3G7B | pdb_00003g7b

Staphylococcus aureus Gyrase B co-complex with METHYL ({5-[4-(4-HYDROXYPIPERIDIN-1-YL)-2-PHENYL-1,3-THIAZOL-5-YL]-1H-PYRAZOL-3-YL}METHYL)CARBAMATE inhibitor

• PDB DOI: https://doi.org/10.2210/pdb3G7B/pdb

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


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

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 
  0.275 (Depositor), 0.279 (DCC) 
• R-Value Work: 
  0.209 (Depositor), 0.218 (DCC) 
• R-Value Observed: 
  0.212 (Depositor) 

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 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: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 43.08 kDa 
• Atom Count: 3,063 
• Modeled Residue Count: 368 
• Deposited Residue Count: 368 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA gyrase subunit B	A, B	184	Staphylococcus aureus	Mutation(s): 0  Gene Names: gyrB EC: 5.99.1.3 (PDB Primary Data), 5.6.2.2 (UniProt)
UniProt
Find proteins for P0A0K8 (Staphylococcus aureus) Explore P0A0K8  Go to UniProtKB:  P0A0K8

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
B47	C [auth A], D [auth B]	methyl ({5-[4-(4-hydroxypiperidin-1-yl)-2-phenyl-1,3-thiazol-5-yl]-1H-pyrazol-3-yl}methyl)carbamate C20 H23 N5 O3 S GFUMDRBVYNGSBP-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free:  0.275 (Depositor), 0.279 (DCC) 
• R-Value Work:  0.209 (Depositor), 0.218 (DCC) 
• R-Value Observed: 0.212 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 144	α = 90
b = 55.84	β = 99.8
c = 50.42	γ = 90

Software Package:

Software Name	Purpose
CNX	refinement

Structure Validation

Entry History 

Deposition Data

• Released Date: 2010-02-09 
Deposition Author(s): Wei, Y., Charisfon, 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: 2024-02-21
  Changes: Data collection, Database references, Derived calculations