6KVP

S. aureus FtsZ in complex with 3-(1-(5-bromo-4-(4-(trifluoromethyl)phenyl)oxazol-2-yl)ethoxy)-2,6-difluorobenzamide (compound 2)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.40 Å
  • R-Value Free: 0.177 
  • R-Value Work: 0.145 
  • R-Value Observed: 0.146 

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Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

Structure-Guided Design of a Fluorescent Probe for the Visualization of FtsZ in Clinically Important Gram-Positive and Gram-Negative Bacterial Pathogens.

Ferrer-Gonzalez, E.Fujita, J.Yoshizawa, T.Nelson, J.M.Pilch, A.J.Hillman, E.Ozawa, M.Kuroda, N.Al-Tameemi, H.M.Boyd, J.M.LaVoie, E.J.Matsumura, H.Pilch, D.S.

(2019) Sci Rep 9: 20092-20092

  • DOI: https://doi.org/10.1038/s41598-019-56557-x
  • Primary Citation of Related Structures:  
    6KVP, 6KVQ

  • PubMed Abstract: 

    Addressing the growing problem of antibiotic resistance requires the development of new drugs with novel antibacterial targets. FtsZ has been identified as an appealing new target for antibacterial agents. Here, we describe the structure-guided design of a new fluorescent probe (BOFP) in which a BODIPY fluorophore has been conjugated to an oxazole-benzamide FtsZ inhibitor. Crystallographic studies have enabled us to identify the optimal position for tethering the fluorophore that facilitates the high-affinity FtsZ binding of BOFP. Fluorescence anisotropy studies demonstrate that BOFP binds the FtsZ proteins from the Gram-positive pathogens Staphylococcus aureus, Enterococcus faecalis, Enterococcus faecium, Streptococcus pyogenes, Streptococcus agalactiae, and Streptococcus pneumoniae with K d values of 0.6-4.6 µM. Significantly, BOFP binds the FtsZ proteins from the Gram-negative pathogens Escherichia coli, Klebsiella pneumoniae, Pseudomonas aeruginosa, and Acinetobacter baumannii with an even higher affinity (K d  = 0.2-0.8 µM). Fluorescence microscopy studies reveal that BOFP can effectively label FtsZ in all the above Gram-positive and Gram-negative pathogens. In addition, BOFP is effective at monitoring the impact of non-fluorescent inhibitors on FtsZ localization in these target pathogens. Viewed as a whole, our results highlight the utility of BOFP as a powerful tool for identifying new broad-spectrum FtsZ inhibitors and understanding their mechanisms of action.


  • Organizational Affiliation

    Department of Pharmacology, Rutgers Robert Wood Johnson Medical School, 675 Hoes Lane, Piscataway, NJ, 08854, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Cell division protein FtsZ308Staphylococcus aureusMutation(s): 0 
Gene Names: ftsZ
UniProt
Find proteins for Q6GHP9 (Staphylococcus aureus (strain MRSA252))
Explore Q6GHP9 
Go to UniProtKB:  Q6GHP9
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ6GHP9
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ZI1 (Subject of Investigation/LOI)
Query on ZI1

Download Ideal Coordinates CCD File 
D [auth A]3-[(1R)-1-[5-bromanyl-4-[4-(trifluoromethyl)phenyl]-1,3-oxazol-2-yl]ethoxy]-2,6-bis(fluoranyl)benzamide
C19 H12 Br F5 N2 O3
VMZXYVWYPGADSK-MRVPVSSYSA-N
GDP
Query on GDP

Download Ideal Coordinates CCD File 
B [auth A]GUANOSINE-5'-DIPHOSPHATE
C10 H15 N5 O11 P2
QGWNDRXFNXRZMB-UUOKFMHZSA-N
CA
Query on CA

Download Ideal Coordinates CCD File 
C [auth A]CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.40 Å
  • R-Value Free: 0.177 
  • R-Value Work: 0.145 
  • R-Value Observed: 0.146 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 70.491α = 90
b = 51.739β = 108.65
c = 86.737γ = 90
Software Package:
Software NamePurpose
HKL-2000data reduction
SCALEPACKdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACTdata extraction

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)United StatesAI118874
Japan Society for the Promotion of ScienceJapan15J00589
Japan Society for the Promotion of ScienceJapan19K16060
Japan Society for the Promotion of ScienceJapan17H05732
Japan Society for the Promotion of ScienceJapan18K06094
Japan Society for the Promotion of ScienceJapan19H04735
Japan Society for the Promotion of ScienceJapan19K07582
Japan Agency for Medical Research and Development (AMED)JapanJP19am0101070

Revision History  (Full details and data files)

  • Version 1.0: 2020-01-15
    Type: Initial release
  • Version 1.1: 2022-03-23
    Changes: Author supporting evidence, Database references
  • Version 1.2: 2023-11-22
    Changes: Data collection, Refinement description