7FJ0 | pdb_00007fj0

Interaction between a fluoroquinolone derivative and RNAs with a single bulge

• PDB DOI: https://doi.org/10.2210/pdb7FJ0/pdb
• NAKB: 7FJ0
• BMRB: 36435

• Classification: RNA
• Organism(s): Mus musculus
• Mutation(s): No 


• Deposited: 2021-08-02 Released: 2021-12-01 
• Deposition Author(s): Nagano, K., Kamimura, T., Kawai, G.
• Funding Organization(s): Not funded

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Experimental Data Snapshot

• Method: SOLUTION NMR
• Conformers Calculated: 100 
• Conformers Submitted: 11 
• Selection Criteria: structures with the lowest energy 

Literature

Interaction between a fluoroquinolone derivative and RNAs with a single bulge.

Nagano, K., Kamimura, T., Kawai, G.

(2022) J Biochem 171: 239-244

• PubMed: 34791286 
• DOI: https://doi.org/10.1093/jb/mvab124
• Primary Citation Related Structures: 
  7FHI, 7FJ0


• 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.

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Organizational Affiliation: 
• Department of Life and Environmental Sciences, Graduate School of Engineering, Chiba Institute of Technology, Chiba 275-0016, Japan.
Veritas In Silico Inc., Tokyo 141-0031, Japan.

Biological Assembly 1  

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: NMR Distance Restraints

Macromolecule Content 

• Total Structure Weight: 6.8 kDa 
• Atom Count: 452 
• Modeled Residue Count: 20 
• Deposited Residue Count: 20 
• Unique nucleic acid chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Length	Organism	Image
RNA (5'-R(*GP*GP*AP*UP*GP*CP*UP*UP*AP*CP*UP*CP*AP*GP*CP*GP*AP*UP*CP*C)-3')	A	20	Mus musculus

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
53D (Subject of Investigation/LOI)	B [auth A]	1-cyclopropyl-N-[3-(dimethylamino)propyl]-7-(4-ethylpiperazin-1-yl)-6-fluoranyl-4-oxidanylidene-quinoline-3-carboxamide C24 H34 F N5 O2 SJAQLOUTDAIPJJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: SOLUTION NMR
• Conformers Calculated: 100 
• Conformers Submitted: 11 
• Selection Criteria: structures with the lowest energy 

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2021-12-01 
Deposition Author(s): Nagano, K., Kamimura, T., Kawai, G.

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Funding Organization	Location	Grant Number
Not funded		--

Revision History  

• Version 1.0: 2021-12-01
  Type: Initial release
  
• Version 1.1: 2022-03-02
  Changes: Database references
• Version 1.2: 2023-06-14
  Changes: Other
• Version 1.3: 2024-05-15
  Changes: Data collection, Database references