5IWM

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Free: 0.224 
  • R-Value Work: 0.180 

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:  

  • 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. ...

    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: Sequence  |  Structure


Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
DNA gyrase subunit B,DNA gyrase subunit B
B, D
202Staphylococcus aureus (strain N315)Mutation(s): 0 
Gene Names: gyrB
EC: 5.6.2.3
Find proteins for P66937 (Staphylococcus aureus (strain N315))
Go to UniProtKB:  P66937
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
DNA gyrase subunit A
A, C
490Staphylococcus aureus (strain N315)Mutation(s): 0 
Gene Names: gyrA
EC: 5.6.2.3
Find proteins for Q99XG5 (Staphylococcus aureus (strain N315))
Go to UniProtKB:  Q99XG5
Entity ID: 3
MoleculeChainsLengthOrganism
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
Entity ID: 4
MoleculeChainsLengthOrganism
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
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MN
Query on MN

Download SDF File 
Download CCD File 
B, D
MANGANESE (II) ION
Mn
WAEMQWOKJMHJLA-UHFFFAOYSA-N
 Ligand Interaction
GOL
Query on GOL

Download SDF File 
Download CCD File 
C
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
6EJ
Query on 6EJ

Download SDF File 
Download CCD File 
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
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Free: 0.224 
  • R-Value Work: 0.180 
  • Space Group: P 61
Unit Cell:
Length (Å)Angle (°)
a = 93.785α = 90.00
b = 93.785β = 90.00
c = 413.350γ = 120.00
Software Package:
Software NamePurpose
MOSFLMdata reduction
REFMACphasing
SCALAdata scaling
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



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 

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