1MN9

NDP kinase mutant (H122G) complex with RTP


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.90 Å
  • R-Value Free: 0.249 
  • R-Value Work: 0.207 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Structural Analysis of the Activation of Ribavirin Analogs by NDP Kinase: Comparison with Other Ribavirin Targets

Gallois-montbrun, S.Chen, Y.Dutartre, H.Sophys, M.Morera, S.Guerreiro, C.Schneider, B.Mulard, L.Janin, J.Veron, M.Deville-bonne, D.Canard, B.

(2003) Mol Pharmacol 63: 538-546

  • DOI: 10.1124/mol.63.3.538
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • Ribavirin used in therapies against hepatitis C virus (HCV) is potentially efficient against other viruses but presents a high cytotoxicity. Several ribavirin triphosphate analogs modified on the ribose moiety were synthesized and tested in vitro on ...

    Ribavirin used in therapies against hepatitis C virus (HCV) is potentially efficient against other viruses but presents a high cytotoxicity. Several ribavirin triphosphate analogs modified on the ribose moiety were synthesized and tested in vitro on the RNA polymerases of HCV, phage T7, and HIV-1 reverse transcriptase. Modified nucleotides with 2'-deoxy, 3'-deoxy, 2',3'-dideoxy, 2',3'-dideoxy-2',3'-dehydro, and 2',3'-epoxy-ribose inhibited the HCV enzyme but not the other two polymerases. They were also analyzed as substrates for nucleoside diphosphate (NDP) kinase, the enzyme responsible for the last step of the cellular activation of antiviral nucleoside analogs. An X-ray structure of NDP kinase complexed with ribavirin triphosphate was determined. It demonstrates that the analog binds as a normal substrate despite the modified base and confirms the crucial role of the 3'-hydroxyl group in the phosphorylation reaction. The 3'-hydroxyl is required for inhibition of the initiation step of RNA synthesis by HCV polymerase, and both sugar hydroxyls must be present to inhibit elongation. The 2'deoxyribavirin is the only derivative efficient in vitro against HCV polymerase and properly activated by NDP kinase.


    Organizational Affiliation

    Unité de Régulation Enzymatique des Activités Cellulaires, Centre National de la Recherche Scientifique Formation de Recherche en Evolution 2364, Institut Pasteur, Paris, France.



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
NDP kinase
A, B, C
155Dictyostelium discoideumMutation(s): 1 
Gene Names: ndkC-1gip17ndkBDDB_G0273069ndkC-2DDB_G0273805
EC: 2.7.4.6
Find proteins for P22887 (Dictyostelium discoideum)
Go to UniProtKB:  P22887
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
RTP
Query on RTP

Download CCD File 
A
RIBAVIRIN TRIPHOSPHATE
C8 H15 N4 O14 P3
MMJOCKKLRMRSEQ-AFCXAGJDSA-N
 Ligand Interaction
MG
Query on MG

Download CCD File 
A, B, C
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
RTPKd :  24000   nM  PDBBind
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.90 Å
  • R-Value Free: 0.249 
  • R-Value Work: 0.207 
  • Space Group: P 31 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 71.731α = 90
b = 71.731β = 90
c = 153.818γ = 120
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
CNSrefinement

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2003-03-18
    Type: Initial release
  • Version 1.1: 2008-04-28
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Derived calculations, Version format compliance