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: 1.80 Å
  • R-Value Free: 0.203 
  • R-Value Work: 0.158 
  • R-Value Observed: 0.162 

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:  
    3N9R, 3N9S

  • 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 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 ...

    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:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Fructose-bisphosphate aldolaseA, B, C [auth K], D [auth P], E [auth U], F [auth Z], G [auth e], H [auth j]307Helicobacter pylori 51Mutation(s): 0 
Gene Names: ALF_HELPYfbaKHP_0173
EC: 4.1.2.13
Find proteins for D0IR47 (Helicobacter pylori (strain 51))
Explore D0IR47 
Go to UniProtKB:  D0IR47
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
TD3
Query on TD3

Download Ideal Coordinates CCD File 
BA [auth U], FA [auth Z], JA [auth e], L [auth A], NA [auth j], P [auth B], T [auth K], X [auth P]2-[hydroxy(4-hydroxybutyl)amino]-2-oxoethyl dihydrogen phosphate
C6 H14 N O7 P
XYJLIJWOOPZDNB-UHFFFAOYSA-N
 Ligand Interaction
ZN
Query on ZN

Download Ideal Coordinates CCD File 
CA [auth Z], GA [auth e], I [auth A], KA [auth j], M [auth B], Q [auth K], U [auth P], Y [auth U]ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
CL
Query on CL

Download Ideal Coordinates CCD File 
AA [auth U], EA [auth Z], IA [auth e], K [auth A], MA [auth j], O [auth B], S [auth K], W [auth P]CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
NA
Query on NA

Download Ideal Coordinates CCD File 
DA [auth Z], HA [auth e], J [auth A], LA [auth j], N [auth B], R [auth K], V [auth P], Z [auth U]SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
TD3Ki :  70   nM  PDBBind
TD3Ki:  5500   nM  Binding MOAD
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.203 
  • R-Value Work: 0.158 
  • R-Value Observed: 0.162 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 51.4α = 98.5
b = 104.4β = 90
c = 111.9γ = 90
Software Package:
Software NamePurpose
SCALAdata scaling
PHENIXrefinement
PDB_EXTRACTdata extraction
XSCALEdata scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

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