5B0X

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 
  • R-Value Work: 0.218 

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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
Expand
  • 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)
Binding MOAD:  5B0X IC50: 20 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.234 
  • R-Value Work: 0.218 
  • 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

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Ligand Structure Quality Assessment 


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