PDBsum entry 3d1v

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protein ligands links
Transferase PDB id
Protein chain
288 a.a. *
SO4 ×3
Waters ×69
* Residue conservation analysis
PDB id:
Name: Transferase
Title: Crystal structure of human pnp complexed with 2-mercapto(3h) quinazolinone
Structure: Purine nucleoside phosphorylase. Chain: a. Synonym: inosine phosphorylase, pnp. Engineered: yes
Source: Homo sapiens. Human. Organism_taxid: 9606. Gene: np, pnp. Expressed in: escherichia coli. Expression_system_taxid: 562.
2.70Å     R-factor:   0.224     R-free:   0.277
Authors: W.F.De Azevedo Jr.,L.A.Basso,D.S.Santos
Key ref: L.F.Timmers et al. (2008). Structural studies of human purine nucleoside phosphorylase: towards a new specific empirical scoring function. Arch Biochem Biophys, 479, 28-38. PubMed id: 18790691 DOI: 10.1016/
06-May-08     Release date:   14-Jul-09    
Go to PROCHECK summary

Protein chain
Pfam   ArchSchema ?
P00491  (PNPH_HUMAN) -  Purine nucleoside phosphorylase
289 a.a.
288 a.a.*
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 1 residue position (black cross)

 Enzyme reactions 
   Enzyme class: E.C.  - Purine-nucleoside phosphorylase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
1. Purine nucleoside + phosphate = purine + alpha-D-ribose 1-phosphate
2. Purine deoxynucleoside + phosphate = purine + 2'-deoxy-alpha-D-ribose 1-phosphate
Purine nucleoside
Bound ligand (Het Group name = D1V)
matches with 50.00% similarity
+ phosphate
= purine
+ alpha-D-ribose 1-phosphate
Purine deoxynucleoside
+ phosphate
= purine
+ 2'-deoxy-alpha-D-ribose 1-phosphate
Molecule diagrams generated from .mol files obtained from the KEGG ftp site
 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     intracellular   5 terms 
  Biological process     small molecule metabolic process   16 terms 
  Biochemical function     catalytic activity     9 terms  


DOI no: 10.1016/ Arch Biochem Biophys 479:28-38 (2008)
PubMed id: 18790691  
Structural studies of human purine nucleoside phosphorylase: towards a new specific empirical scoring function.
L.F.Timmers, R.A.Caceres, A.L.Vivan, L.M.Gava, R.Dias, R.G.Ducati, L.A.Basso, D.S.Santos, Azevedo.
Human purine nucleoside phosphorylase (HsPNP) is a target for inhibitor development aiming at T-cell immune response modulation. In this work, we report the development of a new set of empirical scoring functions and its application to evaluate binding affinities and docking results. To test these new functions, we solved the structure of HsPNP and 2-mercapto-4(3H)-quinazolinone (HsPNP:MQU) binary complex at 2.7A resolution using synchrotron radiation, and used these functions to predict ligand position obtained in docking simulations. We also employed molecular dynamics simulations to analyze HsPNP in two conditions, as apoenzyme and in the binary complex form, in order to assess the structural features responsible for stability. Analysis of the structural differences between systems provides explanation for inhibitor binding. The use of these scoring functions to evaluate binding affinities and molecular docking results may be used to guide future efforts on virtual screening focused on HsPNP.

Literature references that cite this PDB file's key reference

  PubMed id Reference
19669809 F.B.Zanchi, R.A.Caceres, R.G.Stabeli, and Azevedo (2010).
Molecular dynamics studies of a hexameric purine nucleoside phosphorylase.
  J Mol Model, 16, 543-550.  
20210752 M.L.Bellows, and C.A.Floudas (2010).
Computational methods for de novo protein design and its applications to the human immunodeficiency virus 1, purine nucleoside phosphorylase, ubiquitin specific protease 7, and histone demethylases.
  Curr Drug Targets, 11, 264-278.  
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