6HMQ

STRUCTURE OF PROTEIN KINASE CK2 CATALYTIC SUBUNIT (ISOFORM CK2ALPHA'; CSNK2A2 GENE PRODUCT) IN COMPLEX WITH THE BENZOTRIAZOLE-TYPE INHIBITOR MB002

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 0.97 Å
  • R-Value Free: 0.132 
  • R-Value Work: 0.120 
  • R-Value Observed: 0.120 

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


Literature

Diacritic Binding of an Indenoindole Inhibitor by CK2 alpha Paralogs Explored by a Reliable Path to Atomic Resolution CK2 alpha ' 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: 5471-5478

  • DOI: 10.1021/acsomega.8b03415
  • Primary Citation of Related Structures:  
    6HBN, 6HMB, 6HMC, 6HMD, 6HME, 6HMQ

  • PubMed Abstract: 

    • CK2α and CK2α' are the two isoforms of the catalytic subunit of human protein kinase CK2, an important target for cancer therapy. They have similar, albeit not identical functional and structural properties, and were occasionally reported to be inhibited with distinct efficacies by certain ATP-competitive ligands ...

    CK2α and CK2α' are the two isoforms of the catalytic subunit of human protein kinase CK2, an important target for cancer therapy. They have similar, albeit not identical functional and structural properties, and were occasionally reported to be inhibited with distinct efficacies by certain ATP-competitive ligands. Here, we present THN27, an indeno[1,2- b ]indole derivative, as a further inhibitor with basal isoform selectivity. The selectivity disappears when measured using CK2α/CK2α' complexes with CK2β, the regulatory CK2 subunit. Co-crystal structures of THN27 with CK2α and CK2α' reveal that subtle differences in the conformational variability of the interdomain hinge region are correlated with the observed effect. In the case of CK2α', a crystallographically problematic protein so far, this comparative structural analysis required the development of an experimental strategy that finally enables atomic resolution structure determinations with ab initio phasing of potentially any ATP-competitive CK2 inhibitor and possibly many non-ATP-competitive ligands as well bound to CK2α'.

    Related Citations: 
    • Unexpected Binding Mode of a Potent Indeno[1,2-b]indole-Type Inhibitor of Protein Kinase CK2 Revealed by Complex Structures with the Catalytic Subunit CK2alpha and Its Paralog CK2alpha'
      Hochscherf, J., Lindenblatt, D., Witulski, B., Birus, R., Aichele, D., Marminon, C., Bouaziz, Z., Le Borgne, M., Jose, J., Niefind, K.
      (2017) Pharmaceuticals (Basel) 10: --
    • 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: 

    Department für Chemie, Institut für Biochemie, Universität zu Köln, Zülpicher Straße 47, D-50674 Köln, Germany.



Macromolecules
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(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Casein kinase II subunit alpha'A364Homo sapiensMutation(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
GTEx:  ENSG00000070770 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP19784
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 5 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
4B0
Query on 4B0
Download Ideal Coordinates CCD File 
P [auth A]3-(4,5,6,7-tetrabromo-1H-benzotriazol-1-yl)propan-1-ol
C9 H7 Br4 N3 O
VXLNELSTYPRMEW-UHFFFAOYSA-N		 Ligand Interaction
TRS
Query on TRS
Download Ideal Coordinates CCD File 
B [auth A]2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
C4 H12 N O3
LENZDBCJOHFCAS-UHFFFAOYSA-O		 Ligand Interaction
EDO
Query on EDO
Download Ideal Coordinates CCD File 
C [auth A],
D [auth A],
E [auth A],
F [auth A],
G [auth A],
C [auth A],
D [auth A],
E [auth A],
F [auth A],
G [auth A],
H [auth A],
I [auth A],
J [auth A],
K [auth A],
L [auth A]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N		 Ligand Interaction
CL
Query on CL
Download Ideal Coordinates CCD File 
M [auth A],
N [auth A]		CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M		 Ligand Interaction
NA
Query on NA
Download Ideal Coordinates CCD File 
O [auth A]SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N		 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 0.97 Å
  • R-Value Free: 0.132 
  • R-Value Work: 0.120 
  • R-Value Observed: 0.120 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 46.14α = 113.47
b = 47.22β = 90.76
c = 50.29γ = 90.27
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
Aimlessdata scaling
Arcimboldophasing
ARP/wARPmodel building

Structure Validation

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Ligand Structure Quality Assessment 


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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: 2019-03-27
    Type: Initial release
  • Version 1.1: 2019-08-28
    Changes: Author supporting evidence, Data collection
  • Version 1.2: 2019-10-09
    Changes: Data collection, Database references