9U70 | pdb_00009u70

INTERACTION BETWEEN A FLUOROQUINOLONE DERIVATIVE AND RNAS WITH A SINGLE BULGE

• PDB DOI: https://doi.org/10.2210/pdb9U70/pdb
• NAKB: 9U70

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


• Deposited: 2025-03-23 Released: 2025-07-09 
• 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

Interaction between a fluoroquinolone derivative KG022 and RNAs: effect of the bulged residues.

Ichijo, R., Kawai, G.

(2025) J Biochem 178: 229-236

• PubMed: 40566752 
• DOI: https://doi.org/10.1093/jb/mvaf039
• Primary Citation of Related Structures:  
  9U6Z, 9U70


• PubMed Abstract: 
  

  To progress the RNA-binding small molecule drug discovery, the specific interaction between RNAs having a single bulge and a fluoroquinolone derivative, KG022, was analyzed by NMR spectroscopy. In our previous work, it was found that KG022 is located between the two base pairs at the 3' and 5' side of the bulged residue. KG022 prefers G or C as the bulged residue and, in the present study, the reason for this preference was analyzed by using RNAs with modified nucleoside residues as the bulged residue. It was found that the amino groups of bulged guanine and cytidine bases interact with the oxygen atoms of the backbone phosphate groups, and the oxygen and nitrogen atoms of bulged guanine and cytidine bases interact with the piperazine group of KG022. Thus, this work presents an example of the mechanism of the specific recognition of a small molecule by RNAs.

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Organizational Affiliation: 
• Graduate School of Engineering, Chiba Institute of Technology, Tsudanuma 2-17-1, Narashino, Chiba 275-0016, 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: 6.5 kDa 
• Atom Count: 432 
• Modeled Residue Count: 19 
• Deposited Residue Count: 19 
• Unique hybrid chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Length	Organism	Image
DNA/RNA (5'-R(*GP*GP*AP*UP*GP*CP*UP*UP*UP*CP*GP*AP*GP*C)-D(P*G)-R(P*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: 2025-07-09 
Deposition Author(s): Ichijo, R., Kawai, G.

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Funding Organization	Location	Grant Number
Not funded		--

Revision History  

• Version 1.0: 2025-07-09
  Type: Initial release
  
• Version 1.1: 2025-10-15
  Changes: Database references