4BUL

Novel hydroxyl tricyclics (e.g. GSK966587) as potent inhibitors of bacterial type IIA topoisomerases


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.6 Å
  • R-Value Free: 0.183 
  • R-Value Work: 0.144 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Novel Hydroxyl Tricyclics (E.G., Gsk966587) 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.Huang, J.Jones, G.E.Kusalakumari Sukmar, S.K.Spitzfaden, C.Markwell, R.E.Minthorn, E.A.Rittenhouse, S.Gwynn, M.N.Pearson, N.D.

(2013) Bioorg.Med.Chem.Lett. 23: 5437

  • DOI: 10.1016/j.bmcl.2013.07.013

  • PubMed Abstract: 
  • During the course of our research to find novel mode of action antibacterials, we discovered a series of hydroxyl tricyclic compounds that showed good potency against Gram-positive and Gram-negative pathogens. These compounds inhibit bacterial type I ...

    During the course of our research to find novel mode of action antibacterials, we discovered a series of hydroxyl tricyclic compounds that showed good potency against Gram-positive and Gram-negative pathogens. These compounds inhibit bacterial type IIA topoisomerases. Herein we will discuss structure-activity relationships in this series and report advanced studies on compound 1 (GSK966587) which demonstrates good PK and in vivo efficacy properties. X-ray crystallographic studies were used to provide insight into the structural basis for the difference in antibacterial potency between enantiomers.


    Related Citations: 
    • Type Iia Topoisomerase Inhibition by a New Class of Antibacterial Agents.
      Bax, B.D.,Chan, P.F.,Eggleston, D.S.,Fosberry, A.,Gentry, D.R.,Gorrec, F.,Giordano, I.,Hann, M.M.,Hennessy, A.,Hibbs, M.,Huang, J.,Jones, E.,Jones, J.,Brown, K.K.,Lewis, C.J.,May, E.W.,Saunders, M.R.,Singh, O.,Spitzfaden, C.E.,Shen, C.,Shillings, A.,Theobald, A.J.,Wohlkonig, A.,Pearson, N.D.,Gwynn, M.N.
      (2010) Nature 466: 935


    Organizational Affiliation

    Diseases of the Developing World CEDD, GlaxoSmithKline, Madrid, Spain. tim.j.miles@gsk.com




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
DNA GYRASE SUBUNIT B, DNA GYRASE SUBUNIT A
A, C
692Staphylococcus aureus (strain N315)Mutation(s): 1 
Gene Names: gyrA, gyrB
EC: 5.6.2.3 5.6.2.3
Find proteins for Q99XG5 (Staphylococcus aureus (strain N315))
Go to UniProtKB:  Q99XG5
Find proteins for P66937 (Staphylococcus aureus (strain N315))
Go to UniProtKB:  P66937
Entity ID: 2
MoleculeChainsLengthOrganism
5'-D(*TP*GP*TP*GP*CP*GP*GP*TP*GP*TP*AP*CP*CP*TP *AP*CP*GP*GP*CP*T)-3'E,G20synthetic construct
Entity ID: 3
MoleculeChainsLengthOrganism
5'-D(*AP*GP*CP*CP*GP*TP*AP*GP*GP*TP*AP*CP*AP*CP *CP*GP*CP*AP*C)-3'F,H20synthetic construct
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MN
Query on MN

Download SDF File 
Download CCD File 
A, C, E
MANGANESE (II) ION
Mn
WAEMQWOKJMHJLA-UHFFFAOYSA-N
 Ligand Interaction
AE8
Query on AE8

Download SDF File 
Download CCD File 
F
(S)-4-((4-(((2,3-dihydro-[1,4]dioxino[2,3-c]pyridin-7-yl)methyl)amino)piperidin-1-yl)methyl)-3-fluoro-4-hydroxy-4H-pyrrolo[3,2,1-de][1,5]naphthyridin-7(5H)-one
C24 H26 F N5 O4
VJVBZXRLYHVXIQ-DEOSSOPVSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.6 Å
  • R-Value Free: 0.183 
  • R-Value Work: 0.144 
  • Space Group: P 61
Unit Cell:
Length (Å)Angle (°)
a = 93.871α = 90.00
b = 93.871β = 90.00
c = 416.439γ = 120.00
Software Package:
Software NamePurpose
SCALAdata scaling
MOSFLMdata reduction
REFMACphasing
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Revision History 

  • Version 1.0: 2013-08-07
    Type: Initial release
  • Version 1.1: 2013-09-04
    Type: Database references
  • Version 1.2: 2013-09-18
    Type: Database references
  • Version 1.3: 2017-03-15
    Type: Source and taxonomy