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 

Starting Model: experimental
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This is version 1.4 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: https://doi.org/10.1080/15257770903155899
  • Primary Citation of Related Structures:  
    3FKB

  • 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 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:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Nucleoside diphosphate kinase, cytosolic
A, B, C, D, E
A, B, C, D, E, F
155Dictyostelium discoideumMutation(s): 1 
EC: 2.7.4.6
UniProt
Find proteins for P22887 (Dictyostelium discoideum)
Explore P22887 
Go to UniProtKB:  P22887
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP22887
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 5 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
TNV
Query on TNV

Download Ideal Coordinates CCD File 
P [auth D][2-(6-AMINO-9H-PURIN-9-YL)-1-METHYLETHOXY]METHYL-TRIPHOSPHATE
C9 H16 N5 O10 P3
IACQCQDWSIQSRP-ZCFIWIBFSA-N
TNM
Query on TNM

Download Ideal Coordinates CCD File 
G [auth A],
J [auth B],
M [auth C],
T [auth E],
V [auth F]
[(2R)-1-(6-aminopurin-9-yl)propan-2-yl]oxymethyl-phosphonooxy-phosphinic acid
C9 H15 N5 O7 P2
BQDRSOMUPPCKPB-ZCFIWIBFSA-N
GOL
Query on GOL

Download Ideal Coordinates CCD File 
O [auth C],
R [auth D]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
EDO
Query on EDO

Download Ideal Coordinates CCD File 
I [auth A],
L [auth B],
S [auth D],
X [auth F],
Y [auth F]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
MG
Query on MG

Download Ideal Coordinates CCD File 
H [auth A]
K [auth B]
N [auth C]
Q [auth D]
U [auth E]
H [auth A],
K [auth B],
N [auth C],
Q [auth D],
U [auth E],
W [auth F]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
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 = 69.42α = 90
b = 104.57β = 117.96
c = 69.21γ = 90
Software Package:
Software NamePurpose
ADSCdata collection
AMoREphasing
CNSrefinement
MOSFLMdata reduction
SCALAdata scaling

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2009-09-29
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Non-polymer description, Version format compliance
  • Version 1.2: 2012-04-18
    Changes: Database references
  • Version 1.3: 2021-11-10
    Changes: Database references, Derived calculations, Structure summary
  • Version 1.4: 2023-11-01
    Changes: Data collection, Refinement description