7FHI

Interaction between a fluoroquinolone derivative and RNAs with a single bulge

Summary for 7FHI

• Entry DOI: 10.2210/pdb7fhi/pdb
• Descriptor: RNA (5'-R(*GP*GP*AP*UP*GP*CP*UP*UP*AP*CP*UP*CP*AP*GP*CP*CP*AP*UP*CP*C)-3'), 1-cyclopropyl-N-[3-(dimethylamino)propyl]-7-(4-ethylpiperazin-1-yl)-6-fluoranyl-4-oxidanylidene-quinoline-3-carboxamide (2 entities in total)
• Functional Keywords: complex, fluoroquinolone, rna
• Biological source: Mus musculus
• Total number of polymer chains: 1
• Total formula weight: 6763.35

Authors

Nagano, K.,Kamimura, T.,Kawai, G. (deposition date: 2021-07-29, release date: 2021-12-01, Last modification date: 2024-05-15)

Primary citation

Nagano, K.,Kamimura, T.,Kawai, G.
Interaction between a fluoroquinolone derivative and RNAs with a single bulge.
J.Biochem., 171:239-244, 2022

PubMed Abstract: Interaction analysis between small molecules and RNA as well as structure determination of RNA-small molecule complexes will be the clues to search for compounds that bind to specific mRNA or non-coding RNA in drug discovery. In this study, the RNA-binding ability of a fluoroquinolone derivative, KG022, was examined against single-residue bulge-containing hairpin RNAs as RNA models. Nuclear magnetic resonance analysis indicated that KG022 interacts with the RNAs in the vicinity of the bulge residue, with preferring C and G as the bulge residues. The solution structures of the RNA-KG022 complexes showed that the KG022 binds to the RNAs at the bulge-out regions. Each substituent in KG022 interacts with specific position of RNAs around the bulge-out region probably contributing the specificity of the binding. This work provides a novel member for the RNA-targeted small molecules.

PubMed: 34791286
DOI: 10.1093/jb/mvab124

Experimental method

SOLUTION NMR