3FKB

Structure of NDPK H122G and tenofovir-diphosphate


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.65 Å
  • R-Value Free: 0.205 
  • R-Value Work: 0.181 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Nucleoside diphosphate kinase and the activation of antiviral phosphonate analogs of nucleotides: binding mode and phosphorylation of tenofovir derivatives

Koch, K.Chen, Y.X.Feng, J.Y.Borroto-Esoda, K.Deville-Bonne, D.Gallois-Montbrun, S.Janin, J.Morera, S.

(2009) Nucleosides Nucleotides Nucleic Acids 28: 776-792

  • DOI: 10.1080/15257770903155899

  • PubMed Abstract: 
  • Tenofovir is an acyclic phosphonate analog of deoxyadenylate used in AIDS and hepatitis B therapy. We find that tenofovir diphosphate, its active form, can be produced by human nucleoside diphosphate kinase (NDPK), but with low efficiency, and that c ...

    Tenofovir is an acyclic phosphonate analog of deoxyadenylate used in AIDS and hepatitis B therapy. We find that tenofovir diphosphate, its active form, can be produced by human nucleoside diphosphate kinase (NDPK), but with low efficiency, and that creatine kinase is significantly more active. The 1.65 A x-ray structure of NDPK in complex with tenofovir mono- and diphosphate shows that the analogs bind at the same site as natural nucleotides, but in a different conformation, and make only a subset of the Van der Waals and polar interactions made by natural substrates, consistent with their comparatively low affinity for the enzyme.


    Organizational Affiliation

    Yeast Structural Genomics, IBBMC UMR 8619 CNRS, Universite Paris-Sud, Orsay, France.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Nucleoside diphosphate kinase, cytosolic
A, B, C, D, E, F
155Dictyostelium discoideumMutation(s): 1 
Gene Names: ndkC-1, ndkC-2 (gip17, ndkB, gip17, ndkB)
EC: 2.7.4.6
Find proteins for P22887 (Dictyostelium discoideum)
Go to UniProtKB:  P22887
Small Molecules
Ligands 5 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
TNV
Query on TNV

Download SDF File 
Download CCD File 
D
[2-(6-AMINO-9H-PURIN-9-YL)-1-METHYLETHOXY]METHYL-TRIPHOSPHATE
TENOFOVIR-DIPHOSPHATE
C9 H16 N5 O10 P3
IACQCQDWSIQSRP-ZCFIWIBFSA-N
 Ligand Interaction
GOL
Query on GOL

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Download CCD File 
C, D
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
EDO
Query on EDO

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Download CCD File 
A, B, D, F
1,2-ETHANEDIOL
ETHYLENE GLYCOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

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Download CCD File 
A, B, C, D, E, F
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
TNM
Query on TNM

Download SDF File 
Download CCD File 
A, B, C, E, F
[(2R)-1-(6-aminopurin-9-yl)propan-2-yl]oxymethyl-phosphonooxy-phosphinic acid
Tenofovir-monophosphate, PMPA-monophosphate
C9 H15 N5 O7 P2
BQDRSOMUPPCKPB-ZCFIWIBFSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.65 Å
  • R-Value Free: 0.205 
  • R-Value Work: 0.181 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 69.420α = 90.00
b = 104.570β = 117.96
c = 69.210γ = 90.00
Software Package:
Software NamePurpose
SCALAdata scaling
ADSCdata collection
CNSrefinement
AMoREphasing
MOSFLMdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2008-12-16 
  • Released Date: 2009-09-29 
  • Deposition Author(s): Morera, S., Chen, Y.X.

Revision History 

  • Version 1.0: 2009-09-29
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Non-polymer description, Version format compliance
  • Version 1.2: 2012-04-18
    Type: Database references