2QPL

Crystal structure of calf spleen purine nucleoside phosphorylase complexed to a novel purine analogue


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.1 Å
  • R-Value Free: 0.218 
  • R-Value Work: 0.168 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Crystal structure of calf spleen purine nucleoside phosphorylase complexed to a novel purine analogue.

Pereira, H.M.Berdini, V.Cleasby, A.Garratt, R.C.

(2007) Febs Lett. 581: 5082-5086

  • DOI: 10.1016/j.febslet.2007.09.051

  • PubMed Abstract: 
  • The combined use of a rapid virtual screen of a small fragment library together with a single point enzyme assay has been used for the discovery of novel PNP inhibitors. The availability of readily soakable crystals of bovine PNP has allowed the appr ...

    The combined use of a rapid virtual screen of a small fragment library together with a single point enzyme assay has been used for the discovery of novel PNP inhibitors. The availability of readily soakable crystals of bovine PNP has allowed the approach to be experimentally validated by determining the crystal structure of one of the inhibitor-PNP complexes. Comparison of the experimentally determined binding mode with that predicted by the virtual screening shows them to be similar. This represents a starting point for the growth of the ligand into a higher affinity inhibitor.


    Organizational Affiliation

    Instituto de Física de São Carlos, Universidade de São Paulo, Physics and Informatics, Av. Trabalhador Saocarlense 400, Centro CP 369, 13560-970 Sao Carlos, São Paulo, Brazil. hmuniz.pereira@gmail.com




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Purine nucleoside phosphorylase
A
282Bos taurusMutation(s): 0 
Gene Names: PNP (NP)
EC: 2.4.2.1
Find proteins for P55859 (Bos taurus)
Go to Gene View: PNP
Go to UniProtKB:  P55859
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download SDF File 
Download CCD File 
A
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
BTY
Query on BTY

Download SDF File 
Download CCD File 
A
4-amino-7-methylpyrazolo[1,5-a][1,3,5]triazin-2(1H)-one
C6 H7 N5 O
AIOHMASJJVGZOY-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

Download SDF File 
Download CCD File 
A
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
BTYIC50: 18900 nM BINDINGMOAD
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.1 Å
  • R-Value Free: 0.218 
  • R-Value Work: 0.168 
  • Space Group: P 21 3
Unit Cell:
Length (Å)Angle (°)
a = 93.442α = 90.00
b = 93.442β = 90.00
c = 93.442γ = 90.00
Software Package:
Software NamePurpose
ADSCdata collection
PDB_EXTRACTdata extraction
MOSFLMdata reduction
SCALAdata scaling
REFMACrefinement
MOLREPphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2007-12-18
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance