5B0X | pdb_00005b0x

Crystal structure of the CK2a/benzoic acid derivative complex

• PDB DOI: https://doi.org/10.2210/pdb5B0X/pdb

• Classification: TRANSFERASE/TRANSFERASE INHIBITOR
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2015-11-13 Released: 2016-03-30 
• Deposition Author(s): Kinoshita, T., Nakanishi, I.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 
  0.234 (Depositor), 0.243 (DCC) 
• R-Value Work: 
  0.218 (Depositor), 0.227 (DCC) 

Starting Model: experimental

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

• PubMed: 26850376 
• DOI: https://doi.org/10.1016/j.bmc.2016.01.043
• Primary Citation 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.

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Organizational Affiliation: 
• Graduate School of Pharmaceutical Sciences, Kyoto University, Sakyo-ku, Kyoto 606-8501, Japan. Electronic address: [e-mail].
Graduate School of Pharmaceutical Sciences, Kyoto University, Sakyo-ku, Kyoto 606-8501, Japan.
Faculty of Pharmacy, Department of Pharmaceutical Sciences, Kinki University, 3-4-1 Kowakae, Higashi-Osaka, Osaka 577-8502, Japan.
Graduate School of Science, Osaka Prefecture University, 1-1 Gakuen-cho, Naka-ku, Sakai, Osaka 599-8531, Japan.
Graduate School of Pharmaceutical Sciences, Kyoto University, Sakyo-ku, Kyoto 606-8501, Japan. Electronic address: [e-mail].

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 40.83 kDa 
• Atom Count: 2,942 
• Modeled Residue Count: 329 
• Deposited Residue Count: 340 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Casein kinase II subunit alpha	A	340	Homo sapiens	Mutation(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

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
HCK	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
ID	Source	Binding 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), 0.243 (DCC) 
• R-Value Work:  0.218 (Depositor), 0.227 (DCC) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 48.12	α = 90
b = 79.858	β = 90
c = 83.171	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling
MOLREP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2016-03-30 
Deposition Author(s): Kinoshita, T., Nakanishi, I.

Revision History  

• 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