3H30

Crystal structure of the catalytic subunit of human protein kinase CK2 with 5,6-dichloro-1-beta-D-ribofuranosylbenzimidazole

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.56 Å
  • R-Value Free: 0.198 
  • R-Value Work: 0.156 
  • R-Value Observed: 0.157 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history. 


Literature

The CK2alpha/CK2beta Interface of Human Protein Kinase CK2 Harbors a Binding Pocket for Small Molecules

Raaf, J., Brunstein, E., Issinger, O.-G., Niefind, K.

(2008) Chem Biol 15: 111-117

  • DOI: https://doi.org/10.1016/j.chembiol.2007.12.012
  • Primary Citation of Related Structures:  
    3H30

  • PubMed Abstract: 

    • The Ser/Thr kinase CK2 (previously called casein kinase 2) is composed of two catalytic chains (CK2 alpha) attached to a dimer of noncatalytic subunits (CK2 beta). CK2 is involved in suppression of apoptosis, cell survival, and tumorigenesis. To investigate these activities and possibly affect them, selective CK2 inhibitors are required ...

    The Ser/Thr kinase CK2 (previously called casein kinase 2) is composed of two catalytic chains (CK2 alpha) attached to a dimer of noncatalytic subunits (CK2 beta). CK2 is involved in suppression of apoptosis, cell survival, and tumorigenesis. To investigate these activities and possibly affect them, selective CK2 inhibitors are required. An often-used CK2 inhibitor is 5,6-dichloro-1-beta-D-ribofuranosylbenzimidazole (DRB). In a complex structure with human CK2 alpha, DRB binds to the canonical ATP cleft, but additionally it occupies an allosteric site that can be alternatively filled by glycerol. Inhibition kinetic studies corroborate the dual binding mode of the inhibitor. Structural comparisons reveal a surprising conformational plasticity of human CK2 alpha around both DRB binding sites. After local rearrangement, the allosteric site serves as a CK2 beta interface. This opens the potential to construct molecules interfering with the CK2 alpha/CK2 beta interaction.

    Related Citations: 
    • Evolved to be active: sulfate ions define substrate recognition sites of CK2alpha and emphasise its exceptional role within the CMGC family of eukaryotic protein kinases
      Niefind, K., Yde, C.W., Ermakova, I., Issinger, O.-G.
      (2007) J Mol Biol 370: 427
    • Crystal structure of a C-terminal deletion mutant of human protein kinase CK2 catalytic subunit
      Ermakova, I., Boldyreff, B., Issinger, O.-G., Niefind, K.
      (2003) J Mol Biol 330: 925
    Organizational Affiliation: 

    Institut für Biochemie, Universität zu Köln, Zülpicher Str. 47, D-50674 Köln, Germany.



Macromolecules
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Casein kinase II subunit alphaA, B334Homo sapiensMutation(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
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP68400
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
RFZ
Query on RFZ
Download Ideal Coordinates CCD File 
C [auth A],
D [auth A],
S [auth B]		5,6-dichloro-1-beta-D-ribofuranosyl-1H-benzimidazole
C12 H12 Cl2 N2 O4
XHSQDZXAVJRBMX-DDHJBXDOSA-N		 Ligand Interaction
CL
Query on CL
Download Ideal Coordinates CCD File 
AA [auth B],
BA [auth B],
CA [auth B],
DA [auth B],
E [auth A],
AA [auth B],
BA [auth B],
CA [auth B],
DA [auth B],
E [auth A],
EA [auth B],
F [auth A],
FA [auth B],
G [auth A],
GA [auth B],
H [auth A],
HA [auth B],
I [auth A],
IA [auth B],
J [auth A],
JA [auth B],
K [auth A],
KA [auth B],
L [auth A],
M [auth A],
N [auth A],
O [auth A],
P [auth A],
Q [auth A],
R [auth A],
T [auth B],
U [auth B],
V [auth B],
W [auth B],
X [auth B],
Y [auth B],
Z [auth B]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M		 Ligand Interaction
Binding Affinity Annotations 
IDSourceBinding Affinity
RFZ Binding MOAD:  3H30 Ki: 2.92e+4 (nM) from 1 assay(s)
BindingDB:  3H30 Ki: 4500 (nM) from 1 assay(s)
IC50: 1.30e+4 (nM) from 1 assay(s)
PDBBind:  3H30 Ki: 2.92e+4 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.56 Å
  • R-Value Free: 0.198 
  • R-Value Work: 0.156 
  • R-Value Observed: 0.157 
  • Space Group: P 43
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 71.506α = 90
b = 71.506β = 90
c = 125.789γ = 90
Software Package:
Software NamePurpose
MOLREPphasing
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

View Full Validation Report



View more in-depth experimental data
Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2009-05-12
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2017-11-01
    Changes: Refinement description