3G7E

Crystal structure of E. coli Gyrase B co-complexed with PROP-2-YN-1-YL {[5-(4-PIPERIDIN-1-YL-2-PYRIDIN-3-YL-1,3-THIAZOL-5-YL)-1H-PYRAZOL-3-YL]METHYL}CARBAMATE inhibitor

• PDB DOI: https://doi.org/10.2210/pdb3G7E/pdb

• Classification: Isomerase/Isomerase inhibitor
• Organism(s): Escherichia coli
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2009-02-09 Released: 2010-02-09 
• Deposition Author(s): Wei, Y., Charifson, P.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 0.234 
• R-Value Work: 0.206 
• R-Value Observed: 0.208 

Starting Model: experimental

Literature

Discovery of pyrazolthiazoles as novel and potent inhibitors of bacterial gyrase.

Ronkin, S.M., Badia, M., Bellon, S., Grillot, A.L., Gross, C.H., Grossman, T.H., Mani, N., Parsons, J.D., Stamos, D., Trudeau, M., Wei, Y., Charifson, P.S.

(2010) Bioorg Med Chem Lett 20: 2828-2831

• PubMed: 20356737 
• DOI: https://doi.org/10.1016/j.bmcl.2010.03.052
• Primary Citation of Related Structures:  
  3G75, 3G7B, 3G7E


• PubMed Abstract: 
  

  Bacterial DNA gyrase is an attractive target for the investigation of new antibacterial agents. Inhibitors of the GyrB subunit, which contains the ATP-binding site, are described in this communication. Novel, substituted 5-(1H-pyrazol-3-yl)thiazole compounds were identified as inhibitors of bacterial gyrase. Structure-guided optimization led to greater enzymatic potency and moderate antibacterial potency. Data are presented for the demonstration of selective enzyme inhibition of Escherichia coli GyrB over Staphylococcus aureus GyrB.

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Organizational Affiliation: 

Vertex Pharmaceuticals Inc., 130 Waverly Street, Cambridge, MA 02139, USA. [e-mail]

Biological Assembly 1  

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

Biological assembly 1 generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 22.72 kDa 
• Atom Count: 1,679 
• Modelled Residue Count: 203 
• Deposited Residue Count: 203 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA gyrase subunit B	A	203	Escherichia coli	Mutation(s): 0  Gene Names: ECs4634 EC: 5.99.1.3 (PDB Primary Data), 5.6.2.2 (UniProt)
UniProt
Find proteins for C3SLN3 (Escherichia coli) Explore C3SLN3  Go to UniProtKB:  C3SLN3

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
B46	B [auth A]	prop-2-yn-1-yl {[5-(4-piperidin-1-yl-2-pyridin-3-yl-1,3-thiazol-5-yl)-1H-pyrazol-3-yl]methyl}carbamate C21 H22 N6 O2 S DJDJEDRAXXHMHQ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 0.234 
• R-Value Work: 0.206 
• R-Value Observed: 0.208 
• Space Group: P 3₁ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 95.4	α = 90
b = 95.4	β = 90
c = 51.25	γ = 120

Software Package:

Software Name	Purpose
CrystalClear	data collection
AMoRE	phasing
CNX	refinement
DENZO	data reduction
SCALEPACK	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2010-02-09 
Deposition Author(s): Wei, Y., Charifson, P.

Revision History  

• Version 1.0: 2010-02-09
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2013-07-03
  Changes: Database references
• Version 1.3: 2023-09-06
  Changes: Data collection, Database references, Derived calculations, Refinement description