5B0X | pdb_00005b0x

Crystal structure of the CK2a/benzoic acid derivative complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 
    0.234 (Depositor), 0.240 (DCC) 
  • R-Value Work: 
    0.218 (Depositor), 0.230 (DCC) 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted HCKClick on this verticalbar to view details

This is version 1.2 of the entry. See complete history


Literature

Structure-activity relationship study of 4-(thiazol-5-yl)benzoic acid derivatives as potent protein kinase CK2 inhibitors

Ohno, H.Minamiguchi, D.Nakamura, S.Shu, K.Okazaki, S.Honda, M.Misu, R.Moriwaki, H.Nakanishi, S.Oishi, S.Kinoshita, T.Nakanishi, I.Fujii, N.

(2016) Bioorg Med Chem 24: 1136-1141

  • DOI: https://doi.org/10.1016/j.bmc.2016.01.043
  • Primary Citation of Related Structures:  
    5B0X

  • PubMed Abstract: 

    Two classes of modified analogs of 4-(thiazol-5-yl)benzoic acid-type CK2 inhibitors were designed. The azabenzene analogs, pyridine- and pyridazine-carboxylic acid derivatives, showed potent protein kinase CK2 inhibitory activities [IC50 (CK2α)=0.014-0.017μM; IC50 (CK2α')=0.0046-0.010μM]. Introduction of a 2-halo- or 2-methoxy-benzyloxy group at the 3-position of the benzoic acid moiety maintained the potent CK2 inhibitory activities [IC50 (CK2α)=0.014-0.016μM; IC50 (CK2α')=0.0088-0.014μM] and led to antiproliferative activities [CC50 (A549)=1.5-3.3μM] three to six times higher than those of the parent compound.


  • Organizational Affiliation

    Graduate School of Pharmaceutical Sciences, Kyoto University, Sakyo-ku, Kyoto 606-8501, Japan. Electronic address: hohno@pharm.kyoto-u.ac.jp.


Macromolecules
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: 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
GTEx:  ENSG00000101266 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP68400
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
HCK
Query on HCK

Download Ideal Coordinates CCD File 
B [auth A]4-[2-[(4-methoxyphenyl)carbonylamino]-1,3-thiazol-5-yl]benzoic acid
C18 H14 N2 O4 S
UPIVZLFKYMNZDG-UHFFFAOYSA-N
Binding Affinity Annotations 
IDSourceBinding Affinity
HCK BindingDB:  5B0X IC50: min: 11, max: 46 (nM) from 4 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free:  0.234 (Depositor), 0.240 (DCC) 
  • R-Value Work:  0.218 (Depositor), 0.230 (DCC) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 48.12α = 90
b = 79.858β = 90
c = 83.171γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted HCKClick on this verticalbar to view details

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2016-03-30
    Type: Initial release
  • Version 1.1: 2020-02-26
    Changes: Data collection, Database references, Derived calculations
  • Version 1.2: 2023-11-08
    Changes: Data collection, Database references, Refinement description