Crystal structure, conformation, and absolute configuration of kanamycin A

Yoram A. Puius, Todd H. Stievater, Thamarapu Srikrishnan

Research output: Contribution to journalArticlepeer-review

24 Scopus citations


Kanamycin, an antibiotic complex produced by Streptomyces kanamycetius isolated from Japanese soil, was described by Okami and Umezawa as early as 1957 and consists of three components: Kanamycin A (the major component), B, and C. The disulfate salt of kanamycin A [4-O-(6-amino-6-deoxy-α-d-glucopyranosyl)-6-O-(3-amino-3-deoxy-α-d-glucopyranosyl)-2-deoxystreptamine] is a broad-spectrum antibiotic that is used to treat gonorrhea, salmonella, tuberculosis, and many other diseases. Crystals of kanamycin A monosulfate monohydrate obtained from water are triclinic, space group P1, with a = 7.2294(14), b = 12.4922(15), c = 7.1168(9), α = 94.74(1), β = 89.16(1), γ = 91.59(1), V = 640.2(2) Å3, μ(Cu Kα) = 18.4 cm-1, FW 600.6, Dcalc = 1.558 g/cm3, CAD-4 diffractometric data (2693 reflections, 2554 ≥ 3σ(I)), structure by shelx-86 and refined by full-matrix least squares to a final R value of 0.038. The wrong conformer had an R value of 0.043. Both of the d-glucose moieties are attached to the deoxystreptamine by α linkages. This absolute configuration agrees with the earlier determination by both chemical and X-ray methods with photographic data. The (φ{symbol}, ψ) values for the glycosidic linkages are 101.6°, -121.1°, 106.3°, and -140.4°, respectively. Kanamycin interacts with the ribosomal S12 protein to stabilize the codon-anticodon binding between mRNA and the aminoacyl tRNA and inhibits the elongation of peptide chains through a series of reactions resulting in the prevention of ribosomes from moving along mRNA.{A figure is presented}.

Original languageEnglish (US)
Pages (from-to)2871-2875
Number of pages5
JournalCarbohydrate Research
Issue number17
StatePublished - Dec 11 2006
Externally publishedYes


  • Absolute configuration
  • Crystal structure
  • Kanamycin A
  • Stereochemistry

ASJC Scopus subject areas

  • Analytical Chemistry
  • Biochemistry
  • Organic Chemistry


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