9IO0 | pdb_00009io0

INTERACTION BETWEEN A FLUOROQUINOLONE DERIVATIVE KG022 AND RNAS: EFFECT OF BASE PAIRS 5' ADJACENT TO THE BULGE OUT ESIDUES

• PDB DOI: https://doi.org/10.2210/pdb9IO0/pdb
• NAKB: 9IO0
• BMRB: 36681

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


• Deposited: 2024-07-08 Released: 2025-04-02 
• Deposition Author(s): Ichijo, R., 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

Specific Interaction between a Fluoroquinolone Derivative, KG022, and RNAs with a Single Bulge.

Ichijo, R., Kawai, G.

(2025) Biochemistry 64: 2192-2199

• PubMed: 40067027 
• DOI: https://doi.org/10.1021/acs.biochem.4c00669
• Primary Citation Related Structures: 
  9IO0, 9IO1, 9IOR, 9IOS, 9IOU


• PubMed Abstract: 
  

  Small compounds targeting RNAs are recognized as a promising modality in drug discovery. We have found that a fluoroquinolone derivative, KG022, binds to RNAs with single-bulged residues. It has been demonstrated by ¹ H NMR that KG022 binds to RNAs with a bulged G or C and a GC or AU base pair at the 3' adjacent to the bulged residues. In the present study, the effects of the base pairs at the 5' adjacent to the bulged residues on the interaction of KG022 were analyzed mainly by ¹ H NMR. It was found that KG022 prefers UA and CG base pairs at the 5' adjacent to the bulged residues, indicating that a stable complex is formed by the stacking interaction among the fluoroquinolone ring and the purine bases of the 5' and 3' sides. In addition, this was confirmed by analysis of the ¹⁹ F-NMR spectra. Analysis of temperature dependences of NMR spectra revealed that KG022 forms a more stable complex with RNAs having CG base pairs at the 5' adjacent position than those with UA base pairs. This work presented useful information for the development of small molecules having higher affinity to target RNAs.

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Organizational Affiliation: 
• Graduate School of Advanced Engineering, Chiba Institute of Technology, Tsudanuma 2-17-1, Narashino , Chiba275-0016, Japan.

Biological Assembly 1  

Biological assembly 1 assigned by authors and generated by (software)

Biological Assembly Evidence: NMR Distance Restraints

Macromolecule Content 

• Total Structure Weight: 6.51 kDa 
• Atom Count: 433 
• Modeled Residue Count: 19 
• Deposited Residue Count: 19 
• Unique nucleic acid chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Length	Organism	Image
RNA (5'-R(*GP*GP*AP*UP*GP*GP*UP*UP*UP*CP*GP*AP*CP*CP*GP*AP*UP*CP*C)-3')	A	19	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: 2025-04-02 
Deposition Author(s): Ichijo, R., Kawai, G.

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Funding Organization	Location	Grant Number
Not funded		--

Revision History  

• Version 1.0: 2025-04-02
  Type: Initial release
  
• Version 1.1: 2025-06-04
  Changes: Database references