3D1V

Crystal structure of human PNP complexed with 2-mercapto(3H) quinazolinone


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.70 Å
  • R-Value Free: 0.277 
  • R-Value Work: 0.221 
  • R-Value Observed: 0.224 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Structural studies of human purine nucleoside phosphorylase: towards a new specific empirical scoring function

Timmers, L.F.Caceres, R.A.Vivan, A.L.Gava, L.M.Dias, R.Ducati, R.G.Basso, L.A.Santos, D.S.de Azevedo, W.F.

(2008) Arch Biochem Biophys 479: 28-38

  • DOI: 10.1016/j.abb.2008.08.015
  • Primary Citation of Related Structures:  
    3D1V

  • PubMed Abstract: 
  • 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 ...

    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.


    Related Citations: 
    • Crystal Structure of Human Purine Nucleoside Phosphorylase at 2.3A Resolution
      De Azevedo Jr., W.F., Canduri, F., Dos Santos, D.M., Silva, R.G., De Oliveira, J.S., De Carvalho, L.P.S., Basso, L.A., Mendes, M.A., Palma, M.S., Santos, D.S.
      (2003) Biochem Biophys Res Commun 308: 545

    Organizational Affiliation

    Faculdade de Biociências, Laboratório de Bioquímica Estrutural, Pontifícia Universidade Católica do Rio Grande do Sul, Porto Alegre, RS, Brazil.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Purine nucleoside phosphorylaseA289Homo sapiensMutation(s): 0 
Gene Names: NPPNP
EC: 2.4.2.1
Find proteins for P00491 (Homo sapiens)
Explore P00491 
Go to UniProtKB:  P00491
NIH Common Fund Data Resources
PHAROS:  P00491
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
D1V
Query on D1V

Download Ideal Coordinates CCD File 
E [auth A]2-mercapto(3H)quinazolinone
C8 H6 N2 O S
PUPFOFVEHDNUJU-UHFFFAOYSA-N
 Ligand Interaction
SO4
Query on SO4

Download Ideal Coordinates CCD File 
B [auth A], C [auth A], D [auth A]SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
D1VKd :  324000   nM  PDBBind
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.70 Å
  • R-Value Free: 0.277 
  • R-Value Work: 0.221 
  • R-Value Observed: 0.224 
  • Space Group: H 3 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 138.666α = 90
b = 138.666β = 90
c = 159.379γ = 120
Software Package:
Software NamePurpose
AMoREphasing
REFMACrefinement
MOSFLMdata reduction
CCP4data scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2009-07-14
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance