9U6Z | pdb_00009u6z

INTERACTION BETWEEN A FLUOROQUINOLONE DERIVATIVE AND RNAS WITH A SINGLE BULGE

  • 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

Experimental Data Snapshot

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

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history. 


Literature

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

Ichijo, R., Kawai, G.

(2025) J Biochem 178: 229-236

  • 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.

    • Organizational Affiliation: 
    • Graduate School of Engineering, Chiba Institute of Technology, Tsudanuma 2-17-1, Narashino, Chiba 275-0016, Japan.

Macromolecules

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Entity ID: 1
MoleculeChains LengthOrganismImage
DNA/RNA (5'-R(*GP*GP*AP*UP*GP*CP*UP*UP*UP*CP*GP*AP*GP*C)-D(P*C)-R(P*AP*UP*CP*C)-3')19Mus musculus
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
53D (Subject of Investigation/LOI)
Query on 53D
Download Ideal Coordinates CCD File 
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

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Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
Not funded--

Revision History  (Full details and data files)

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