3C56

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

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.207 
  • R-Value Work: 0.172 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.3 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
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PH4 (Subject of Investigation/LOI)
Query on PH4

Download Ideal Coordinates CCD File 
D [auth A], F [auth B]3-{hydroxy[(phosphonooxy)acetyl]amino}propyl dihydrogen phosphate
C5 H13 N O10 P2
IISKWLQYGVRJHI-UHFFFAOYSA-N
 Ligand Interaction
ZN
Query on ZN

Download Ideal Coordinates CCD File 
C [auth A], E [auth B]ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
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

  • Method: X-RAY DIFFRACTION
  • 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
PHENIXrefinement
PDB_EXTRACTdata extraction
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
CNSrefinement

Structure Validation

View Full Validation Report



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