Crystal structure of CK2alpha with pyradine derivative

Experimental Data Snapshot

  • Resolution: 2.60 Å
  • R-Value Free: 0.263 
  • R-Value Work: 0.236 

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A detailed thermodynamic profile of cyclopentyl and isopropyl derivatives binding to CK2 kinase

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

(2011) Mol Cell Biochem 356: 97-105

  • DOI: https://doi.org/10.1007/s11010-011-0960-9
  • Primary Citation of Related Structures:  
    3AT2, 3AT3, 3AT4

  • PubMed Abstract: 

    The detailed understanding of the molecular features of a ligand binding to a target protein, facilitates the successful design of potent and selective inhibitors. We present a case study of ATP-competitive kinase inhibitors that include a pyradine moiety. These compounds have similar chemical structure, except for distinct terminal hydrophobic cyclopentyl or isopropyl groups, and block kinase activity of casein kinase 2 subunit α (CK2α), which is a target for several diseases, such as cancer and glomerulonephritis. Although these compounds display similar inhibitory potency against CK2α, the crystal structures reveal that the cyclopentyl derivative gains more favorable interactions compared with the isopropyl derivative, because of the additional ethylene moiety. The structural observations and biological data are consistent with the thermodynamic profiles of these inhibitors in binding to CK2α, revealing that the enthalpic advantage of the cyclopentyl derivative is accompanied with a lower entropic loss. Computational analyses indicated that the relative enthalpic gain of the cyclopentyl derivative arises from an enhancement of a wide range of van der Waals interactions from the whole complex. Conversely, the relative entropy loss of the cyclopentyl derivative arises from a decrease in the molecular fluctuation and higher conformational restriction in the active site of CK2α. These structural insights, in combination with thermodynamic and computational observations, should be helpful in developing potent and selective CK2α inhibitors.

  • Organizational Affiliation

    Graduate School of Science, Osaka Prefecture University, 1-1 Gakuen-cho, Naka-ku, Sakai, Osaka 599-8531, Japan. kinotk@b.s.osakafu-u.ac.jp

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Casein kinase II subunit alpha340Homo 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 ATK

Download Ideal Coordinates CCD File 
B [auth A](1-{6-[6-(cyclopentylamino)-1H-indazol-1-yl]pyrazin-2-yl}-1H-pyrrol-3-yl)acetic acid
C22 H22 N6 O2
Binding Affinity Annotations 
IDSourceBinding Affinity
ATK PDBBind:  3AT3 IC50: 9.2 (nM) from 1 assay(s)
BindingDB:  3AT3 IC50: min: 110, max: 190 (nM) from 2 assay(s)
Experimental Data & Validation

Experimental Data

  • Resolution: 2.60 Å
  • R-Value Free: 0.263 
  • R-Value Work: 0.236 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 51.169α = 90
b = 78.483β = 90
c = 80.374γ = 90
Software Package:
Software NamePurpose
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

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Ligand Structure Quality Assessment 

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2011-11-09
    Type: Initial release
  • Version 1.1: 2023-11-01
    Changes: Data collection, Database references, Derived calculations, Refinement description