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- PDB-9io1: INTERACTION BETWEEN A FLUOROQUINOLONE DERIVATIVE KG022 AND RNAS: ... -

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Basic information

Entry
Database: PDB / ID: 9io1
TitleINTERACTION BETWEEN A FLUOROQUINOLONE DERIVATIVE KG022 AND RNAS: EFFECT OF BASE PAIRS 5' ADJACENT TO THE BULGE OUT RESIDUES
ComponentsRNA (5'-R(*GP*GP*AP*UP*AP*CP*UP*UP*UP*CP*GP*AP*GP*UP*CP*AP*UP*CP*C)-3')
KeywordsRNA / FLUOROQUINOLONE / INTERACTION / SPECIFICITY
Function / homologyChem-53D / RNA / RNA (> 10)
Function and homology information
Biological speciesMus musculus (house mouse)
MethodSOLUTION NMR / na
AuthorsIchijo, R. / Kawai, G.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Biochemistry / Year: 2025
Title: Specific Interaction between a Fluoroquinolone Derivative, KG022, and RNAs with a Single Bulge.
Authors: Ichijo, R. / Kawai, G.
History
DepositionJul 8, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 2, 2025Provider: repository / Type: Initial release
Revision 1.1Jun 4, 2025Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: RNA (5'-R(*GP*GP*AP*UP*AP*CP*UP*UP*UP*CP*GP*AP*GP*UP*CP*AP*UP*CP*C)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)6,4592
Polymers6,0161
Non-polymers4441
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: NMR Distance Restraints, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)11 / 100structures with the lowest energy
RepresentativeModel #1minimized average structure

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Components

#1: RNA chain RNA (5'-R(*GP*GP*AP*UP*AP*CP*UP*UP*UP*CP*GP*AP*GP*UP*CP*AP*UP*CP*C)-3')


Mass: 6015.592 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Mus musculus (house mouse)
#2: Chemical ChemComp-53D / 1-cyclopropyl-N-[3-(dimethylamino)propyl]-7-(4-ethylpiperazin-1-yl)-6-fluoranyl-4-oxidanylidene-quinoline-3-carboxamide


Mass: 443.557 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C24H34FN5O2 / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic12D 1H-1H NOESY
121isotropic12D 1H-1H TOCSY

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Sample preparation

DetailsType: solution
Contents: 0.44 mM RNA (5'-R(*GP*GP*AP*UP*AP*CP*UP*UP*UP*CP*GP*AP*GP*UP*CP*AP*UP*CP*C)-3'), 0.66 mM 53D, 95% H2O/5% D2O
Label: sample1 / Solvent system: 95% H2O/5% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.44 mMRNA (5'-R(*GP*GP*AP*UP*AP*CP*UP*UP*UP*CP*GP*AP*GP*UP*CP*AP*UP*CP*C)-3')none1
0.66 mM53Dnone1
Sample conditionsIonic strength: 50 mM / Label: condition1 / pH: 6.5 / Pressure: 1 atm / Temperature: 288 K

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NMR measurement

NMR spectrometerType: Bruker AVANCE NEO / Manufacturer: Bruker / Model: AVANCE NEO / Field strength: 600 MHz

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Processing

NMR software
NameVersionDeveloperClassification
Sparky3Goddardchemical shift assignment
CNS1.3Brunger, Adams, Clore, Gros, Nilges and Readstructure calculation
Sparky3Goddardpeak picking
RefinementMethod: na / Software ordinal: 2
NMR representativeSelection criteria: minimized average structure
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 11

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