4MOT

Structure of Streptococcus pneumonia pare in complex with AZ13072886


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.75 Å
  • R-Value Free: 0.228 
  • R-Value Work: 0.190 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

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

  • DOI: 10.1016/j.bmcl.2013.12.080

  • 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 thiaz ...

    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.


    Organizational Affiliation

    DMPK and Animal Sciences, AstraZeneca India Pvt. Ltd, Bellary Road, Hebbal, Bangalore 560024, India.,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.,Department of Medicinal Chemistry, AstraZeneca India Pvt. Ltd, Bellary Road, Hebbal, Bangalore 560024, India. Electronic address: Sandeep.ghorpade@astrazeneca.com.,Discovery Sciences, AstraZeneca, Alderley Park, Macclesfield, UK.,Biosciences, Infection iMed, AstraZeneca, Waltham, MA, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Topoisomerase IV subunit B
A
226Streptococcus pneumoniae (strain ATCC BAA-255 / R6)Mutation(s): 0 
Gene Names: parE
EC: 5.6.2.3
Find proteins for Q8DQB5 (Streptococcus pneumoniae (strain ATCC BAA-255 / R6))
Go to UniProtKB:  Q8DQB5
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
2B7
Query on 2B7

Download SDF File 
Download CCD File 
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
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
2B7IC50: 50 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.75 Å
  • R-Value Free: 0.228 
  • R-Value Work: 0.190 
  • Space Group: C 2 2 21
Unit Cell:
Length (Å)Angle (°)
a = 73.603α = 90.00
b = 94.571β = 90.00
c = 61.001γ = 90.00
Software Package:
Software NamePurpose
d*TREKdata reduction
AMoREphasing
StructureStudiodata collection
REFMACrefinement
d*TREKdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2013-11-20
    Type: Initial release
  • Version 1.1: 2013-11-27
    Type: Data collection
  • Version 1.2: 2014-02-12
    Type: Database references
  • Version 1.3: 2018-01-24
    Type: Structure summary