High salt structure of human protein kinase CK2alpha in complex with 3-aminopropyl-4,5,6,7-tetrabromobenzimidazol

Experimental Data Snapshot

  • Resolution: 2.30 Å
  • R-Value Free: 0.263 
  • R-Value Work: 0.219 
  • R-Value Observed: 0.222 

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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.Tolzer, C.Niefind, K.Bretner, M.

(2018) Bioorg Chem 80: 266-275

  • DOI: https://doi.org/10.1016/j.bioorg.2018.06.022
  • Primary Citation of Related Structures:  
    5OWH, 5OWL

  • PubMed Abstract: 

    The new aminoalkyl-substituted derivatives of known CK2 inhibitors 4,5,6,7-tetrabromo-1H-benzimidazole (TBBi) and 4,5,6,7-tetrabromo-1H-benzotriazole (TBBt) were synthesized, and their influence on the activity of recombinant human CK2 α, CK2 holoenzyme and PIM1 kinases was evaluated. All derivatives inhibited the activity of studied kinases and the most efficient were aminopropyl-derivatives 8b and 14b. These compounds also exerted inhibition of cancer cell lines - CCRF-CEM (acute lymphoblastoid leukemia), MCF-7 (human breast cancer), and PC-3 (prostate cancer) proliferation and their EC 50 is comparable with the value for clinically studied CK2 inhibitor CX-4945. Preliminary structure activity relationship analysis indicated that the spacer length affected antitumor potency, and two to three methylene units were more favorable. The complex of CK2 α 1-335 /8b was crystallized, both under high-salt conditions and under low-salt conditions giving crystals which diffracted X-rays to about 2.4 Å resolution, what enabled the determination of the corresponding 3D-structures.

  • Organizational Affiliation

    Faculty of Chemistry, Warsaw University of Technology, Noakowskiego 3, 00-664 Warsaw, Poland. Electronic address: mbretner@ch.pw.edu.pl.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Casein kinase II subunit alpha335Homo sapiensMutation(s): 0 
Gene Names: CSNK2A1CK2A1
UniProt & NIH Common Fund Data Resources
Find proteins for P68400 (Homo sapiens)
Explore P68400 
Go to UniProtKB:  P68400
PHAROS:  P68400
GTEx:  ENSG00000101266 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP68400
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on B0K

Download Ideal Coordinates CCD File 
B [auth A]3-[4,5,6,7-tetrakis(bromanyl)benzimidazol-1-yl]propan-1-amine
C10 H9 Br4 N3
Query on CL

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Experimental Data & Validation

Experimental Data

  • Resolution: 2.30 Å
  • R-Value Free: 0.263 
  • R-Value Work: 0.219 
  • R-Value Observed: 0.222 
  • Space Group: P 43 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 71.661α = 90
b = 71.661β = 90
c = 133.107γ = 90
Software Package:
Software NamePurpose
XDSdata reduction
Aimlessdata scaling

Structure Validation

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Ligand Structure Quality Assessment 

Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
German Research FoundationGermanyNI 643/4-2

Revision History  (Full details and data files)

  • Version 1.0: 2018-07-25
    Type: Initial release
  • Version 1.1: 2024-01-17
    Changes: Data collection, Database references, Refinement description