2A7Q

Crystal structure of human dCK complexed with clofarabine and ADP

Summary for 2A7Q

• Entry DOI: 10.2210/pdb2a7q/pdb
• Related: 1P5Z 1p60 1p61 1p62
• Descriptor: Deoxycytidine kinase, MAGNESIUM ION, ADENOSINE-5'-DIPHOSPHATE, ... (5 entities in total)
• Functional Keywords: alpha/beta parallel beta-sheet of 5 strands, transferase
• Biological source: Homo sapiens (human)
• Cellular location: Nucleus: P27707
• Total number of polymer chains: 1
• Total formula weight: 31589.96

Authors

Zhang, Y.,Secrist III, J.A.,Ealick, S.E. (deposition date: 2005-07-05, release date: 2006-01-24, Last modification date: 2023-08-23)

Primary citation

Zhang, Y.,Secrist, J.A.,Ealick, S.E.
The structure of human deoxycytidine kinase in complex with clofarabine reveals key interactions for prodrug activation.
Acta Crystallogr.,Sect.D, 62:133-139, 2006

PubMed Abstract: Clofarabine [2-chloro-9-(2-deoxy-2-fluoro-beta-D-arabinofuranosyl)-9H-purin-6-amine] is a hybrid of the widely used anticancer drugs cladribine and fludarabine. It is the precursor of an effective chemotherapeutic agent for leukemias and other hematological malignancies and received accelerated approval by the FDA for the treatment of pediatric patients with relapsed or refractory acute lymphoblastic leukemia. Clofarabine is phosphorylated intracellularly by human deoxycytidine kinase (dCK) to the 5'-monophosphate, which is the rate-limiting step in activation of the prodrug. dCK has a broad substrate specificity, with a much higher activity to deoxycytidine than to deoxyadenosine and deoxyguanosine. As a purine-nucleoside analog, clofarabine is a better substrate of dCK than deoxycytidine. The crystal structure of dCK has been solved previously in complex with pyrimidine nucleosides and ADP [Sabini et al. (2003), Nature Struct. Biol. 10, 513-519]. In the current study, the crystal structure of clofarabine- and ADP-bound dCK was solved to 2.55 angstroms by molecular replacement. It appears that the enzyme takes the same conformation as in the structures of the pyrimidine nucleoside-bound complexes. The interactions between 2-Cl and its surrounding hydrophobic residues contribute to the high catalytic efficiency of dCK for clofarabine.

PubMed: 16421443
DOI: 10.1107/S0907444905034293

Experimental method

X-RAY DIFFRACTION (2.55 Å)