3C52

Class II fructose-1,6-bisphosphate aldolase from helicobacter pylori in complex with phosphoglycolohydroxamic acid, a competitive inhibitor


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.249 
  • R-Value Work: 0.204 

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Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

Synthesis and Biochemical Evaluation of Selective Inhibitors of Class II Fructose Bisphosphate Aldolases: Towards New Synthetic Antibiotics.

Fonvielle, M.Coincon, M.Daher, R.Desbenoit, N.Kosieradzka, K.Barilone, N.Gicquel, B.Sygusch, J.Jackson, M.Therisod, M.

(2008) Chemistry 14: 8521-8529

  • DOI: 10.1002/chem.200800857
  • Primary Citation of Related Structures:  
    3C4U, 3C52, 3C56

  • PubMed Abstract: 
  • We report the synthesis and biochemical evaluation of selective inhibitors of class II (zinc-dependent) fructose bisphosphate aldolases. The most active compound is a simplified analogue of fructose bisphosphate, bearing a well-positioned metal chelating group ...

    We report the synthesis and biochemical evaluation of selective inhibitors of class II (zinc-dependent) fructose bisphosphate aldolases. The most active compound is a simplified analogue of fructose bisphosphate, bearing a well-positioned metal chelating group. It is a powerful and highly selective competitive inhibitor of isolated class II aldolases. We report crystallographic studies of this inhibitor bound in the active site of the Helicobacter pylori enzyme. The compound also shows activity against Mycobacterium tuberculosis isolates.


    Organizational Affiliation

    LCBB-ICMMO, UMR 8182, Université Paris-Sud, Orsay, France.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Fructose-bisphosphate aldolaseA, B307Helicobacter pyloriMutation(s): 0 
Gene Names: fba
EC: 4.1.2.13
UniProt
Find proteins for P56109 (Helicobacter pylori (strain ATCC 700392 / 26695))
Explore P56109 
Go to UniProtKB:  P56109
Protein Feature View
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  • Reference Sequence
Small Molecules
Binding Affinity Annotations 
IDSourceBinding Affinity
PGH PDBBind:  3C52 Ki: 50 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.249 
  • R-Value Work: 0.204 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 39.242α = 90
b = 85.305β = 100.16
c = 90.818γ = 90
Software Package:
Software NamePurpose
CNSrefinement
PDB_EXTRACTdata extraction
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
andrefinement

Structure Validation

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Ligand Structure Quality Assessment  



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2008-08-26
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2012-07-25
    Changes: Structure summary