1P62

Structure of human dCK complexed with gemcitabine and ADP-MG


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.207 
  • R-Value Work: 0.179 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Structure of human dCK suggests strategies to improve anticancer and antiviral therapy

Sabini, E.Ort, S.Monnerjahn, C.Konrad, M.Lavie, A.

(2003) Nat.Struct.Mol.Biol. 10: 513-519

  • DOI: 10.1038/nsb942
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Human deoxycytidine kinase (dCK) phosphorylates the natural deoxyribonucleosides deoxycytidine (dC), deoxyguanosine (dG) and deoxyadenosine (dA) and is an essential enzyme for the phosphorylation of numerous nucleoside analog prodrugs routinely used ...

    Human deoxycytidine kinase (dCK) phosphorylates the natural deoxyribonucleosides deoxycytidine (dC), deoxyguanosine (dG) and deoxyadenosine (dA) and is an essential enzyme for the phosphorylation of numerous nucleoside analog prodrugs routinely used in cancer and antiviral chemotherapy. For many of these compounds, the phosphorylation step catalyzed by dCK is the rate-limiting step in their overall activation pathway. To determine the factors that limit the phosphorylation efficiency of the prodrug, we solved the crystal structure of dCK to a resolution of 1.6 A in complex with its physiological substrate deoxycytidine and with the prodrugs AraC and gemcitabine. The structures reveal the determinants of dCK substrate specificity. Especially relevant to new prodrug development is the interaction between Arg128 and the hydrogen-bond acceptor at the sugar 2'-arabinosyl position of AraC and gemcitabine. On the basis of the structures, we designed a catalytically superior dCK variant that could be used in suicide gene-therapy applications.


    Organizational Affiliation

    University of Illinois at Chicago, Department of Biochemistry and Molecular Biology, 1819 West Polk Street, Chicago, Illinois 60612, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Deoxycytidine kinase
B
263Homo sapiensGene Names: DCK
EC: 2.7.1.74
Find proteins for P27707 (Homo sapiens)
Go to Gene View: DCK
Go to UniProtKB:  P27707
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ADP
Query on ADP

Download SDF File 
Download CCD File 
B
ADENOSINE-5'-DIPHOSPHATE
C10 H15 N5 O10 P2
XTWYTFMLZFPYCI-KQYNXXCUSA-N
 Ligand Interaction
MG
Query on MG

Download SDF File 
Download CCD File 
B
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
GEO
Query on GEO

Download SDF File 
Download CCD File 
B
GEMCITABINE
2',2'-DIFLUORODEOXYCYTIDINE
C9 H11 F2 N3 O4
SDUQYLNIPVEERB-QPPQHZFASA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.207 
  • R-Value Work: 0.179 
  • Space Group: P 43 21 2
Unit Cell:
Length (Å)Angle (°)
a = 81.200α = 90.00
b = 81.200β = 90.00
c = 94.600γ = 90.00
Software Package:
Software NamePurpose
SOLVEphasing
XDSdata scaling
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2003-07-01
    Type: Initial release
  • Version 1.1: 2008-04-29
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Derived calculations, Version format compliance