3U2D

S. aureus GyrB ATPase domain in complex with small molecule inhibitor


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.85 Å
  • R-Value Free: 0.232 
  • R-Value Work: 0.201 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Pyrrolamide DNA gyrase inhibitors: fragment-based nuclear magnetic resonance screening to identify antibacterial agents.

Eakin, A.E.Green, O.Hales, N.Walkup, G.K.Bist, S.Singh, A.Mullen, G.Bryant, J.Embrey, K.Gao, N.Breeze, A.Timms, D.Andrews, B.Uria-Nickelsen, M.Demeritt, J.Loch, J.T.Hull, K.Blodgett, A.Illingworth, R.N.Prince, B.Boriack-Sjodin, P.A.Hauck, S.Macpherson, L.J.Ni, H.Sherer, B.

(2012) Antimicrob.Agents Chemother. 56: 1240-1246

  • DOI: 10.1128/AAC.05485-11
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • DNA gyrase is an essential enzyme in bacteria, and its inhibition results in the disruption of DNA synthesis and, subsequently, cell death. The pyrrolamides are a novel class of antibacterial agents targeting DNA gyrase. These compounds were identifi ...

    DNA gyrase is an essential enzyme in bacteria, and its inhibition results in the disruption of DNA synthesis and, subsequently, cell death. The pyrrolamides are a novel class of antibacterial agents targeting DNA gyrase. These compounds were identified by a fragment-based lead generation (FBLG) approach using nuclear magnetic resonance (NMR) screening to identify low-molecular-weight compounds that bind to the ATP pocket of DNA gyrase. A pyrrole hit with a binding constant of 1 mM formed the basis of the design and synthesis of a focused library of compounds that resulted in the rapid identification of a lead compound that inhibited DNA gyrase with a 50% inhibitory concentration (IC(50)) of 3 μM. The potency of the lead compound was further optimized by utilizing iterative X-ray crystallography to yield DNA gyrase inhibitors that also displayed antibacterial activity. Spontaneous mutants were isolated in Staphylococcus aureus by plating on agar plates containing pyrrolamide 4 at the MIC. The resistant variants displayed 4- to 8-fold-increased MIC values relative to the parent strain. DNA sequencing revealed two independent point mutations in the pyrrolamide binding region of the gyrB genes from these variants, supporting the hypothesis that the mode of action of these compounds was inhibition of DNA gyrase. Efficacy of a representative pyrrolamide was demonstrated against Streptococcus pneumoniae in a mouse lung infection model. These data demonstrate that the pyrrolamides are a novel class of DNA gyrase inhibitors with the potential to deliver future antibacterial agents targeting multiple clinical indications.


    Organizational Affiliation

    Infection Innovative Medicines Unit, AstraZeneca R&D Boston, Waltham, Massachusetts, USA. Ann.Eakin@astrazeneca.com




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
DNA gyrase subunit B
A, B
198Staphylococcus aureusMutation(s): 0 
Gene Names: gyrB
EC: 5.6.2.3
Find proteins for P0A0K8 (Staphylococcus aureus)
Go to UniProtKB:  P0A0K8
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
08B
Query on 08B

Download SDF File 
Download CCD File 
A, B
4-bromo-5-methyl-N-[1-(3-nitropyridin-2-yl)piperidin-4-yl]-1H-pyrrole-2-carboxamide
C16 H18 Br N5 O3
AUXATGQLTJKTRN-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

Download SDF File 
Download CCD File 
A, B
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.85 Å
  • R-Value Free: 0.232 
  • R-Value Work: 0.201 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 143.487α = 90.00
b = 55.646β = 100.38
c = 51.103γ = 90.00
Software Package:
Software NamePurpose
d*TREKdata reduction
REFMACrefinement
d*TREKdata scaling
AMoREphasing
JDirectordata collection
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2012-01-11
    Type: Initial release
  • Version 1.1: 2012-02-29
    Type: Database references
  • Version 1.2: 2017-08-09
    Type: Refinement description, Source and taxonomy