Structure of human dCK complexed with 2'-Deoxycytidine and ADP, Space group C 2 2 21

Experimental Data Snapshot

  • Resolution: 1.96 Å
  • R-Value Free: 0.203 
  • R-Value Work: 0.161 
  • R-Value Observed: 0.165 

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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 Biol 10: 513-519

  • DOI: https://doi.org/10.1038/nsb942
  • Primary Citation of Related Structures:  
    1P5Z, 1P60, 1P61, 1P62

  • 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 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.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Deoxycytidine kinase
A, B
263Homo sapiensMutation(s): 0 
Gene Names: DCK
UniProt & NIH Common Fund Data Resources
Find proteins for P27707 (Homo sapiens)
Explore P27707 
Go to UniProtKB:  P27707
PHAROS:  P27707
GTEx:  ENSG00000156136 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP27707
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 1.96 Å
  • R-Value Free: 0.203 
  • R-Value Work: 0.161 
  • R-Value Observed: 0.165 
  • Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 52.714α = 90
b = 132.808β = 90
c = 157.565γ = 90
Software Package:
Software NamePurpose
XDSdata 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: 2003-07-01
    Type: Initial release
  • Version 1.1: 2008-04-29
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2024-02-14
    Changes: Data collection, Database references, Derived calculations