4KPF

Novel fluoroquinolones in complex with topoisomerase IV from S. pneumoniae and E-site G-gate


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.24 Å
  • R-Value Free: 0.184 
  • R-Value Work: 0.162 
  • R-Value Observed: 0.163 

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Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

Exploring the active site of the Streptococcus pneumoniae topoisomerase IV-DNA cleavage complex with novel 7,8-bridged fluoroquinolones.

Laponogov, I.Pan, X.S.Veselkov, D.A.Cirz, R.T.Wagman, A.Moser, H.E.Fisher, L.M.Sanderson, M.R.

(2016) Open Biol 6

  • DOI: https://doi.org/10.1098/rsob.160157
  • Primary Citation of Related Structures:  
    3RAD, 4KPE, 4KPF

  • PubMed Abstract: 

    As part of a programme of synthesizing and investigating the biological properties of new fluoroquinolone antibacterials and their targeting of topoisomerase IV from Streptococcus pneumoniae, we have solved the X-ray structure of the complexes of two new 7,8-bridged fluoroquinolones (with restricted C7 group rotation favouring tight binding) in complex with the topoisomerase IV from S. pneumoniae and an 18-base-pair DNA binding site-the E-site-found by our DNA mapping studies to bind drug strongly in the presence of topoisomerase IV (Leo et al. 2005 J. Biol. Chem. 280, 14 252-14 263, doi:10.1074/jbc.M500156200). Although the degree of antibiotic resistance towards fluoroquinolones is much lower than that of β-lactams and a range of ribosome-bound antibiotics, there is a pressing need to increase the diversity of members of this successful clinically used class of drugs. The quinolone moiety of the new 7,8-bridged agents ACHN-245 and ACHN-454 binds similarly to that of clinafloxocin, levofloxacin, moxifloxacin and trovofloxacin but the cyclic scaffold offers the possibility of chemical modification to produce interactions with other topoisomerase residues at the active site.


  • Organizational Affiliation

    Randall Division of Cell and Molecular Biophysics, King's College, Guy's Campus, London Bridge, London SE1 1UL, UK Molecular and Clinical Sciences Research Institute, St George's, University of London, Cranmer Terrace, London SW17 0RE, UK.


Macromolecules

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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
ParC55
A, B
496Streptococcus pneumoniae TIGR4Mutation(s): 0 
Gene Names: parCSP_0855
EC: 5.6.2.2
UniProt
Find proteins for P72525 (Streptococcus pneumoniae serotype 4 (strain ATCC BAA-334 / TIGR4))
Explore P72525 
Go to UniProtKB:  P72525
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP72525
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
ParE30
C, D
268Streptococcus pneumoniae TIGR4Mutation(s): 0 
Gene Names: parE
EC: 5.6.2.2
UniProt
Find proteins for Q59961 (Streptococcus pneumoniae serotype 4 (strain ATCC BAA-334 / TIGR4))
Explore Q59961 
Go to UniProtKB:  Q59961
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ59961
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  • Reference Sequence

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Entity ID: 3
MoleculeChains LengthOrganismImage
E-site17synthetic construct
Sequence Annotations
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  • Reference Sequence

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Entity ID: 4
MoleculeChains LengthOrganismImage
E-site211synthetic construct
Sequence Annotations
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  • Reference Sequence

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Entity ID: 5
MoleculeChains LengthOrganismImage
E-site37synthetic construct
Sequence Annotations
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  • Reference Sequence

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Entity ID: 6
MoleculeChains LengthOrganismImage
E-site411synthetic construct
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
1UV
Query on 1UV

Download Ideal Coordinates CCD File 
O [auth H],
P [auth H]
(3aS,4R)-4-amino-13-cyclopropyl-8-fluoro-10-oxo-3a,4,5,6,10,13-hexahydro-1H,3H-pyrrolo[2',1':3,4][1,4]oxazepino[5,6-h]quinoline-11-carboxylic acid
C19 H20 F N3 O4
DXDXKLSOWWPCNV-HUUCEWRRSA-N
MG
Query on MG

Download Ideal Coordinates CCD File 
I [auth A]
J [auth A]
K [auth B]
L [auth C]
M [auth D]
I [auth A],
J [auth A],
K [auth B],
L [auth C],
M [auth D],
N [auth G]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.24 Å
  • R-Value Free: 0.184 
  • R-Value Work: 0.162 
  • R-Value Observed: 0.163 
  • Space Group: P 31 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 157.86α = 90
b = 157.86β = 90
c = 210.78γ = 120
Software Package:
Software NamePurpose
GDEdata collection
PHASERphasing
PHENIXrefinement
XDSdata reduction
XSCALEdata scaling

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2014-11-26
    Type: Initial release
  • Version 1.1: 2018-10-03
    Changes: Data collection, Database references, Source and taxonomy
  • Version 1.2: 2024-10-16
    Changes: Data collection, Database references, Derived calculations, Structure summary