4O7U

Etherocomplex of Enteroccocus faecalis thymidylate synthase with 5-hydroxymethilene-6-hydrofolic acid and the phtalimidic inhibitor SS7


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 0.287 
  • R-Value Work: 0.212 
  • R-Value Observed: 0.216 

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Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

X-ray crystal structures of Enterococcus faecalis thymidylate synthase with folate binding site inhibitors.

Catalano, A.Luciani, R.Carocci, A.Cortesi, D.Pozzi, C.Borsari, C.Ferrari, S.Mangani, S.

(2016) Eur J Med Chem 123: 649-664

  • DOI: https://doi.org/10.1016/j.ejmech.2016.07.066
  • Primary Citation of Related Structures:  
    4O7U, 5J7W

  • PubMed Abstract: 

    Infections caused by Enterococcus faecalis (Ef) represent nowadays a relevant health problem. We selected Thymidylate synthase (TS) from this organism as a potential specific target for antibacterial therapy. We have previously demonstrated that species-specific inhibition of the protein can be achieved despite the relatively high structural similarity among bacterial TSs and human TS. We had previously obtained the EfTS crystal structure of the protein in complex with the metabolite 5-formyl-tetrahydrofolate (5-FTHF) suggesting the protein role as metabolite reservoir; however, protein-inhibitors complexes were still missing. In the present work we identified some inhibitors bearing the phthalimidic core from our in-house library and we performed crystallographic screening towards EfTS. We obtained two X-ray crystallographic structures: the first with a weak phthalimidic inhibitor bound in one subunit and 5-hydroxymethylene-6-hydrofolic acid (5-HMHF) in the other subunit; a second X-ray structure complex with methotrexate. The structural information achieved confirm the role of EfTS as an enzyme involved in the folate pool system and provide a structural basis for structure-based drug design.


  • Organizational Affiliation

    Dipartimento di Farmacia-Scienze del Farmaco, Università degli Studi di Bari "Aldo Moro", Via Orabona 4, 70125 Bari, Italy.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Thymidylate synthase
A, B, C, D
315Enterococcus faecalis V583Mutation(s): 0 
Gene Names: thyAEF_1576
EC: 2.1.1.45
UniProt
Find proteins for Q834R3 (Enterococcus faecalis (strain ATCC 700802 / V583))
Explore Q834R3 
Go to UniProtKB:  Q834R3
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ834R3
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
THF
Query on THF

Download Ideal Coordinates CCD File 
G [auth B]5-HYDROXYMETHYLENE-6-HYDROFOLIC ACID
C20 H23 N7 O7
IIEPLRAFVCMHQF-STQMWFEESA-N
SS7
Query on SS7

Download Ideal Coordinates CCD File 
K [auth D]4-{[(2S)-2-(1,3-dioxo-1,3-dihydro-2H-isoindol-2-yl)propyl]oxy}-3,5-dimethylphenyl acetate
C21 H21 N O5
UICXIWCGDWFHDK-AWEZNQCLSA-N
SO4
Query on SO4

Download Ideal Coordinates CCD File 
E [auth A],
F [auth A],
H [auth C],
J [auth D]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
EDO
Query on EDO

Download Ideal Coordinates CCD File 
I [auth C],
L [auth D]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 0.287 
  • R-Value Work: 0.212 
  • R-Value Observed: 0.216 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 72.082α = 90
b = 94.225β = 94.33
c = 96.816γ = 90
Software Package:
Software NamePurpose
DNAdata collection
MOLREPphasing
REFMACrefinement
MOSFLMdata reduction
SCALAdata 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: 2014-12-31
    Type: Initial release
  • Version 1.1: 2016-10-05
    Changes: Database references
  • Version 1.2: 2024-02-28
    Changes: Data collection, Database references, Derived calculations