3DJF | pdb_00003djf

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 
    0.259 (Depositor), 0.249 (DCC) 
  • R-Value Work: 
    0.201 (Depositor), 0.194 (DCC) 
  • R-Value Observed: 
    0.204 (Depositor) 

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Ligand Structure Quality Assessment 


This is version 1.2 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: https://doi.org/10.1016/j.bmc.2010.01.022
  • Primary Citation Related Structures: 
    3DJF, 3IEX

  • 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 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

Macromolecule Content 

  • Total Structure Weight: 94.74 kDa 
  • Atom Count: 6,754 
  • Modeled Residue Count: 832 
  • Deposited Residue Count: 861 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Purine-nucleoside phosphorylase
A, B, C
287Schistosoma mansoniMutation(s): 0 
EC: 2.4.2.1
UniProt
Find proteins for Q9BMI9 (Schistosoma mansoni)
Explore Q9BMI9 
Go to UniProtKB:  Q9BMI9
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9BMI9
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
BC3

Query on BC3



Download:Ideal Coordinates CCD File
F [auth A],
H [auth B],
K [auth C]
2-amino-7-(pyridin-3-ylmethyl)-3,5-dihydro-4H-pyrrolo[3,2-d]pyrimidin-4-one
C12 H11 N5 O
DOHVAKFYAHLCJP-UHFFFAOYSA-N
SO4

Query on SO4



Download:Ideal Coordinates CCD File
D [auth A],
I [auth C]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
DMS

Query on DMS



Download:Ideal Coordinates CCD File
E [auth A],
G [auth B],
J [auth C]
DIMETHYL SULFOXIDE
C2 H6 O S
IAZDPXIOMUYVGZ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free:  0.259 (Depositor), 0.249 (DCC) 
  • R-Value Work:  0.201 (Depositor), 0.194 (DCC) 
  • R-Value Observed: 0.204 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 49.577α = 90
b = 132.953β = 90
c = 121.154γ = 90
Software Package:
Software NamePurpose
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
PHENIXrefinement
PDB_EXTRACTdata extraction
MAR345dtbdata collection

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2009-06-30
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2024-02-21
    Changes: Data collection, Database references, Derived calculations