6YD5

SaFtsZ-UCM151 (comp. 18)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.55 Å
  • R-Value Free: 0.234 
  • R-Value Work: 0.184 
  • R-Value Observed: 0.186 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


Literature

Targeting the FtsZ Allosteric Binding Site with a Novel Fluorescence Polarization Screen, Cytological and Structural Approaches for Antibacterial Discovery.

Huecas, S.Araujo-Bazan, L.Ruiz, F.M.Ruiz-Avila, L.B.Martinez, R.F.Escobar-Pena, A.Artola, M.Vazquez-Villa, H.Martin-Fontecha, M.Fernandez-Tornero, C.Lopez-Rodriguez, M.L.Andreu, J.M.

(2021) J Med Chem 64: 5730-5745

  • DOI: https://doi.org/10.1021/acs.jmedchem.0c02207
  • Primary Citation of Related Structures:  
    6YD1, 6YD5, 6YD6

  • PubMed Abstract: 

    Bacterial resistance to antibiotics makes previously manageable infections again disabling and lethal, highlighting the need for new antibacterial strategies. In this regard, inhibition of the bacterial division process by targeting key protein FtsZ has been recognized as an attractive approach for discovering new antibiotics. Binding of small molecules to the cleft between the N-terminal guanosine triphosphate (GTP)-binding and the C-terminal subdomains allosterically impairs the FtsZ function, eventually inhibiting bacterial division. Nonetheless, the lack of appropriate chemical tools to develop a binding screen against this site has hampered the discovery of FtsZ antibacterial inhibitors. Herein, we describe the first competitive binding assay to identify FtsZ allosteric ligands interacting with the interdomain cleft, based on the use of specific high-affinity fluorescent probes. This novel assay, together with phenotypic profiling and X-ray crystallographic insights, enables the identification and characterization of FtsZ inhibitors of bacterial division aiming at the discovery of more effective antibacterials.


  • Organizational Affiliation

    Centro de Investigaciones Biológicas Margarita Salas, CSIC, Ramiro de Maeztu 9, 28040 Madrid, Spain.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Cell division protein FtsZ307Staphylococcus aureusMutation(s): 0 
Gene Names: ftsZ
UniProt
Find proteins for Q2FZ89 (Staphylococcus aureus (strain NCTC 8325 / PS 47))
Explore Q2FZ89 
Go to UniProtKB:  Q2FZ89
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ2FZ89
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 5 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
GDP
Query on GDP

Download Ideal Coordinates CCD File 
B [auth A]GUANOSINE-5'-DIPHOSPHATE
C10 H15 N5 O11 P2
QGWNDRXFNXRZMB-UUOKFMHZSA-N
OM8 (Subject of Investigation/LOI)
Query on OM8

Download Ideal Coordinates CCD File 
E [auth A]3-[(3-chlorophenyl)methoxy]-2,6-bis(fluoranyl)benzamide
C14 H10 Cl F2 N O2
QPJFTLSXPCJEKL-UHFFFAOYSA-N
MB3
Query on MB3

Download Ideal Coordinates CCD File 
C [auth A]1-methylpyrrolidin-2-one
C5 H9 N O
SECXISVLQFMRJM-UHFFFAOYSA-N
EDO
Query on EDO

Download Ideal Coordinates CCD File 
F [auth A]1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
K
Query on K

Download Ideal Coordinates CCD File 
D [auth A]POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.55 Å
  • R-Value Free: 0.234 
  • R-Value Work: 0.184 
  • R-Value Observed: 0.186 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 72.404α = 90
b = 50.182β = 111.49
c = 88.6γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
PHENIXrefinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2021-07-28
    Type: Initial release
  • Version 1.1: 2024-01-24
    Changes: Data collection, Database references, Refinement description