Lividomycin aptamer

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Description

In 1996, Lato, S. M., & Ellington, A. D.isolated RNA molecules capable of binding to rifamycin led to the discovery of the SLB10-1 aptamer in vitro. a lividomycin aptamer was iteratively isolated from a random sequence pool. The consensus sequence of this and other anti-aminoglycoside aptamers was used as the basis for a comprehensive search of natural sequence databases. A high degree of similarity was found between aptamers and genomic sequences from a variety of organisms[1].



SELEX

Lato, S. M., & Ellington, A. D. used in vitro screening from a pool of RNAs that would contain 30 random sequence positions, after which 10 aptamers were cloned, 13 clones were sequenced, and 12 proved to be identical aptamers, one being an unrelated species. After ten rounds of selection and amplification, a predominant aptamer species, SLB10-1, was identified[1].

Detailed information are accessible on SELEX page.



Structure

The sequence and secondary prediction structure of the aptamer will be shown here, here we used ribodraw to complete the figure. The 2D structure of the figure is based on the article by ribodraw tool to draw. SLB10-1 aptamer was named by Lato, S. M., & Ellington, A. D[1].

5'-GGGAAUGGAUCCACAUCUACGAAUUCAACGAGUGCAGUGGGAAACAGGUCUUUGGCUUCACUGCAGACUUGACGAAGCUU-3'

drawing


Ligand information

SELEX ligand

This compound belongs to the class of organic compounds known as 4,5-disubstituted 2-deoxystreptamines. These are 2-deoxystreptamine aminoglycosides that a glycosidically linked to a pyranose of furanose unit at the C4- and C5-positions.-----From Drugbank

PubChem CID: a unique identifier for substances in the PubChem database.

CAS number: a global registry number for chemical substances.

Drugbank: a comprehensive database with detailed information on drugs and drug targets.

Name Molecular Formula Molecular Weight CAS Solubility PubChem Drugbank ID
Lividomycin C29H55N5O18 761.8 g/mol 36441-41-5 Difficult to dissolve in water 72394 DB04728
drawing

Similar compound

We screened the compounds with great similarity to by using the ZINC database and showed some of the compounds' structure diagrams. For some CAS numbers not available, we will supplement them with Pubchem CID. For another compound, we used a similar compound query method from the PubChem database.

ZINC ID: a compound identifier used by the ZINC database, one of the largest repositories for virtual screening of drug-like molecules.

PubChem CID: a unique identifier for substances in the PubChem database.

CAS number: a global registry number for chemical substances.

ZINC ID Name CAS Pubchem CID Structure
ZINC253673980 lividomycin A 36441-41-5 72394 drawing
ZINC255211892 (2R,3S,4R,5S,6R)-2-[(2R,3S,4R,5S,6R)-5-amino-2-(aminomethyl)-6-[(2S,3R,4S,5S)-5-[(1R,2S,3R,5S,6S)-3,5-diamino-2-[(2R,3S,4R,5S,6S)-3-amino-4,5-dihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy-6-hydroxycyclohexyl]oxy-4-hydroxy-2-(hydroxymethyl)oxolan-3-yl]oxy-4-hydroxyoxan-3-yl]oxy-6-(hydroxymethyl)oxane-3,4,5-triol NA 162929092 drawing
ZINC257402766 (2R,3S,4R,5R,6S)-2-[(2S,3R,4S,5R,6R)-5-amino-2-(aminomethyl)-6-[(2S,3S,4R,5R)-5-[(1R,2S,3S,5R,6R)-3,5-diamino-2-[(2R,3S,5R,6R)-3-amino-5-hydroxy-6-(hydroxymethyl)oxan-2-yl]oxy-6-hydroxycyclohexyl]oxy-4-hydroxy-2-(hydroxymethyl)oxolan-3-yl]oxy-4-hydroxyoxan-3-yl]oxy-6-(hydroxymethyl)oxane-3,4,5-triol NA 125038099 drawing
ZINC257402767 (2R,3S,4R,5R,6S)-2-[(2S,3R,4S,5R,6R)-5-amino-2-(aminomethyl)-6-[(2S,3S,4R,5R)-5-[(1R,2S,3S,5R,6R)-3,5-diamino-2-[(2R,3S,5S,6R)-3-amino-5-hydroxy-6-(hydroxymethyl)oxan-2-yl]oxy-6-hydroxycyclohexyl]oxy-4-hydroxy-2-(hydroxymethyl)oxolan-3-yl]oxy-4-hydroxyoxan-3-yl]oxy-6-(hydroxymethyl)oxane-3,4,5-triol NA 125038100 drawing
ZINC257402768 (2R,3S,4R,5R,6S)-2-[(2S,3R,4S,5R,6R)-5-amino-2-(aminomethyl)-6-[(2S,3S,4R,5R)-5-[(1R,2S,3S,5R,6R)-3,5-diamino-2-[(2R,3S,5S,6S)-3-amino-5-hydroxy-6-(hydroxymethyl)oxan-2-yl]oxy-6-hydroxycyclohexyl]oxy-4-hydroxy-2-(hydroxymethyl)oxolan-3-yl]oxy-4-hydroxyoxan-3-yl]oxy-6-(hydroxymethyl)oxane-3,4,5-triol NA 125038101 drawing
ZINC257402769 (2R,3S,4R,5R,6S)-2-[(2S,3R,4S,5R,6R)-5-amino-2-(aminomethyl)-6-[(2S,3S,4R,5R)-5-[(1R,2S,3S,5R,6R)-3,5-diamino-2-[(2R,3S,5R,6S)-3-amino-5-hydroxy-6-(hydroxymethyl)oxan-2-yl]oxy-6-hydroxycyclohexyl]oxy-4-hydroxy-2-(hydroxymethyl)oxolan-3-yl]oxy-4-hydroxyoxan-3-yl]oxy-6-(hydroxymethyl)oxane-3,4,5-triol NA 125038102 drawing


References

[1] Screening chemical libraries for nucleic-acid-binding drugs by in vitro selection: a test case with lividomycin.
Lato, S. M., & Ellington, A. D.
Molecular diversity, 2(1-2), 103–110. (1996)