Crystal structure and conformational analysis of doxorubicin nitrate

Logesh Mathivathanan; Guang Yang; Fenfei Leng; Raphael G Raptis

doi:10.1107/S2056989018002955

Crystal structure and conformational analysis of doxorubicin nitrate

Acta Crystallogr E Crystallogr Commun. 2018 Feb 28;74(Pt 3):400-405. doi: 10.1107/S2056989018002955. eCollection 2018 Mar 1.

Authors

Logesh Mathivathanan¹, Guang Yang^{1

2}, Fenfei Leng¹, Raphael G Raptis¹

Affiliations

¹ Department of Chemistry and Biochemistry and Biomolecular Sciences Institute, Florida International University, 11200 SW 8th St, Miami, FL 33199, USA.
² College of Chemistry and Molecular Engineering, Zhengzhou University, Zhengzhou, Henan, 450001, People's Republic of China.

Abstract

Crystal structure determination of doxorubicin nitrate, (DoxH)NO₃, systematic name (7S,9S)-7-{[(2R,4S,5S,6S)-4-azaniumyl-5-hy-droxy-6-methyl-oxan-2-yl]-oxy}-6,9,11-trihy-droxy-9-(2-hy-droxy-acet-yl)-4-meth-oxy-8,10-di-hydro-7H-tetra-cen-5,12-dione nitrate, shows two formula units present in the asymmetric unit. In the crystal lattice, hydrogen-bonded pairs of (DoxH⁺) cations and segregation of the aglycone and sugar moieties are observed. Inspection of mol-ecular overlays reveals that the conformation of (DoxH)NO₃ resembles that of DNA-inter-calated, but not of protein-docked (DoxH)⁺. The structure was refined as a two-component twin.

Keywords: anthracycline; conformation; crystal structure; doxorubicin; intercalation.

Grants and funding

This work was funded by China Scholarship Council grant 201707045007 to G. Yang.