H-triazolo[4,5-b]pyridines and 1H-imidazo[4,5-b]pyridines were synthesised as analogues of known CK2 inhibitors: 4,5,6,7-tetrabromo-1H-benzotriazole (TBBt) and 4,5,6,7-tetrabromo-1H-benzimidazole (TBBi). Their influence on the activity of recombinant human CK2α, CK2α' and PIM1 kinases was determined. The most active inhibitors were di- and trihalogenated 1H-triazolo[4,5-b]pyridines (4a, 5a and 10a) with IC ₅₀ values 2.56, 3.82 and 3.26 μM respectively for CK2α. Furthermore, effect on viability of cancer cell lines MCF-7 (human breast adenocarcinoma) and CCRF-CEM (T lymphoblast leukemia) of all final compounds was evaluated. Finally, three crystal structures of complexes of CK2α ^1-335 with inhibitors 4a, 5a and 10a were obtained. In addition, new protocol was used to obtain high-resolution crystal structures of CK2α' ^Cys336Ser in complex with four inhibitors (4a, 5a, 5b, 10a).

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Related Citations: 

• Biological properties and structural study of new aminoalkyl derivatives of benzimidazole and benzotriazole, dual inhibitors of CK2 and PIM1 kinases.
  Chojnacki, K., Winska, P., Wielechowska, M., Lukowska-Chojnacka, E., Toelzer, C., Niefind, K., Bretner, M.
  (2018) Bioorg Chem 80: 266

• Diacritic Binding of an Indenoindole Inhibitor by CK2alpha Paralogs Explored by a Reliable Path to Atomic Resolution CK2alpha' Structures.
  Lindenblatt, D., Nickelsen, A., Applegate, V.M., Hochscherf, J., Witulski, B., Bouaziz, Z., Marminon, C., Bretner, M., Le Borgne, M., Jose, J., Niefind, K.
  (2019) ACS Omega 4: 5471

• Structural and Mechanistic Basis of the Inhibitory Potency of Selected 2-Aminothiazole Compounds on Protein Kinase CK2.
  Lindenblatt, D., Nickelsen, A., Applegate, V.M., Jose, J., Niefind, K.
  (2020) J Med Chem 63: 7766

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Organizational Affiliation: 

Faculty of Chemistry, Warsaw University of Technology, Noakowskiego St. 3, 00-664 Warsaw, Poland.

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: 43.62 kDa 
• Atom Count: 3,257 
• Modelled 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

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
QXW (Subject of Investigation/LOI)	B [auth A]	5,6-dibromo-1H-triazolo[4,5-b]pyridine C5 H2 Br2 N4 WKRYLZOTKJYHJM-UHFFFAOYSA-N
EDO	C [auth A], D [auth A], E [auth A], F [auth A], G [auth A], H [auth A]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N
CL	I [auth A], J [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M
NA	K [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
QXW	Binding MOAD:  7A1B	IC50: 2360 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.29 Å
• R-Value Free: 0.193 
• R-Value Work: 0.157 
• R-Value Observed: 0.158 
• Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 46.256	α = 113.229
b = 47.593	β = 89.996
c = 50.55	γ = 91.127

Software Package:

Software Name	Purpose
XDS	data reduction
Aimless	data scaling
Arcimboldo	phasing
PHENIX	refinement

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2020-12-09 
Deposition Author(s): Niefind, K., Lindenblatt, D., Toelzer, C., Bretner, M., Chojnacki, K., Wielechowska, M., Winska, P.

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

Revision History  

• Version 1.0: 2020-12-09
  Type: Initial release
  
• Version 1.1: 2020-12-23
  Changes: Database references
• Version 1.2: 2021-01-13
  Changes: Database references