Class II fructose-1,6-bisphosphate aldolase from helicobacter pylori in complex with N-(3-Hydroxypropyl)-glycolohydroxamic acid bisphosphate, a competitive inhibitor

Experimental Data Snapshot

  • Resolution: 2.30 Å
  • R-Value Free: 0.207 
  • R-Value Work: 0.172 

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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: https://doi.org/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. 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.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Fructose-bisphosphate aldolase
A, B
307Helicobacter pyloriMutation(s): 0 
Gene Names: fba
Find proteins for P56109 (Helicobacter pylori (strain ATCC 700392 / 26695))
Explore P56109 
Go to UniProtKB:  P56109
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP56109
Sequence Annotations
  • Reference Sequence
Small Molecules
Binding Affinity Annotations 
IDSourceBinding Affinity
PH4 Binding MOAD:  3C56 Ki: 13 (nM) from 1 assay(s)
PDBBind:  3C56 Ki: 13 (nM) from 1 assay(s)
BindingDB:  3C56 Ki: 13 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Resolution: 2.30 Å
  • R-Value Free: 0.207 
  • R-Value Work: 0.172 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 39.222α = 82.9
b = 62.005β = 79.77
c = 65.615γ = 71.03
Software Package:
Software NamePurpose
PDB_EXTRACTdata extraction
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

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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: 2018-01-24
    Changes: Structure summary
  • Version 1.3: 2019-07-24
    Changes: Data collection, Refinement description