6F96

Crystal Structure of E. coli GyraseB 24kDa in complex with 6-[(ethylcarbamoyl)amino]-4-[(4-methoxyphenyl)amino]-N-(pyridin-3-yl)pyridine-3-carboxamide

• PDB DOI: https://doi.org/10.2210/pdb6F96/pdb

• Classification: ISOMERASE
• Organism(s): Escherichia coli O157:H7
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2017-12-14 Released: 2019-01-30 
• Deposition Author(s): Narramore, S.K., Stevenson, C.E.M., Lawson, D.M., Maxwell, A., Fishwick, C.W.G.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free: 0.238 
• R-Value Work: 0.207 
• R-Value Observed: 0.209 

Starting Model: experimental

Literature

New insights into the binding mode of pyridine-3-carboxamide inhibitors of E. coli DNA gyrase.

Narramore, S., Stevenson, C.E.M., Maxwell, A., Lawson, D.M., Fishwick, C.W.G.

(2019) Bioorg Med Chem 27: 3546-3550

• PubMed: 31257079 
• DOI: https://doi.org/10.1016/j.bmc.2019.06.015
• Primary Citation of Related Structures:  
  6F86, 6F8J, 6F94, 6F96


• PubMed Abstract: 
  

  Previously we have reported on a series of pyridine-3-carboxamide inhibitors of DNA gyrase and DNA topoisomerase IV that were designed using a computational de novo design approach and which showed promising antibacterial properties. Herein we describe the synthesis of additional examples from this series aimed specifically at DNA gyrase, along with crystal structures confirming the predicted mode of binding and in vitro ADME data which describe the drug-likeness of these compounds.

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Organizational Affiliation: 

School of Chemistry and the Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds LS2 9JT, UK.

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: 24.68 kDa 
• Atom Count: 1,577 
• Modelled Residue Count: 187 
• Deposited Residue Count: 221 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA gyrase subunit B	A	221	Escherichia coli O157:H7	Mutation(s): 0  Gene Names: gyrB, Z5190, ECs4634 EC: 5.99.1.3 (PDB Primary Data), 5.6.2.2 (UniProt)
UniProt
Find proteins for P0AES6 (Escherichia coli (strain K12)) Explore P0AES6  Go to UniProtKB:  P0AES6

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
D0K	B [auth A]	6-(ethylcarbamoylamino)-4-[(4-methoxyphenyl)amino]-~{N}-pyridin-3-yl-pyridine-3-carboxamide C21 H22 N6 O3 FSOAZMGZMXDGQX-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free: 0.238 
• R-Value Work: 0.207 
• R-Value Observed: 0.209 
• Space Group: P 3₂ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 100.2	α = 90
b = 100.2	β = 90
c = 50.27	γ = 120

Software Package:

Software Name	Purpose
XDS	data reduction
Aimless	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction

Structure Validation

Entry History 

Deposition Data

• Released Date: 2019-01-30 
Deposition Author(s): Narramore, S.K., Stevenson, C.E.M., Lawson, D.M., Maxwell, A., Fishwick, C.W.G.

Revision History  

• Version 1.0: 2019-01-30
  Type: Initial release
  
• Version 1.1: 2019-07-10
  Changes: Data collection, Database references
• Version 1.2: 2019-08-07
  Changes: Data collection, Database references
• Version 1.3: 2024-01-17
  Changes: Data collection, Database references, Refinement description