3DJF

Crystal Structure of Schistosoma mansoni Purine Nucleoside Phosphorylase in a complex with BCX-34


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.302 Å
  • R-Value Free: 0.259 
  • R-Value Work: 0.201 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Structural basis for selective inhibition of purine nucleoside phosphorylase from Schistosoma mansoni: kinetic and structural studies.

Castilho, M.S.Postigo, M.P.Pereira, H.M.Oliva, G.Andricopulo, A.D.

(2010) Bioorg.Med.Chem. 18: 1421-1427

  • DOI: 10.1016/j.bmc.2010.01.022
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Selectivity plays a crucial role in the design of enzyme inhibitors as novel antiparasitic agents, particularly in cases where the target enzyme is also present in the human host. Purine nucleoside phosphorylase from Schistosoma mansoni (SmPNP) is an ...

    Selectivity plays a crucial role in the design of enzyme inhibitors as novel antiparasitic agents, particularly in cases where the target enzyme is also present in the human host. Purine nucleoside phosphorylase from Schistosoma mansoni (SmPNP) is an attractive target for the discovery of potential antischistosomal agents. In the present work, kinetic studies were carried out in order to determine the inhibitory potency, mode of action and enzyme selectivity of a series of inhibitors of SmPNP. In addition, crystallographic studies provided important structural insights for rational inhibitor design, revealing consistent structural differences in the binding mode of the inhibitors in the active sites of the SmPNP and human PNP (HsPNP) structures. The molecular information gathered in this work should be useful for future medicinal chemistry efforts in the design of new inhibitors of SmPNP having increased affinity and selectivity.


    Organizational Affiliation

    Universidade Federal da Bahia, Faculdade de Farmácia, R. Barão de Jeremoabo, Salvador-BA, Brazil. castilho@ufba.br




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Purine-nucleoside phosphorylase
A, B, C
287Schistosoma mansoniMutation(s): 0 
EC: 2.4.2.1
Find proteins for Q9BMI9 (Schistosoma mansoni)
Go to UniProtKB:  Q9BMI9
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
BC3
Query on BC3

Download SDF File 
Download CCD File 
A, B, C
2-amino-7-(pyridin-3-ylmethyl)-3,5-dihydro-4H-pyrrolo[3,2-d]pyrimidin-4-one
peldesine,BCX-34
C12 H11 N5 O
DOHVAKFYAHLCJP-UHFFFAOYSA-N
 Ligand Interaction
SO4
Query on SO4

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Download CCD File 
A, C
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
DMS
Query on DMS

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Download CCD File 
A, B, C
DIMETHYL SULFOXIDE
C2 H6 O S
IAZDPXIOMUYVGZ-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
BC3IC50: 800 nM BINDINGMOAD
BC3IC50: 800 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.302 Å
  • R-Value Free: 0.259 
  • R-Value Work: 0.201 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 49.577α = 90.00
b = 132.953β = 90.00
c = 121.154γ = 90.00
Software Package:
Software NamePurpose
PHASERphasing
MOSFLMdata reduction
PDB_EXTRACTdata extraction
SCALAdata scaling
MAR345dtbdata collection
PHENIXrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2009-06-30
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance