5IWM

2.5A structure of GSK945237 with S.aureus DNA gyrase and DNA.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.224 
  • R-Value Work: 0.180 
  • R-Value Observed: 0.182 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Novel tricyclics (e.g., GSK945237) as potent inhibitors of bacterial type IIA topoisomerases.

Miles, T.J.Hennessy, A.J.Bax, B.Brooks, G.Brown, B.S.Brown, P.Cailleau, N.Chen, D.Dabbs, S.Davies, D.T.Esken, J.M.Giordano, I.Hoover, J.L.Jones, G.E.Kusalakumari Sukmar, S.K.Markwell, R.E.Minthorn, E.A.Rittenhouse, S.Gwynn, M.N.Pearson, N.D.

(2016) Bioorg Med Chem Lett 26: 2464-2469

  • DOI: 10.1016/j.bmcl.2016.03.106
  • Primary Citation of Related Structures:  
    5IWM, 5IWI

  • PubMed Abstract: 
  • During the course of our research on the lead optimisation of the NBTI (Novel Bacterial Type II Topoisomerase Inhibitors) class of antibacterials, we discovered a series of tricyclic compounds that showed good Gram-positive and Gram-negative potency. Herein we will discuss the various subunits that were investigated in this series and report advanced studies on compound 1 (GSK945237) which demonstrates good PK and in vivo efficacy properties ...

    During the course of our research on the lead optimisation of the NBTI (Novel Bacterial Type II Topoisomerase Inhibitors) class of antibacterials, we discovered a series of tricyclic compounds that showed good Gram-positive and Gram-negative potency. Herein we will discuss the various subunits that were investigated in this series and report advanced studies on compound 1 (GSK945237) which demonstrates good PK and in vivo efficacy properties.


    Organizational Affiliation

    Infectious Diseases CEDD, GlaxoSmithKline, 1250 South Collegeville Road, Collegeville, PA 19426, USA.



Macromolecules

Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
DNA gyrase subunit B,DNA gyrase subunit BA [auth B], C [auth D]202Staphylococcus aureus subsp. aureus N315Mutation(s): 0 
Gene Names: gyrBSA0005
EC: 5.99.1.3 (PDB Primary Data), 5.6.2.2 (UniProt)
UniProt
Find proteins for P66937 (Staphylococcus aureus (strain N315))
Explore P66937 
Go to UniProtKB:  P66937
Protein Feature View
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
DNA gyrase subunit AB [auth A], D [auth C]490Staphylococcus aureusMutation(s): 0 
Gene Names: gyrASA0006
EC: 5.99.1.3 (PDB Primary Data), 5.6.2.2 (UniProt)
UniProt
Find proteins for Q99XG5 (Staphylococcus aureus (strain N315))
Explore Q99XG5 
Go to UniProtKB:  Q99XG5
Protein Feature View
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  • Reference Sequence
  • Find similar nucleic acids by:  Sequence   |   Structure
  • Entity ID: 3
    MoleculeChainsLengthOrganismImage
    DNA (5'-D(*AP*GP*CP*CP*GP*TP*AP*GP*GP*TP*TP*CP*AP*CP*CP*GP*CP*AP*CP*A)-3')E20synthetic construct
    Protein Feature View
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    • Reference Sequence
    • Find similar nucleic acids by:  Sequence   |   Structure
    • Entity ID: 4
      MoleculeChainsLengthOrganismImage
      DNA (5'-D(*TP*GP*TP*GP*CP*GP*GP*TP*GP*AP*AP*CP*CP*TP*AP*CP*GP*GP*CP*T)-3')F20synthetic construct
      Protein Feature View
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      • Reference Sequence
      Small Molecules
      Ligands 3 Unique
      IDChainsName / Formula / InChI Key2D Diagram3D Interactions
      6EJ
      Query on 6EJ

      Download Ideal Coordinates CCD File 
      J [auth F](1R)-1-[(4-{[(6,7-dihydro[1,4]dioxino[2,3-c]pyridazin-3-yl)methyl]amino}piperidin-1-yl)methyl]-9-fluoro-1,2-dihydro-4H-pyrrolo[3,2,1-ij]quinolin-4-one
      C24 H26 F N5 O3
      SRICOHRDRMZREQ-MRXNPFEDSA-N
       Ligand Interaction
      GOL
      Query on GOL

      Download Ideal Coordinates CCD File 
      I [auth C]GLYCEROL
      C3 H8 O3
      PEDCQBHIVMGVHV-UHFFFAOYSA-N
       Ligand Interaction
      MN
      Query on MN

      Download Ideal Coordinates CCD File 
      G [auth B], H [auth D]MANGANESE (II) ION
      Mn
      WAEMQWOKJMHJLA-UHFFFAOYSA-N
       Ligand Interaction
      Experimental Data & Validation

      Experimental Data

      • Method: X-RAY DIFFRACTION
      • Resolution: 2.50 Å
      • R-Value Free: 0.224 
      • R-Value Work: 0.180 
      • R-Value Observed: 0.182 
      • Space Group: P 61
      Unit Cell:
      Length ( Å )Angle ( ˚ )
      a = 93.785α = 90
      b = 93.785β = 90
      c = 413.35γ = 120
      Software Package:
      Software NamePurpose
      REFMACrefinement
      MOSFLMdata reduction
      SCALAdata scaling
      REFMACphasing

      Structure Validation

      View Full Validation Report



      Entry History 

      Deposition Data

      • Deposited Date: 2016-03-22 
      • Released Date: 2016-05-25 
      • Deposition Author(s): Bax, B.D., Miles, T.J.

      Revision History  (Full details and data files)

      • Version 1.0: 2016-05-25
        Type: Initial release
      • Version 1.1: 2016-06-29
        Changes: Database references