2W5U

Flavodoxin from Helicobacter pylori in complex with the C3 inhibitor


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.62 Å
  • R-Value Free: 0.264 
  • R-Value Work: 0.227 
  • R-Value Observed: 0.227 

wwPDB Validation 3D Report Full Report


This is version 1.5 of the entry. See complete history


Literature

Discovery of Specific Flavodoxin Inhibitors as Potential Therapeutic Agents Against Helicobacter Pylori Infection.

Cremades, N.Velazquez-Campoy, A.Martinez-Julvez, M.Neira, J.L.Perez-Dorado, I.Hermoso, J.Jimenez, P.Lanas, A.Hoffman, P.S.Sancho, J.

(2009) ACS Chem Biol 4: 928

  • DOI: 10.1021/cb900166q
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • Helicobacter pylori establishes life-long infections in the gastric mucosa of over 1 billion people worldwide. In many cases, without specific antimicrobial intervention, H. pylori infected individuals will develop type B gastritis, chronic peptic ul ...

    Helicobacter pylori establishes life-long infections in the gastric mucosa of over 1 billion people worldwide. In many cases, without specific antimicrobial intervention, H. pylori infected individuals will develop type B gastritis, chronic peptic ulcers and, more rarely, gastric neoplasias. Conventional antimicrobial therapy has been complicated by dramatic increases in resistance to macrolides, metronidazole and fluoroquinolones. Here, we report the development of novel therapeutics that specifically target the unique flavodoxin component of an essential metabolic pathway of H. pylori. With the use of high-throughput screening methodology, we have tested 10,000 chemicals and have identified 29 compounds that bind flavodoxin, four of which interrupted in vitro electron transfer to flavodoxin physiological partners. Three of these compounds are bactericidal and promisingly selective for H. pylori. The minimal inhibitory concentrations of two of them are 10 times lower than their minimal cytotoxic concentrations for HeLa cells. Importantly, neither of the four inhibitors is toxic for mice after administration of 1-10 mg kg(-1) doses twice a day for 5 days. Enzymatic, thermodynamic and structural characterization of the inhibitor-flavodoxin complexes suggests these compounds could act by modifying the redox potentials of flavodoxin. These newly discovered inhibitors represent promising selective leads against the different diseases associated to H. pylori infection.


    Related Citations: 
    • Common Conformational Changes in Flavodoxins Induced by Fmn and Anion Binding: The Structure of Helicobacter Pylori Apoflavodoxin.
      Martinez-Julvez, M., Cremades, N., Bueno, M., Perez-Dorado, I., Maya, C., Cuesta-Lopez, S., Prada, D., Falo, F., Hermoso, J.A., Sancho, J.
      (2007) Proteins 69: 581
    • Towards a New Therapeutic Target: Helicobacter Pylori Flavodoxin.
      Cremades, N., Bueno, M., Toja, M., Sancho, J.
      (2005) Biophys Chem 115: 267

    Organizational Affiliation

    Departamento de Bioquimica y Biologia Molecular y Celular, Facultad de Ciencias, Universidad de Zaragoza, Spain.



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
FlavodoxinA, B164Helicobacter pyloriMutation(s): 0 
Find proteins for O25776 (Helicobacter pylori (strain ATCC 700392 / 26695))
Explore O25776 
Go to UniProtKB:  O25776
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
FMN
Query on FMN

Download CCD File 
A, B
FLAVIN MONONUCLEOTIDE
C17 H21 N4 O9 P
FVTCRASFADXXNN-SCRDCRAPSA-N
 Ligand Interaction
IC3
Query on IC3

Download CCD File 
A
[2-(5-amino-4-cyano-1H-pyrazol-1-yl)-5-(trifluoromethyl)phenyl](hydroxy)oxoammonium
C11 H7 F3 N5 O2
XSUKDZBLRKXERL-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.62 Å
  • R-Value Free: 0.264 
  • R-Value Work: 0.227 
  • R-Value Observed: 0.227 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 38.533α = 90
b = 50.967β = 98.64
c = 72.806γ = 90
Software Package:
Software NamePurpose
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2009-12-22
    Type: Initial release
  • Version 1.1: 2011-05-08
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2017-06-14
    Changes: Derived calculations, Source and taxonomy, Structure summary
  • Version 1.4: 2017-07-05
    Changes: Data collection
  • Version 1.5: 2018-02-07
    Changes: Database references