5YIG

Crystal structure of Streptococcus pneumonia ParE with inhibitor

• PDB DOI: https://doi.org/10.2210/pdb5YIG/pdb

• Classification: ANTIMICROBIAL PROTEIN
• Organism(s): Streptococcus pneumoniae GA47502
• Expression System: Escherichia coli K-12
• Mutation(s): No 


• Deposited: 2017-10-04 Released: 2018-09-05 
• Deposition Author(s): Cherian, J., Tan, Y., Hill, J.
• Funding Organization(s): Astar

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.80 Å
• R-Value Free: 
  0.255 (Depositor), 0.260 (DCC) 
• R-Value Work: 
  0.206 (Depositor), 0.210 (DCC) 
• R-Value Observed: 
  0.211 (Depositor) 

Literature

Discovery of dual GyrB/ParE inhibitors active against Gram-negative bacteria.

Ho, S.Y., Wang, W., Ng, F.M., Wong, Y.X., Poh, Z.Y., Tan, S.W.E., Ang, S.H., Liew, S.S., Joyner Wong, Y.S., Tan, Y., Poulsen, A., Pendharkar, V., Sangthongpitag, K., Manchester, J., Basarab, G., Hill, J., Keller, T.H., Cherian, J.

(2018) Eur J Med Chem 157: 610-621

• PubMed: 30125722 
• DOI: https://doi.org/10.1016/j.ejmech.2018.08.025
• Primary Citation of Related Structures:  
  5YIG


• PubMed Abstract: 
  

  Even though many GyrB and ParE inhibitors have been reported in the literature, few possess activity against Gram-negative bacteria. This is primarily due to limited permeability across Gram-negative bacterial membrane as well as bacterial efflux mechanisms. Permeability of compounds across Gram-negative bacterial membranes depends on many factors including physicochemical properties of the inhibitors. Herein, we show the optimization of pyridylureas leading to compounds with potent activity against Gram-negative bacterial species such as P.aeruginosa, E.coli and A.baumannii.

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Organizational Affiliation: 

Experimental Therapeutics Centre, 13 Biopolis Way, Nanos 13866, Singapore.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 46.67 kDa 
• Atom Count: 3,119 
• Modelled Residue Count: 386 
• Deposited Residue Count: 420 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA topoisomerase 4 subunit B	A, B	210	Streptococcus pneumoniae GA47502	Mutation(s): 0  Gene Names: parE, SPAR98_0871 EC: 5.99.1.3

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
54B	C [auth A], D [auth B]	1-ethyl-3-[5-[2-[(1S,5R)-3-methyl-3,8-diazabicyclo[3.2.1]octan-8-yl]-5-(2-oxidanylidene-3H-1,3,4-oxadiazol-5-yl)pyridin-3-yl]-4-[4-(trifluoromethyl)-1,3-thiazol-2-yl]pyridin-2-yl]urea C26 H26 F3 N9 O3 S IDALGTCHRLCQSK-GASCZTMLSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.80 Å
• R-Value Free:  0.255 (Depositor), 0.260 (DCC) 
• R-Value Work:  0.206 (Depositor), 0.210 (DCC) 
• R-Value Observed: 0.211 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 43.394	α = 90
b = 61.98	β = 99.03
c = 84.824	γ = 90

Software Package:

Software Name	Purpose
SAINT	data scaling
PHASER	phasing
PHENIX	refinement
PDB_EXTRACT	data extraction
d*TREK	data collection
Coot	model building

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2018-09-05 
Deposition Author(s): Cherian, J., Tan, Y., Hill, J.

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Funding Organization	Location	Grant Number
Astar	Singapore	--

Revision History  

• Version 1.0: 2018-09-05
  Type: Initial release
  
• Version 1.1: 2024-03-27
  Changes: Data collection, Database references, Refinement description