4MB9

Structure of Streptococcus pneumonia ParE in complex with AZ13102335


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.85 Å
  • R-Value Free: 0.242 
  • R-Value Work: 0.195 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Thiazolopyridine Ureas as Novel Antitubercular Agents Acting through Inhibition of DNA Gyrase B.

Kale, M.G.Raichurkar, A.Hameed, S.P.Waterson, D.McKinney, D.Manjunatha, M.R.Kranthi, U.Koushik, K.Jena, L.K.Shinde, V.Rudrapatna, S.Barde, S.Humnabadkar, V.Madhavapeddi, P.Basavarajappa, H.Ghosh, A.Ramya, V.Guptha, S.Sharma, S.Vachaspati, P.Kumar, K.N.Giridhar, J.Reddy, J.Panduga, V.Ganguly, S.Ahuja, V.Gaonkar, S.Kumar, C.N.Ogg, D.Tucker, J.A.Boriack-Sjodin, P.A.de Sousa, S.M.Sambandamurthy, V.K.Ghorpade, S.R.

(2013) J.Med.Chem. 56: 8834-8848

  • DOI: 10.1021/jm401268f
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • A pharmacophore-based search led to the identification of thiazolopyridine ureas as a novel scaffold with antitubercular activity acting through inhibition of DNA Gyrase B (GyrB) ATPase. Evaluation of the binding mode of thiazolopyridines in a Mycoba ...

    A pharmacophore-based search led to the identification of thiazolopyridine ureas as a novel scaffold with antitubercular activity acting through inhibition of DNA Gyrase B (GyrB) ATPase. Evaluation of the binding mode of thiazolopyridines in a Mycobacterium tuberculosis (Mtb) GyrB homology model prompted exploration of the side chains at the thiazolopyridine ring C-5 position to access the ribose/solvent pocket. Potent compounds with GyrB IC50 ≤ 1 nM and Mtb MIC ≤ 0.1 μM were obtained with certain combinations of side chains at the C-5 position and heterocycles at the C-6 position of the thiazolopyridine core. Substitutions at C-5 also enabled optimization of the physicochemical properties. Representative compounds were cocrystallized with Streptococcus pneumoniae (Spn) ParE; these confirmed the binding modes predicted by the homology model. The target link to GyrB was confirmed by genetic mapping of the mutations conferring resistance to thiazolopyridine ureas. The compounds are bactericidal in vitro and efficacious in vivo in an acute murine model of tuberculosis.


    Organizational Affiliation

    Department of Medicinal Chemistry, ‡Department of Biosciences, and §DMPK and Animal Sciences, AstraZeneca India Pvt. Ltd. , Bellary Road, Hebbal, Bangalore 560024, India.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
DNA topoisomerase IV, B subunit
A
226N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download SDF File 
Download CCD File 
A
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
28F
Query on 28F

Download SDF File 
Download CCD File 
A
1-ethyl-3-{6-(pyrimidin-5-yl)-5-[(3R)-tetrahydrofuran-3-ylmethoxy][1,3]thiazolo[5,4-b]pyridin-2-yl}urea
C18 H20 N6 O3 S
GVEJQEIIQCQRCC-LLVKDONJSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
28FIC50: 10 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.85 Å
  • R-Value Free: 0.242 
  • R-Value Work: 0.195 
  • Space Group: C 2 2 21
Unit Cell:
Length (Å)Angle (°)
a = 73.397α = 90.00
b = 94.279β = 90.00
c = 60.535γ = 90.00
Software Package:
Software NamePurpose
REFMACrefinement
AMoREphasing
d*TREKdata scaling
StructureStudiodata collection
d*TREKdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2013-08-19 
  • Released Date: 2013-10-16 
  • Deposition Author(s): Ogg, D., Tucker, J.

Revision History 

  • Version 1.0: 2013-10-16
    Type: Initial release
  • Version 1.1: 2014-01-15
    Type: Database references
  • Version 1.2: 2015-04-29
    Type: Data collection