3E3B

Crystal structure of catalytic subunit of human protein kinase CK2alpha prime with a potent indazole-derivative inhibitor

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.2 Å
  • R-Value Free: 0.274 
  • R-Value Work: 0.248 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history. 

Literature

Structure of human protein kinase CK2alpha2 with a potent indazole-derivative inhibitor

Nakaniwa, T., Kinoshita, T., Sekiguchi, Y., Tada, T., Nakanishi, I., Kitaura, K., Suzuki, Y., Ohno, H., Hirasawa, A., Tsujimoto, G.

(2009) Acta Crystallogr.,Sect.F 65: 75-79

  • DOI: 10.1107/S1744309108043194

  • PubMed Abstract: 

    • Casein kinase 2 (CK2) is a serine/threonine kinase that functions as a heterotetramer composed of two catalytic subunits (CK2alpha1 or CK2alpha2) and two regulatory subunits (CK2beta). The two isozymes CK2alpha1 and CK2alpha2 play distinguishable rol ...

    Casein kinase 2 (CK2) is a serine/threonine kinase that functions as a heterotetramer composed of two catalytic subunits (CK2alpha1 or CK2alpha2) and two regulatory subunits (CK2beta). The two isozymes CK2alpha1 and CK2alpha2 play distinguishable roles in healthy subjects and in patients with diseases such as cancer, respectively. In order to develop novel CK2alpha1-selective inhibitors, the crystal structure of human CK2alpha2 (hCK2alpha2) complexed with a potent CK2alpha inhibitor which binds to the active site of hCK2alpha2 was determined and compared with that of human CK2alpha1. While the two isozymes exhibited a high similarity with regard to the active site, the largest structural difference between the isoforms occurred in the beta4-beta5 loop responsible for the CK2alpha-CK2beta interface. The top of the N-terminal segment interacted with the beta4-beta5 loop via a hydrogen bond in hCK2alpha2 but not in hCK2alpha1. Thus, the CK2alpha-CK2beta interface is a likely target candidate for the production of selective CK2alpha1 inhibitors.

    Organizational Affiliation: 

    Graduate School of Sciences, Osaka Prefecture University, Osaka 599-8530, Japan.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Casein kinase II subunit alpha'
X
339Homo sapiensMutation(s): 0 
Gene Names: CSNK2A2 (CK2A2)
EC: 2.7.11.1
Find proteins for P19784 (Homo sapiens)
Go to Gene View: CSNK2A2
Go to UniProtKB:  P19784
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CCK
Query on CCK
Download SDF File 
Download CCD File 
X
[1-(6-{6-[(1-methylethyl)amino]-1H-indazol-1-yl}pyrazin-2-yl)-1H-pyrrol-3-yl]acetic acid
C20 H20 N6 O2
BBYRUZKRFAIQSR-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
CCKIC50: 11 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.2 Å
  • R-Value Free: 0.274 
  • R-Value Work: 0.248 
  • Space Group: P 21 21 2
Unit Cell:
Length (Å)Angle (°)
a = 69.813α = 90.00
b = 102.126β = 90.00
c = 46.618γ = 90.00
Software Package:
Software NamePurpose
HKL-2000data scaling
CNXrefinement
ADSCdata collection
MOLREPphasing
HKL-2000data reduction

Structure Validation

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View more in-depth experimental data

Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2009-03-03
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance