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


Ligand Structure Quality Assessment 


This is version 1.2 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: https://doi.org/10.1016/j.bmcl.2016.03.106
  • Primary Citation of Related Structures:  
    5IWI, 5IWM

  • 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.


  • Organizational Affiliation

    Diseases of the Developing World CEDD, GlaxoSmithKline, Calle Severo Ochoa, 2, 28760 Tres Cantos, Madrid, Spain. Electronic address: tim.j.miles@gsk.com.


Macromolecules

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence 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
UniProt
Find proteins for P66937 (Staphylococcus aureus (strain N315))
Explore P66937 
Go to UniProtKB:  P66937
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP66937
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
DNA gyrase subunit AB [auth A],
D [auth C]
490Staphylococcus aureusMutation(s): 0 
Gene Names: gyrASA0006
EC: 5.99.1.3
UniProt
Find proteins for Q99XG5 (Staphylococcus aureus (strain N315))
Explore Q99XG5 
Go to UniProtKB:  Q99XG5
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ99XG5
Sequence Annotations
Expand
  • Reference Sequence

Find similar nucleic acids by:  Sequence   |   3D Structure  

Entity ID: 3
MoleculeChains LengthOrganismImage
DNA (5'-D(*AP*GP*CP*CP*GP*TP*AP*GP*GP*TP*TP*CP*AP*CP*CP*GP*CP*AP*CP*A)-3')20synthetic construct
Sequence Annotations
Expand
  • Reference Sequence

Find similar nucleic acids by:  Sequence   |   3D Structure  

Entity ID: 4
MoleculeChains LengthOrganismImage
DNA (5'-D(*TP*GP*TP*GP*CP*GP*GP*TP*GP*AP*AP*CP*CP*TP*AP*CP*GP*GP*CP*T)-3')20synthetic construct
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / 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
GOL
Query on GOL

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

Download Ideal Coordinates CCD File 
G [auth B],
H [auth D]
MANGANESE (II) ION
Mn
WAEMQWOKJMHJLA-UHFFFAOYSA-N
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



Ligand Structure Quality Assessment 


Entry History 

Deposition Data

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
  • Version 1.2: 2024-01-10
    Changes: Advisory, Data collection, Database references, Derived calculations, Refinement description