1PWY

CRYSTAL STRUCTURE OF HUMAN PNP COMPLEXED WITH ACYCLOVIR


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.301 
  • R-Value Work: 0.215 
  • R-Value Observed: 0.215 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Crystal structure of human purine nucleoside phosphorylase complexed with acyclovir.

dos Santos, D.M.Canduri, F.Pereira, J.H.Vinicius Bertacine Dias, M.Silva, R.G.Mendes, M.A.Palma, M.S.Basso, L.A.de Azevedo, W.F.Santos, D.S.

(2003) Biochem Biophys Res Commun 308: 553-559

  • DOI: 10.1016/s0006-291x(03)01433-5
  • Primary Citation of Related Structures:  
    1PWY

  • PubMed Abstract: 
  • In human, purine nucleoside phosphorylase (HsPNP) is responsible for degradation of deoxyguanosine and genetic deficiency of this enzyme leads to profound T-cell mediated immunosuppression. PNP is therefore a target for inhibitor development aiming at T-cell immune response modulation and has been submitted to extensive structure-based drug design ...

    In human, purine nucleoside phosphorylase (HsPNP) is responsible for degradation of deoxyguanosine and genetic deficiency of this enzyme leads to profound T-cell mediated immunosuppression. PNP is therefore a target for inhibitor development aiming at T-cell immune response modulation and has been submitted to extensive structure-based drug design. This work reports the first crystallographic study of human PNP complexed with acyclovir (HsPNP:Acy). Acyclovir is a potent clinically useful inhibitor of replicant herpes simplex virus that also inhibits human PNP but with a relatively lower inhibitory activity (K(i)=90 microM). Analysis of the structural differences among the HsPNP:Acy complex, PNP apoenzyme, and HsPNP:Immucillin-H provides explanation for inhibitor binding, refines the purine-binding site, and can be used for future inhibitor design.


    Related Citations: 
    • Application of Crystallographic and Modeling Methods in the Design of Purine Nucleoside Phosphorylase Inhibitors
      Ealick, S.E., Babu, Y.S., Bugg, C.E., Erion, M.D., Guida, W.C., Montgomery, J.A., Secrist III, J.A.
      (1991) Proc Natl Acad Sci U S A 88: 11540

    Organizational Affiliation

    Departamento de Física, UNESP, São José do Rio Preto, SP, Brazil.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Purine nucleoside phosphorylaseA [auth E]288Homo sapiensMutation(s): 0 
Gene Names: PNPNP
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
AC2
Query on AC2

Download Ideal Coordinates CCD File 
E9-HYROXYETHOXYMETHYLGUANINE
C8 H11 N5 O3
MKUXAQIIEYXACX-UHFFFAOYSA-N
 Ligand Interaction
SO4
Query on SO4

Download Ideal Coordinates CCD File 
B [auth E], C [auth E], D [auth E]SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
AC2Ki:  180000   nM  BindingDB
AC2Ki :  90000   nM  PDBBind
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.301 
  • R-Value Work: 0.215 
  • R-Value Observed: 0.215 
  • Space Group: H 3 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 139.06α = 90
b = 139.06β = 90
c = 160.57γ = 120
Software Package:
Software NamePurpose
MOSFLMdata reduction
SCALAdata scaling
AMoREphasing
X-PLORrefinement
CCP4data scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2004-03-23
    Type: Initial release
  • Version 1.1: 2008-04-29
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Derived calculations, Version format compliance
  • Version 1.3: 2018-01-24
    Changes: Database references