4EMV | pdb_00004emv

Crystal structure of a topoisomerase ATP inhibitor

• PDB DOI: https://doi.org/10.2210/pdb4EMV/pdb

• Classification: ISOMERASE/ISOMERASE INHIBITOR
• Organism(s): Streptococcus pneumoniae GA47373
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2012-04-12 Released: 2012-08-01 
• Deposition Author(s): Boriack-Sjodin, P.A., Manchester, J., Hull, K.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free: 
  0.223 (Depositor), 0.226 (DCC) 
• R-Value Work: 
  0.189 (Depositor), 0.196 (DCC) 
• R-Value Observed: 
  0.191 (Depositor) 

Literature

Discovery of a novel azaindole class of antibacterial agents targeting the ATPase domains of DNA gyrase and Topoisomerase IV.

Manchester, J.I., Dussault, D.D., Rose, J.A., Boriack-Sjodin, P.A., Uria-Nickelsen, M., Ioannidis, G., Bist, S., Fleming, P., Hull, K.G.

(2012) Bioorg Med Chem Lett 22: 5150-5156

• PubMed: 22814212 
• DOI: https://doi.org/10.1016/j.bmcl.2012.05.128
• Primary Citation Related Structures: 
  4EM7, 4EMV


• PubMed Abstract: 
  

  We present the discovery and optimization of a novel series of bacterial topoisomerase inhibitors. Starting from a virtual screening hit, activity was optimized through a combination of structure-based design and physical property optimization. Synthesis of fewer than a dozen compounds was required to achieve inhibition of the growth of methicillin-resistant Staphyloccus aureus (MRSA) at compound concentrations of 1.56 μM. These compounds simultaneously inhibit DNA gyrase and Topoisomerase IV at similar nanomolar concentrations, reducing the likelihood of the spontaneous occurrence of target-based mutations resulting in antibiotic resistance, an increasing threat in the treatment of serious infections.

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Organizational Affiliation: 
• Infection Innovative Medicines Unit, AstraZeneca R&D Boston, Waltham, MA 02451, USA. [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: 25.05 kDa 
• Atom Count: 1,760 
• Modeled Residue Count: 196 
• Deposited Residue Count: 226 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA topoisomerase IV, B subunit	A	226	Streptococcus pneumoniae GA47373	Mutation(s): 0  Gene Names: ParE, SPAR94_0831 EC: 5.99.1

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
0R9	B [auth A]	5-{2-(ethylcarbamoyl)-4-[3-(trifluoromethyl)-1H-pyrazol-1-yl]-1H-pyrrolo[2,3-b]pyridin-5-yl}pyridine-3-carboxylic acid C20 H15 F3 N6 O3 QEODWPGJXCSBCR-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free:  0.223 (Depositor), 0.226 (DCC) 
• R-Value Work:  0.189 (Depositor), 0.196 (DCC) 
• R-Value Observed: 0.191 (Depositor) 

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 73.297	α = 90
b = 94.92	β = 90
c = 61.247	γ = 90

Software Package:

Software Name	Purpose
MOSFLM	data reduction
SCALA	data scaling
AMoRE	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction

Structure Validation

Entry History 

Deposition Data

• Released Date: 2012-08-01 
Deposition Author(s): Boriack-Sjodin, P.A., Manchester, J., Hull, K.

Revision History  

• Version 1.0: 2012-08-01
  Type: Initial release
  
• Version 1.1: 2024-02-28
  Changes: Data collection, Database references, Derived calculations