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Record Information
Creation Date2009-07-30 17:58:47 UTC
Update Date2014-12-24 20:26:07 UTC
Accession NumberT3D3495
Common NameCiprofloxacin
ClassSmall Molecule
DescriptionCiprofloxacin is only found in individuals that have used or taken this drug. It is a broad-spectrum antimicrobial carboxyfluoroquinoline. The bactericidal action of ciprofloxacin results from inhibition of the enzymes topoisomerase II (DNA gyrase) and topoisomerase IV, which are required for bacterial DNA replication, transcription, repair, strand supercoiling repair, and recombination.
Compound Type
  • Amide
  • Amine
  • Anti-Infective Agent
  • Drug
  • Ester
  • Metabolite
  • Nucleic Acid Synthesis Inhibitor
  • Organic Compound
  • Organofluoride
  • Quinolone
  • Synthetic Compound
Chemical Structure
1-Cyclopropyl-6-fluoro-1,4-dihydro-4-oxo-7-(1-piperazinyl)-3-quinolinecarboxylic acid
1-Cyclopropyl-6-fluoro-4-oxo-7-(piperazin-1-yl)-1,4-dihydroquinoline-3-carboxylic acid
1-Cyclopropyl-6-fluoro-4-oxo-7-piperazin-1-yl-1,4-dihydro-quinoline-3-carboxylic acid
1-CYCLOPROPYL-6-fluoro-4-oxo-7-piperazin-1-yl-1,4-dihydroquinoline-3-carboxylic acid
1-Cyclopropyl-6-fluoro-4-oxo-7-piperazin-1-ylquinoline-3-carboxylic acid
1-Cyclopropyl-6-fluoro-7-(4-methyl-piperazin-1-yl)-4-oxo-1,4-dihydro-quinoline-3-carboxylic acid
1-Cyclopropyl-6-fluoro-7-hexahydro-1-pyrazinyl-4-oxo-1,4-dihydro-3-quinolinecarboxylic acid
Ciprofloxacin monohydrochloride
Proquin XR
Chemical FormulaC17H18FN3O3
Average Molecular Mass331.342 g/mol
Monoisotopic Mass331.133 g/mol
CAS Registry Number85721-33-1
IUPAC Name1-cyclopropyl-6-fluoro-4-oxo-7-(piperazin-1-yl)-1,4-dihydroquinoline-3-carboxylic acid
Traditional Nameciprofloxacin
InChI IdentifierInChI=1S/C17H18FN3O3/c18-13-7-11-14(8-15(13)20-5-3-19-4-6-20)21(10-1-2-10)9-12(16(11)22)17(23)24/h7-10,19H,1-6H2,(H,23,24)
Chemical Taxonomy
Description belongs to the class of organic compounds known as quinoline carboxylic acids. These are quinolines in which the quinoline ring system is substituted by a carboxyl group at one or more positions.
KingdomOrganic compounds
Super ClassOrganoheterocyclic compounds
ClassQuinolines and derivatives
Sub ClassQuinoline carboxylic acids
Direct ParentQuinoline carboxylic acids
Alternative Parents
  • Quinoline-3-carboxylic acid
  • Fluoroquinolone
  • N-arylpiperazine
  • Aminoquinoline
  • Haloquinoline
  • Dihydroquinolone
  • Dihydroquinoline
  • Pyridine carboxylic acid
  • Pyridine carboxylic acid or derivatives
  • Tertiary aliphatic/aromatic amine
  • Dialkylarylamine
  • Aryl fluoride
  • Aryl halide
  • 1,4-diazinane
  • Piperazine
  • Pyridine
  • Benzenoid
  • Vinylogous amide
  • Heteroaromatic compound
  • Amino acid or derivatives
  • Amino acid
  • Tertiary amine
  • Azacycle
  • Secondary amine
  • Carboxylic acid derivative
  • Monocarboxylic acid or derivatives
  • Carboxylic acid
  • Secondary aliphatic amine
  • Amine
  • Organic oxygen compound
  • Organic nitrogen compound
  • Organopnictogen compound
  • Organic oxide
  • Organohalogen compound
  • Organofluoride
  • Organonitrogen compound
  • Organooxygen compound
  • Hydrocarbon derivative
  • Aromatic heteropolycyclic compound
Molecular FrameworkAromatic heteropolycyclic compounds
External Descriptors
Biological Properties
StatusDetected and Not Quantified
Cellular Locations
  • Cytoplasm
  • Extracellular
  • Membrane
Biofluid LocationsNot Available
Tissue LocationsNot Available
PathwaysNot Available
Biological Roles
Chemical Roles
Physical Properties
AppearanceWhite powder.
Experimental Properties
Melting Point255-257°C
Boiling PointNot Available
Solubility3E+004 mg/L (at 20°C)
Predicted Properties
Water Solubility1.35 g/LALOGPS
pKa (Strongest Acidic)5.76ChemAxon
pKa (Strongest Basic)8.68ChemAxon
Physiological Charge0ChemAxon
Hydrogen Acceptor Count6ChemAxon
Hydrogen Donor Count2ChemAxon
Polar Surface Area72.88 ŲChemAxon
Rotatable Bond Count3ChemAxon
Refractivity87.94 m³·mol⁻¹ChemAxon
Polarizability33.12 ųChemAxon
Number of Rings4ChemAxon
Rule of FiveYesChemAxon
Ghose FilterYesChemAxon
Veber's RuleYesChemAxon
MDDR-like RuleYesChemAxon
Spectrum TypeDescriptionSplash KeyView
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (Non-derivatized) - 70eV, Positivesplash10-0006-1093000000-862dc160dc8f327d0da9JSpectraViewer
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (1 TMS) - 70eV, Positivesplash10-022j-4019000000-459673fa2b66361777e0JSpectraViewer
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (Non-derivatized) - 70eV, PositiveNot AvailableJSpectraViewer
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-qTof , Positivesplash10-056r-0495500000-f7ac02c54627a27faafaJSpectraViewer | MoNA
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-qTof , Positivesplash10-001i-0397000000-0e08dc88a42e413750ceJSpectraViewer | MoNA
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-QTOF , positivesplash10-001i-0029000000-1366c290ed86c001f05bJSpectraViewer | MoNA
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-ITFT , positivesplash10-03dr-0069000000-a523751ea781088af897JSpectraViewer | MoNA
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-ITFT , positivesplash10-001i-0009000000-f29d9954b2b055b62079JSpectraViewer | MoNA
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-ITFT , positivesplash10-01qi-0039000000-9cb66ef0790c686ea2b2JSpectraViewer | MoNA
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-ITFT , positivesplash10-03di-0089000000-c501b014ce11307842e1JSpectraViewer | MoNA
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-ITFT , positivesplash10-001i-0092000000-3f2bc2af8897693f406aJSpectraViewer | MoNA
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-ITFT , positivesplash10-001i-0290000000-97cd08c23e39dd2412ecJSpectraViewer | MoNA
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-ITFT , positivesplash10-001i-0690000000-c683e1591a42526bd85dJSpectraViewer | MoNA
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-ITFT , positivesplash10-001i-0009000000-c8783567d83c0158dc21JSpectraViewer | MoNA
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-ITFT , positivesplash10-01qi-0049000000-0c3e1fd26ebdc13a760eJSpectraViewer | MoNA
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-ITFT , positivesplash10-03di-0079000000-84eeb4205e8a902133ecJSpectraViewer | MoNA
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-ITFT , positivesplash10-001i-0192000000-3bebeb08e817739aa5f7JSpectraViewer | MoNA
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-ITFT , positivesplash10-001i-0290000000-40a5de8dd981d46dbe88JSpectraViewer | MoNA
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-ITFT , positivesplash10-001i-0690000000-827770181ddec7977048JSpectraViewer | MoNA
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-ITFT , positivesplash10-03dr-0079000000-b9937740f37fc8a939a6JSpectraViewer | MoNA
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-QQ , positivesplash10-001i-0009000000-06b6d10cecb7c9cab240JSpectraViewer | MoNA
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-QQ , positivesplash10-001i-0129000000-61453c8af95773ec6b29JSpectraViewer | MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Positivesplash10-001i-0019000000-5a787abad4fcc942c621JSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Positivesplash10-01q3-5095000000-6f0602f7f1a4d5ec09d5JSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Positivesplash10-0006-9060000000-456e228fa5da21a2f38eJSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Negativesplash10-0019-0095000000-dc014ca1a9ae0d764286JSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Negativesplash10-000i-1090000000-7ff4f51210f601baeaa1JSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Negativesplash10-0f76-5090000000-57a89bf3c6736c060e9aJSpectraViewer
1D NMR13C NMR SpectrumNot AvailableJSpectraViewer
1D NMR1H NMR SpectrumNot AvailableJSpectraViewer
1D NMR13C NMR SpectrumNot AvailableJSpectraViewer
1D NMR1H NMR SpectrumNot AvailableJSpectraViewer
1D NMR13C NMR SpectrumNot AvailableJSpectraViewer
1D NMR1H NMR SpectrumNot AvailableJSpectraViewer
1D NMR13C NMR SpectrumNot AvailableJSpectraViewer
1D NMR1H NMR SpectrumNot AvailableJSpectraViewer
1D NMR13C NMR SpectrumNot AvailableJSpectraViewer
1D NMR1H NMR SpectrumNot AvailableJSpectraViewer
1D NMR13C NMR SpectrumNot AvailableJSpectraViewer
1D NMR1H NMR SpectrumNot AvailableJSpectraViewer
1D NMR13C NMR SpectrumNot AvailableJSpectraViewer
1D NMR1H NMR SpectrumNot AvailableJSpectraViewer
1D NMR13C NMR SpectrumNot AvailableJSpectraViewer
1D NMR1H NMR SpectrumNot AvailableJSpectraViewer
1D NMR13C NMR SpectrumNot AvailableJSpectraViewer
1D NMR1H NMR SpectrumNot AvailableJSpectraViewer
1D NMR13C NMR SpectrumNot AvailableJSpectraViewer
1D NMR1H NMR SpectrumNot AvailableJSpectraViewer
Toxicity Profile
Route of ExposureEye contact; parenteral (intravenous injection); oral. Rapidly and well absorbed from the gastrointestinal tract after oral administration. The absolute bioavailability is approximately 70% with no substantial loss by first pass metabolism.
Mechanism of ToxicityThe bactericidal action of ciprofloxacin results from inhibition of the enzymes topoisomerase II (DNA gyrase) and topoisomerase IV, which are required for bacterial DNA replication, transcription, repair, strand supercoiling repair, and recombination.
MetabolismHepatic. Four metabolites have been identified in human urine which together account for approximately 15% of an oral dose. The metabolites have antimicrobial activity, but are less active than unchanged ciprofloxacin. Route of Elimination: Approximately 40 to 50% of an orally administered dose is excreted in the urine as unchanged drug. Half Life: 4 hours
Toxicity ValuesNot Available
Lethal DoseNot Available
Carcinogenicity (IARC Classification)No indication of carcinogenicity to humans (not listed by IARC).
Uses/SourcesFor the treatment of the following infections caused by susceptible organisms: urinary tract infections, acute uncomplicated cystitis, chronic bacterial prostatitis, lower respiratory tract infections, acute sinusitis, skin and skin structure infections, bone and joint infections, complicated intra-abdominal infections (used in combination with metronidazole), infectious diarrhea, typhoid fever (enteric fever), uncomplicated cervical and urethral gonorrhea, and inhalational anthrax (post-exposure).
Minimum Risk LevelNot Available
Health EffectsInflammation of the skin (exfoliative dermatitis)
SymptomsThe major adverse effect seen with use of is gastrointestinal irritation, common with many antibiotics.
TreatmentNot Available
Normal Concentrations
Not Available
Abnormal Concentrations
Not Available
DrugBank IDDB00537
PubChem Compound ID2764
ChemSpider ID2662
UniProt IDNot Available
ChEBI ID100241
BioCyc IDNot Available
CTD IDNot Available
Stitch IDCiprofloxacin
ACToR IDNot Available
Wikipedia LinkCiprofloxacin
Synthesis Reference

General References
  1. Drusano GL, Standiford HC, Plaisance K, Forrest A, Leslie J, Caldwell J: Absolute oral bioavailability of ciprofloxacin. Antimicrob Agents Chemother. 1986 Sep;30(3):444-6. [3777908 ]
  2. Hilliard JJ, Krause HM, Bernstein JI, Fernandez JA, Nguyen V, Ohemeng KA, Barrett JF: A comparison of active site binding of 4-quinolones and novel flavone gyrase inhibitors to DNA gyrase. Adv Exp Med Biol. 1995;390:59-69. [8718602 ]
  3. Spivey JM, Cummings DM, Pierson NR: Failure of prostatitis treatment secondary to probable ciprofloxacin-sucralfate drug interaction. Pharmacotherapy. 1996 Mar-Apr;16(2):314-6. [8820479 ]
  4. Brouwers JR: Drug interactions with quinolone antibacterials. Drug Saf. 1992 Jul-Aug;7(4):268-81. [1524699 ]
  5. [Link]
Gene Regulation
Up-Regulated Genes
GeneGene SymbolGene IDInteractionChromosomeDetails
Down-Regulated Genes
GeneGene SymbolGene IDInteractionChromosomeDetails


General Function:
Voltage-gated potassium channel activity involved in ventricular cardiac muscle cell action potential repolarization
Specific Function:
Pore-forming (alpha) subunit of voltage-gated inwardly rectifying potassium channel. Channel properties are modulated by cAMP and subunit assembly. Mediates the rapidly activating component of the delayed rectifying potassium current in heart (IKr). Isoforms USO have no channel activity by themself, but modulates channel characteristics by forming heterotetramers with other isoforms which are retained intracellularly and undergo ubiquitin-dependent degradation.
Gene Name:
Uniprot ID:
Molecular Weight:
126653.52 Da
Binding/Activity Constants
TypeValueAssay TypeAssay Source
Inhibitory>100 uMNot AvailableBindingDB 21690
IC50954.99259 uMNot AvailableBindingDB 21690
IC50954.993 uMNot AvailableBindingDB 21690
IC50>30 uMNot AvailableBindingDB 21690
  1. Tobita M, Nishikawa T, Nagashima R: A discriminant model constructed by the support vector machine method for HERG potassium channel inhibitors. Bioorg Med Chem Lett. 2005 Jun 2;15(11):2886-90. [15911273 ]
  2. Jia L, Sun H: Support vector machines classification of hERG liabilities based on atom types. Bioorg Med Chem. 2008 Jun 1;16(11):6252-60. doi: 10.1016/j.bmc.2008.04.028. Epub 2008 Apr 16. [18448342 ]
  3. Keseru GM: Prediction of hERG potassium channel affinity by traditional and hologram qSAR methods. Bioorg Med Chem Lett. 2003 Aug 18;13(16):2773-5. [12873512 ]
  4. Wiles JA, Phadke AS, Bradbury BJ, Pucci MJ, Thanassi JA, Deshpande M: Selenophene-containing inhibitors of type IIA bacterial topoisomerases. J Med Chem. 2011 May 12;54(9):3418-25. doi: 10.1021/jm2002124. Epub 2011 Apr 13. [21443219 ]
  5. Murphy ST, Case HL, Ellsworth E, Hagen S, Huband M, Joannides T, Limberakis C, Marotti KR, Ottolini AM, Rauckhorst M, Starr J, Stier M, Taylor C, Zhu T, Blaser A, Denny WA, Lu GL, Smaill JB, Rivault F: The synthesis and biological evaluation of novel series of nitrile-containing fluoroquinolones as antibacterial agents. Bioorg Med Chem Lett. 2007 Apr 15;17(8):2150-5. Epub 2007 Feb 2. [17303420 ]
General Function:
Toxic substance binding
Specific Function:
Serum albumin, the main protein of plasma, has a good binding capacity for water, Ca(2+), Na(+), K(+), fatty acids, hormones, bilirubin and drugs. Its main function is the regulation of the colloidal osmotic pressure of blood. Major zinc transporter in plasma, typically binds about 80% of all plasma zinc.
Gene Name:
Uniprot ID:
Molecular Weight:
69365.94 Da
  1. Fick AC, Reinscheid UM: Characterization of the binding epitope of ciprofloxacin bound to human serum albumin. J Pharm Biomed Anal. 2006 Jun 7;41(3):1025-8. Epub 2006 Feb 21. [16497464 ]
  2. Ahmad B, Parveen S, Khan RH: Effect of albumin conformation on the binding of ciprofloxacin to human serum albumin: a novel approach directly assigning binding site. Biomacromolecules. 2006 Apr;7(4):1350-6. [16602760 ]
  3. Kumar PV, Jain NK: Suppression of agglomeration of ciprofloxacin-loaded human serum albumin nanoparticles. AAPS PharmSciTech. 2007 Mar 2;8(1):17. [17408217 ]
  4. Wang Z, Zhu Y, Ding S, He F, Beier RC, Li J, Jiang H, Feng C, Wan Y, Zhang S, Kai Z, Yang X, Shen J: Development of a monoclonal antibody-based broad-specificity ELISA for fluoroquinolone antibiotics in foods and molecular modeling studies of cross-reactive compounds. Anal Chem. 2007 Jun 15;79(12):4471-83. Epub 2007 May 19. [17511422 ]
General Function:
Ubiquitin binding
Specific Function:
Control of topological states of DNA by transient breakage and subsequent rejoining of DNA strands. Topoisomerase II makes double-strand breaks. Essential during mitosis and meiosis for proper segregation of daughter chromosomes. May play a role in regulating the period length of ARNTL/BMAL1 transcriptional oscillation (By similarity).
Gene Name:
Uniprot ID:
Molecular Weight:
174383.88 Da
  1. Chen X, Ji ZL, Chen YZ: TTD: Therapeutic Target Database. Nucleic Acids Res. 2002 Jan 1;30(1):412-5. [11752352 ]
  2. Gentry AC, Pitts SL, Jablonsky MJ, Bailly C, Graves DE, Osheroff N: Interactions between the etoposide derivative F14512 and human type II topoisomerases: implications for the C4 spermine moiety in promoting enzyme-mediated DNA cleavage. Biochemistry. 2011 Apr 19;50(15):3240-9. doi: 10.1021/bi200094z. Epub 2011 Mar 28. [21413765 ]