2QPL

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

• PDB DOI: https://doi.org/10.2210/pdb2QPL/pdb

• Classification: TRANSFERASE
• Organism(s): Bos taurus
• Mutation(s): No 


• Deposited: 2007-07-24 Released: 2007-12-18 
• Deposition Author(s): Pereira, H.M., Berdini, V., Cleasby, A., Garratt, R.C.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 0.218 
• R-Value Work: 0.168 
• R-Value Observed: 0.170 

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

• PubMed: 17927987 
• DOI: https://doi.org/10.1016/j.febslet.2007.09.051
• Primary Citation of Related Structures:  
  2QPL


• 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 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.

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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. [e-mail]

Biological Assembly 1  

Global Symmetry: Cyclic - C3  (Explore in 3D)
Global Stoichiometry: Homo 3-mer - A3 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 31.71 kDa 
• Atom Count: 2,259 
• Modelled Residue Count: 266 
• Deposited Residue Count: 282 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Purine nucleoside phosphorylase	A	282	Bos taurus	Mutation(s): 0  EC: 2.4.2.1
UniProt
Find proteins for P55859 (Bos taurus) Explore P55859  Go to UniProtKB:  P55859

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
BTY	D [auth A]	4-amino-7-methylpyrazolo[1,5-a][1,3,5]triazin-2(1H)-one C6 H7 N5 O AIOHMASJJVGZOY-UHFFFAOYSA-N
SO4	B [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
MG	C [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
BTY	Binding MOAD:  2QPL	IC50: 1.89e+4 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 0.218 
• R-Value Work: 0.168 
• R-Value Observed: 0.170 
• Space Group: P 2₁ 3

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 93.442	α = 90
b = 93.442	β = 90
c = 93.442	γ = 90

Software Package:

Software Name	Purpose
MOSFLM	data reduction
SCALA	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
ADSC	data collection
MOLREP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2007-12-18 
Deposition Author(s): Pereira, H.M., Berdini, V., Cleasby, A., Garratt, R.C.

Revision History  

• Version 1.0: 2007-12-18
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2023-08-30
  Changes: Data collection, Database references, Derived calculations, Refinement description
• Version 1.3: 2023-11-29
  Changes: Database references