4MOT | pdb_00004mot

Structure of Streptococcus pneumonia pare in complex with AZ13072886

• PDB DOI: https://doi.org/10.2210/pdb4MOT/pdb

• Classification: ISOMERASE/ISOMERASE INHIBITOR
• Organism(s): Streptococcus pneumoniae R6
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2013-09-12 Released: 2013-11-20 
• Deposition Author(s): Ogg, D., Boriack-Sjodin, P.A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.75 Å
• R-Value Free: 
  0.228 (Depositor), 0.236 (DCC) 
• R-Value Work: 
  0.190 (Depositor), 0.202 (DCC) 
• R-Value Observed: 
  0.192 (Depositor) 

Literature

Thiazolopyridone ureas as DNA gyrase B inhibitors: Optimization of antitubercular activity and efficacy.

Kale, R.R., Kale, M.G., Waterson, D., Raichurkar, A., Hameed, S.P., Manjunatha, M.R., Kishore Reddy, B.K., Malolanarasimhan, K., Shinde, V., Koushik, K., Jena, L.K., Menasinakai, S., Humnabadkar, V., Madhavapeddi, P., Basavarajappa, H., Sharma, S., Nandishaiah, R., Mahesh Kumar, K.N., Ganguly, S., Ahuja, V., Gaonkar, S., Naveen Kumar, C.N., Ogg, D., Boriack-Sjodin, P.A., Sambandamurthy, V.K., de Sousa, S.M., Ghorpade, S.R.

(2014) Bioorg Med Chem Lett 24: 870-879

• PubMed: 24405701 
• DOI: https://doi.org/10.1016/j.bmcl.2013.12.080
• Primary Citation Related Structures: 
  4MOT


• PubMed Abstract: 
  

  Scaffold hopping from the thiazolopyridine ureas led to thiazolopyridone ureas with potent antitubercular activity acting through inhibition of DNA GyrB ATPase activity. Structural diversity was introduced, by extension of substituents from the thiazolopyridone N-4 position, to access hydrophobic interactions in the ribose pocket of the ATP binding region of GyrB. Further optimization of hydrogen bond interactions with arginines in site-2 of GyrB active site pocket led to potent inhibition of the enzyme (IC50 2 nM) along with potent cellular activity (MIC=0.1 μM) against Mycobacterium tuberculosis (Mtb). Efficacy was demonstrated in an acute mouse model of tuberculosis on oral administration.

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Organizational Affiliation: 
• Department of Medicinal Chemistry, AstraZeneca India Pvt. Ltd, Bellary Road, Hebbal, Bangalore 560024, India.
Department of Biosciences, AstraZeneca India Pvt. Ltd, Bellary Road, Hebbal, Bangalore 560024, India.
DMPK and Animal Sciences, AstraZeneca India Pvt. Ltd, Bellary Road, Hebbal, Bangalore 560024, India.
Discovery Sciences, AstraZeneca, Alderley Park, Macclesfield, UK.
Biosciences, Infection iMed, AstraZeneca, Waltham, MA, USA.
Department of Medicinal Chemistry, AstraZeneca India Pvt. Ltd, Bellary Road, Hebbal, Bangalore 560024, India. 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: 25 kDa 
• Atom Count: 1,626 
• Modeled Residue Count: 193 
• Deposited Residue Count: 226 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Topoisomerase IV subunit B	A	226	Streptococcus pneumoniae R6	Mutation(s): 0  Gene Names: parE, spar94_0831, spr0756 EC: 5.99.1 (PDB Primary Data), 5.6.2.2 (UniProt)
UniProt
Find proteins for Q8DQB5 (Streptococcus pneumoniae (strain ATCC BAA-255 / R6)) Explore Q8DQB5  Go to UniProtKB:  Q8DQB5

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
2B7	B [auth A]	1-[4-(3-methylbutyl)-5-oxo-6-(pyridin-3-yl)-4,5-dihydro[1,3]thiazolo[5,4-b]pyridin-2-yl]-3-prop-2-en-1-ylurea C20 H23 N5 O2 S HDSYKPYXRVXIRI-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.75 Å
• R-Value Free:  0.228 (Depositor), 0.236 (DCC) 
• R-Value Work:  0.190 (Depositor), 0.202 (DCC) 
• R-Value Observed: 0.192 (Depositor) 

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 73.603	α = 90
b = 94.571	β = 90
c = 61.001	γ = 90

Software Package:

Software Name	Purpose
StructureStudio	data collection
AMoRE	phasing
REFMAC	refinement
d*TREK	data reduction
d*TREK	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2013-11-20 
Deposition Author(s): Ogg, D., Boriack-Sjodin, P.A.

Revision History  

• Version 1.0: 2013-11-20
  Type: Initial release
  
• Version 1.1: 2013-11-27
  Changes: Data collection
• Version 1.2: 2014-02-12
  Changes: Database references
• Version 1.3: 2018-01-24
  Changes: Structure summary
• Version 1.4: 2024-02-28
  Changes: Data collection, Database references, Derived calculations