3N9R | pdb_00003n9r

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 (Depositor), 0.201 (DCC) 
  • R-Value Work: 
    0.158 (Depositor), 0.158 (DCC) 
  • R-Value Observed: 
    0.162 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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Ligand Structure Quality Assessment 


This is version 1.2 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: https://doi.org/10.1021/jm1009814
  • Primary Citation 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. 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.

Macromolecule Content 

  • Total Structure Weight: 273.34 kDa 
  • Atom Count: 21,263 
  • Modeled Residue Count: 2,376 
  • Deposited Residue Count: 2,456 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Fructose-bisphosphate aldolase307Helicobacter pylori 51Mutation(s): 0 
Gene Names: ALF_HELPY
EC: 4.1.2.13

Small Molecules

Ligands 4 Unique
IDChains Name / 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]
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
ZN

Query on ZN



Download:Ideal Coordinates CCD File
CA [auth Z]
GA [auth e]
I [auth A]
KA [auth j]
M [auth B]
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
CL

Query on CL



Download:Ideal Coordinates CCD File
AA [auth U]
EA [auth Z]
IA [auth e]
K [auth A]
MA [auth j]
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
NA

Query on NA



Download:Ideal Coordinates CCD File
DA [auth Z]
HA [auth e]
J [auth A]
LA [auth j]
N [auth B]
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

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free:  0.203 (Depositor), 0.201 (DCC) 
  • R-Value Work:  0.158 (Depositor), 0.158 (DCC) 
  • R-Value Observed: 0.162 (Depositor) 
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

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Ligand Structure Quality Assessment 


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
  • Version 1.2: 2023-09-06
    Changes: Data collection, Database references, Derived calculations, Refinement description