7OOZ

Purine nucleoside phosphorylase(DeoD-type) from H. pylori with 6-benzyloxo-2-chloropurine


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free: 0.188 
  • R-Value Work: 0.161 
  • R-Value Observed: 0.162 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


Literature

Interactions of 2,6-substituted purines with purine nucleoside phosphorylase from Helicobacter pylori in solution and in the crystal, and the effects of these compounds on cell cultures of this bacterium.

Narczyk, M.Wojtys, M.I.Lescic Asler, I.Zinic, B.Luic, M.Jagusztyn-Krynicka, E.K.Stefanic, Z.Bzowska, A.

(2022) J Enzyme Inhib Med Chem 37: 1083-1097

  • DOI: https://doi.org/10.1080/14756366.2022.2061965
  • Primary Citation of Related Structures:  
    7OOY, 7OOZ, 7OP9, 7OPA

  • PubMed Abstract: 

    Helicobacter pylori represents a global health threat with around 50% of the world population infected. Due to the increasing number of antibiotic-resistant strains, new strategies for eradication of H. pylori are needed. In this study, we suggest purine nucleoside phosphorylase (PNP) as a possible new drug target, by characterising its interactions with 2- and/or 6-substituted purines as well as the effect of these compounds on bacterial growth. Inhibition constants are in the micromolar range, the lowest being that of 6-benzylthio-2-chloropurine. This compound also inhibits H. pylori 26695 growth at the lowest concentration. X-ray structures of the complexes of PNP with the investigated compounds allowed the identification of interactions of inhibitors in the enzyme's base-binding site and the suggestion of structures that could bind to the enzyme more tightly. Our findings prove the potential of PNP inhibitors in the design of drugs against H. pylori .


  • Organizational Affiliation

    Division of Biophysics, Institute of Experimental Physics, Faculty of Physics, University of Warsaw, Warsaw, Poland.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Purine nucleoside phosphorylase DeoD-type
A, B
233Helicobacter pylori 26695Mutation(s): 0 
Gene Names: deoDHP_1178
EC: 2.4.2.1
UniProt
Find proteins for P56463 (Helicobacter pylori (strain ATCC 700392 / 26695))
Explore P56463 
Go to UniProtKB:  P56463
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP56463
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 5 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
05Q (Subject of Investigation/LOI)
Query on 05Q

Download Ideal Coordinates CCD File 
M [auth B]6-benzyloxo-2-chloropurine
C12 H9 Cl N4 O
XKVATRYEPITAPH-UHFFFAOYSA-N
TRS
Query on TRS

Download Ideal Coordinates CCD File 
N [auth B]2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
C4 H12 N O3
LENZDBCJOHFCAS-UHFFFAOYSA-O
PO4
Query on PO4

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O [auth B]PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
GOL
Query on GOL

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C [auth A]
D [auth A]
E [auth A]
F [auth A]
G [auth A]
C [auth A],
D [auth A],
E [auth A],
F [auth A],
G [auth A],
H [auth A],
I [auth A],
J [auth A],
L [auth B],
P [auth B],
Q [auth B],
R [auth B],
S [auth B],
T [auth B],
U [auth B],
V [auth B],
W [auth B],
X [auth B]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
MG
Query on MG

Download Ideal Coordinates CCD File 
K [auth A]MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free: 0.188 
  • R-Value Work: 0.161 
  • R-Value Observed: 0.162 
  • Space Group: P 21 3
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 113.736α = 90
b = 113.736β = 90
c = 113.736γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XSCALEdata scaling
PDB_EXTRACTdata extraction
XDSdata reduction
MOLREPphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Polish National Science CentrePoland2015/18/M/NZ1/00776
Croatian Science FoundationCroatiaIP-2013-11-7423, IP-2019-04-6764
Ministry of Science and Higher Education (Poland)PolandBST-173300/BF

Revision History  (Full details and data files)

  • Version 1.0: 2022-05-04
    Type: Initial release
  • Version 1.1: 2024-01-31
    Changes: Data collection, Refinement description