2VPP

Drosophila melanogaster deoxyribonucleoside kinase successfully activates gemcitabine in transduced cancer cell lines


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.2 Å
  • R-Value Free: 0.253 
  • R-Value Work: 0.207 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Drosophila Melanogaster Deoxyribonucleoside Kinase Activates Gemcitabine.

Knecht, W.Mikkelsen, N.E.Clausen, A.Willer, M.Eklund, H.Gojkovic, Z.Piskur, J.

(2009) Biochem.Biophys.Res.Commun. 382: 430

  • DOI: 10.1016/j.bbrc.2009.03.041

  • PubMed Abstract: 
  • Drosophila melanogaster multisubstrate deoxyribonucleoside kinase (Dm-dNK) can additionally sensitize human cancer cell lines towards the anti-cancer drug gemcitabine. We show that this property is based on the Dm-dNK ability to efficiently phosphory ...

    Drosophila melanogaster multisubstrate deoxyribonucleoside kinase (Dm-dNK) can additionally sensitize human cancer cell lines towards the anti-cancer drug gemcitabine. We show that this property is based on the Dm-dNK ability to efficiently phosphorylate gemcitabine. The 2.2A resolution structure of Dm-dNK in complex with gemcitabine shows that the residues Tyr70 and Arg105 play a crucial role in the firm positioning of gemcitabine by extra interactions made by the fluoride atoms. This explains why gemcitabine is a good substrate for Dm-dNK.


    Organizational Affiliation

    BioCentrum-DTU, Technical University of Denmark, Lyngby, Denmark.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
DEOXYNUCLEOSIDE KINASE
A, B
230Drosophila melanogasterMutation(s): 0 
Gene Names: dnk
EC: 2.7.1.145
Find proteins for Q9XZT6 (Drosophila melanogaster)
Go to UniProtKB:  Q9XZT6
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download SDF File 
Download CCD File 
A, B
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
GEO
Query on GEO

Download SDF File 
Download CCD File 
A, B
GEMCITABINE
2',2'-DIFLUORODEOXYCYTIDINE
C9 H11 F2 N3 O4
SDUQYLNIPVEERB-QPPQHZFASA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
GEOIC50: 760 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.2 Å
  • R-Value Free: 0.253 
  • R-Value Work: 0.207 
  • Space Group: P 21 21 2
Unit Cell:
Length (Å)Angle (°)
a = 120.106α = 90.00
b = 62.298β = 90.00
c = 68.078γ = 90.00
Software Package:
Software NamePurpose
PHASERphasing
MOSFLMdata reduction
REFMACrefinement
SCALAdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2009-03-24
    Type: Initial release
  • Version 1.1: 2011-05-08
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance