3N9R

Class II fructose-1,6-bisphosphate aldolase from helicobacter pylori in complex with N-(4-hydroxybutyl)-phosphoglycolohydroxamic acid, a competitive inhibitor


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.8 Å
  • R-Value Free: 0.203 
  • R-Value Work: 0.158 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Rational Design, Synthesis, and Evaluation of New Selective Inhibitors of Microbial Class II (Zinc Dependent) Fructose Bis-phosphate Aldolases.

Daher, R.Fonvielle, M.Gest, P.M.Guerin, M.E.Jackson, M.Sygusch, J.Therisod, M.

(2010) J.Med.Chem. 53: 7836-7842

  • DOI: 10.1021/jm1009814
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • We report the synthesis and biochemical evaluation of several selective inhibitors of class II (zinc dependent) fructose bis-phosphate aldolases (Fba). The products were designed as transition-state analogues of the catalyzed reaction, structurally r ...

    We report the synthesis and biochemical evaluation of several selective inhibitors of class II (zinc dependent) fructose bis-phosphate aldolases (Fba). The products were designed as transition-state analogues of the catalyzed reaction, structurally related to the substrate fructose bis-phosphate (or sedoheptulose bis-phosphate) and based on an N-substituted hydroxamic acid, as a chelator of the zinc ion present in active site. The compounds synthesized were tested on class II Fbas from various pathogenic microorganisms and, by comparison, on a mammalian class I Fba. The best inhibitor shows K(i) against class II Fbas from various pathogens in the nM range, with very high selectivity (up to 10(5)). Structural analyses of inhibitors in complex with aldolases rationalize and corroborate the enzymatic kinetics results. These inhibitors represent lead compounds for the preparation of new synthetic antibiotics, notably for tuberculosis prophylaxis.


    Organizational Affiliation

    ECBB, ICMMO, Univ Paris-Sud, UMR 8182, F-91405 Orsay, France.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Fructose-bisphosphate aldolase
A, B, K, P, U, Z, e, j
307Helicobacter pylori (strain 51)Mutation(s): 0 
Gene Names: fba
Find proteins for D0IR47 (Helicobacter pylori (strain 51))
Go to UniProtKB:  D0IR47
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

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Download CCD File 
A, B, e, j, K, P, U, Z
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
NA
Query on NA

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Download CCD File 
A, B, e, j, K, P, U, Z
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
CL
Query on CL

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Download CCD File 
A, B, e, j, K, P, U, Z
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
TD3
Query on TD3

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Download CCD File 
A, B, e, j, K, P, U, Z
2-[hydroxy(4-hydroxybutyl)amino]-2-oxoethyl dihydrogen phosphate
C6 H14 N O7 P
XYJLIJWOOPZDNB-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
TD3Ki: 5500 nM BINDINGMOAD
TD3Ki: 70 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.8 Å
  • R-Value Free: 0.203 
  • R-Value Work: 0.158 
  • Space Group: P 1
Unit Cell:
Length (Å)Angle (°)
a = 51.400α = 98.50
b = 104.400β = 90.00
c = 111.900γ = 90.00
Software Package:
Software NamePurpose
PHENIXrefinement
SCALAdata scaling
XSCALEdata scaling
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2010-11-17
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance