Human CK2 catalytic domain in complex with a pyridocarbazole derivative inhibitor

Experimental Data Snapshot

  • Resolution: 1.85 Å
  • R-Value Free: 0.242 
  • R-Value Work: 0.196 
  • R-Value Observed: 0.201 

wwPDB Validation   3D Report Full Report

Ligand Structure Quality Assessment 

This is version 1.2 of the entry. See complete history


Antitumor activity of pyridocarbazole and benzopyridoindole derivatives that inhibit protein kinase CK2.

Prudent, R.Moucadel, V.Nguyen, C.H.Barette, C.Schmidt, F.Florent, J.C.Lafanechere, L.Sautel, C.F.Duchemin-Pelletier, E.Spreux, E.Filhol, O.Reiser, J.B.Cochet, C.

(2010) Cancer Res 70: 9865-9874

  • DOI: https://doi.org/10.1158/0008-5472.CAN-10-0917
  • Primary Citation of Related Structures:  
    3OWJ, 3OWK, 3OWL

  • PubMed Abstract: 

    The alkyloid compound ellipticine derived from the berrywood tree is a topoisomerase II poison that is used in ovarian and breast cancer treatment. In this study, we report the identification of ellipticine derivatives and their tetracyclic angular benzopyridoindole analogues as novel ATP-competitive inhibitors of the protein kinase CK2. In vitro and in vivo assays showed that these compounds have a good pharmacologic profile, causing a marked inhibition of CK2 activity associated with cell cycle arrest and apoptosis in human cancer cells. Further, in vivo assays demonstrate antitumor activity in a mouse xenograft model of human glioblastoma. Finally, crystal structures of CK2-inhibitor complex provide structural insights on the molecular basis of CK2 inhibition. Our work lays the foundation for development of clinically useful CK2 inhibitors derived from a well-studied scaffold with suitable pharmacokinetics parameters.

  • Organizational Affiliation

    INSERM, U873, Grenoble, France.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
CSNK2A1 protein331Homo sapiensMutation(s): 0 
Gene Names: CSNK2A1
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 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on 1EL

Download Ideal Coordinates CCD File 
B [auth A]9-hydroxy-5,11-dimethyl-4,6-dihydro-1H-pyrido[4,3-b]carbazol-1-one
C17 H14 N2 O2
Binding Affinity Annotations 
IDSourceBinding Affinity
1EL Binding MOAD:  3OWJ Ki: 860 (nM) from 1 assay(s)
PDBBind:  3OWJ Ki: 860 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Resolution: 1.85 Å
  • R-Value Free: 0.242 
  • R-Value Work: 0.196 
  • R-Value Observed: 0.201 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 58.51α = 90
b = 46.03β = 111.79
c = 63.62γ = 90
Software Package:
Software NamePurpose
ADSCdata collection
XDSdata reduction
XDSdata scaling

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment 

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2010-12-15
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2024-02-21
    Changes: Data collection, Database references, Derived calculations