Fluorescein isothiocyanate (CHEM001409)

IdentificationTaxonomyBiological PropertiesPhysical PropertiesToxicity ProfileSpectraConcentrationsLinksReferencesTargets (39)XML
Record Information
Version1.0
Creation Date2009-06-22 16:08:23 UTC
Update Date2016-11-09 01:08:32 UTC
Accession NumberCHEM001409
Identification
Common NameFluorescein isothiocyanate
ClassSmall Molecule
DescriptionFluorescein isothiocyanate is a chemical compound derived from fluorescein and containing cyanide. It is used in flow cytometry. (3)
Contaminant Sources
  • T3DB toxins
  • ToxCast & Tox21 Chemicals
Contaminant Type
  • Aromatic Hydrocarbon
  • Cyanide Compound
  • Ester
  • Ether
  • Industrial/Workplace Toxin
  • Organic Compound
  • Pollutant
  • Synthetic Compound
Chemical Structure
Thumb
MOLSDFPDBSMILESInChI
Synonyms
ValueSource
2-(6-Hydroxy-3-oxo-(3H)-xanthen-9-yl)-5-isothiocyanatobenzoic acidChEBI
3',6'-Dihydroxy-5-isothiocyanatospiro(isobenzofuran-1(3H),9'-(9H)xanthen)-3-oneChEBI
5-FITCChEBI
5-IsothiocyanatofluoresceinChEBI
F5ITCChEBI
FITC isomer 1ChEBI
FITC-IChEBI
Fluorescein isothiocyanate isomer 1ChEBI
Fluorescein-5-isothiocyanatChEBI
Fluoreszein-5-isothiocyanatChEBI
2-(6-Hydroxy-3-oxo-(3H)-xanthen-9-yl)-5-isothiocyanatobenzoateGenerator
Fluorescein isothiocyanic acid isomer 1Generator
Fluorescein-5-isothiocyanic acidGenerator
Fluorescein isothiocyanic acidHMDB
Fluorescein 5 isothiocyanateHMDB
Hydrochloride, fluorescein-5-isothiocyanateHMDB
5 IsothiocyanatofluoresceinHMDB
Fluorescein (5 or 6)-isothiocyanateHMDB
Fluorescein 5 isothiocyanate hydrochlorideHMDB
Fluorescein-5-isothiocyanate hydrochlorideHMDB
FITCHMDB
Fluorescein-5-isothiocyanateChEBI
Chemical FormulaC21H11NO5S
Average Molecular Mass389.381 g/mol
Monoisotopic Mass389.036 g/mol
CAS Registry Number27072-45-3
IUPAC Name3',6'-dihydroxy-5-isothiocyanato-3H-spiro[2-benzofuran-1,9'-xanthene]-3-one
Traditional NameFITC
SMILESOC1=CC=C2C(OC3=CC(O)=CC=C3C22OC(=O)C3=CC(=CC=C23)N=C=S)=C1
InChI IdentifierInChI=1S/C21H11NO5S/c23-12-2-5-16-18(8-12)26-19-9-13(24)3-6-17(19)21(16)15-4-1-11(22-10-28)7-14(15)20(25)27-21/h1-9,23-24H
InChI KeyMHMNJMPURVTYEJ-UHFFFAOYSA-N
Chemical Taxonomy
Description belongs to the class of organic compounds known as xanthenes. These are polycyclic aromatic compounds containing a xanthene moiety, which consists of two benzene rings joined to each other by a pyran ring.
KingdomOrganic compounds
Super ClassOrganoheterocyclic compounds
ClassBenzopyrans
Sub Class1-benzopyrans
Direct ParentXanthenes
Alternative Parents
Substituents
  • Xanthene
  • Diaryl ether
  • Benzofuranone
  • Phthalide
  • Isobenzofuranone
  • Isobenzofuran
  • Isocoumaran
  • 1-hydroxy-2-unsubstituted benzenoid
  • Benzenoid
  • Carboxylic acid ester
  • Isothiocyanate
  • Lactone
  • Carboxylic acid derivative
  • Ether
  • Oxacycle
  • Organic 1,3-dipolar compound
  • Monocarboxylic acid or derivatives
  • Propargyl-type 1,3-dipolar organic compound
  • Hydrocarbon derivative
  • Organic nitrogen compound
  • Organonitrogen compound
  • Organooxygen compound
  • Organosulfur compound
  • Organic oxygen compound
  • Organopnictogen compound
  • Organic oxide
  • Aromatic heteropolycyclic compound
Molecular FrameworkAromatic heteropolycyclic compounds
External Descriptors
Biological Properties
StatusDetected and Not Quantified
OriginExogenous
Cellular Locations
  • Membrane
Biofluid LocationsNot Available
Tissue LocationsNot Available
PathwaysNot Available
Applications
Biological Roles
Chemical RolesNot Available
Physical Properties
StateSolid
AppearanceWhite powder.
Experimental Properties
PropertyValue
Melting PointNot Available
Boiling PointNot Available
SolubilityNot Available
Predicted Properties
PropertyValueSource
Water Solubility0.014 g/LALOGPS
logP4.74ALOGPS
logP4.9ChemAxon
logS-4.4ALOGPS
pKa (Strongest Acidic)8.72ChemAxon
pKa (Strongest Basic)-0.28ChemAxon
Physiological Charge0ChemAxon
Hydrogen Acceptor Count4ChemAxon
Hydrogen Donor Count2ChemAxon
Polar Surface Area88.35 ŲChemAxon
Rotatable Bond Count1ChemAxon
Refractivity108.28 m³·mol⁻¹ChemAxon
Polarizability38.67 ųChemAxon
Number of Rings5ChemAxon
Bioavailability1ChemAxon
Rule of FiveYesChemAxon
Ghose FilterYesChemAxon
Veber's RuleNoChemAxon
MDDR-like RuleNoChemAxon
Spectra
Spectra
Spectrum TypeDescriptionSplash KeyView
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (Non-derivatized) - 70eV, Positivesplash10-004i-0696000000-9221205003537ed61c88Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (Non-derivatized) - 70eV, PositiveNot AvailableSpectrum
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (TMS_1_1) - 70eV, PositiveNot AvailableSpectrum
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (TMS_2_1) - 70eV, PositiveNot AvailableSpectrum
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (TBDMS_1_1) - 70eV, PositiveNot AvailableSpectrum
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (TBDMS_2_1) - 70eV, PositiveNot AvailableSpectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Positivesplash10-0006-0009000000-ec9e6b5b7132f279ae1cSpectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Positivesplash10-0006-0009000000-cc7d614d815df8851277Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Positivesplash10-0002-0009000000-5a83b0be852433d3e372Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Negativesplash10-000i-0009000000-35fe5f4e68825b96842fSpectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Negativesplash10-000f-0009000000-04ff70861c0d803ee0f1Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Negativesplash10-0006-0009000000-8fa6671f7739900d864fSpectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Positivesplash10-0006-0009000000-986590fd2c3cb586ce6cSpectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Positivesplash10-0006-0009000000-986590fd2c3cb586ce6cSpectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Positivesplash10-01ot-0019000000-420a6431e7cd56fd3bb0Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Negativesplash10-000i-0009000000-13e20f0880930e8f260dSpectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Negativesplash10-000i-0009000000-13e20f0880930e8f260dSpectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Negativesplash10-002u-1139000000-002ba3d4d330dcb453a9Spectrum
Toxicity Profile
Route of ExposureOral (1) ; inhalation (1) ; dermal (1)
Mechanism of ToxicityCyanide is an inhibitor of cytochrome c oxidase in the fourth complex of the electron transport chain (found in the membrane of the mitochondria of eukaryotic cells). It complexes with the ferric iron atom in this enzyme. The binding of cyanide to this cytochrome prevents transport of electrons from cytochrome c oxidase to oxygen. As a result, the electron transport chain is disrupted and the cell can no longer aerobically produce ATP for energy. Tissues that mainly depend on aerobic respiration, such as the central nervous system and the heart, are particularly affected. Cyanide is also known produce some of its toxic effects by binding to catalase, glutathione peroxidase, methemoglobin, hydroxocobalamin, phosphatase, tyrosinase, ascorbic acid oxidase, xanthine oxidase, succinic dehydrogenase, and Cu/Zn superoxide dismutase. Cyanide binds to the ferric ion of methemoglobin to form inactive cyanmethemoglobin. (2)
MetabolismCyanide is rapidly alsorbed through oral, inhalation, and dermal routes and distributed throughout the body. Cyanide is mainly metabolized into thiocyanate by either rhodanese or 3-mercaptopyruvate sulfur transferase. Cyanide metabolites are excreted in the urine. (1)
Toxicity ValuesNot Available
Lethal Dose200 to 300 milligrams for an adult human (cyanide salts). (4)
Carcinogenicity (IARC Classification)No indication of carcinogenicity to humans (not listed by IARC).
Uses/SourcesFluorescein isothiocyanate is used in flow cytometry. (3)
Minimum Risk LevelNot Available
Health EffectsExposure to high levels of cyanide for a short time harms the brain and heart and can even cause coma, seizures, apnea, cardiac arrest and death. Chronic inhalation of cyanide causes breathing difficulties, chest pain, vomiting, blood changes, headaches, and enlargement of the thyroid gland. Skin contact with cyanide salts can irritate and produce sores. (1, 2)
SymptomsCyanide poisoning is identified by rapid, deep breathing and shortness of breath, general weakness, giddiness, headaches, vertigo, confusion, convulsions/seizures and eventually loss of consciousness. (1, 2)
TreatmentEYES: irrigate opened eyes for several minutes under running water. INGESTION: do not induce vomiting. Rinse mouth with water (never give anything by mouth to an unconscious person). Seek immediate medical advice. SKIN: should be treated immediately by rinsing the affected parts in cold running water for at least 15 minutes, followed by thorough washing with soap and water. If necessary, the person should shower and change contaminated clothing and shoes, and then must seek medical attention. INHALATION: supply fresh air. If required provide artificial respiration.
Concentrations
Not Available
DrugBank IDNot Available
HMDB IDHMDB0246165
FooDB IDNot Available
Phenol Explorer IDNot Available
KNApSAcK IDNot Available
BiGG IDNot Available
BioCyc IDNot Available
METLIN IDNot Available
PDB IDNot Available
Wikipedia LinkFluorescein isothiocyanate
Chemspider ID17686
ChEBI ID37918
PubChem Compound ID18730
Kegg Compound IDNot Available
YMDB IDNot Available
ECMDB IDNot Available
References
Synthesis ReferenceNot Available
MSDSNot Available
General References
1. https://www.ncbi.nlm.nih.gov/pubmed/?term=11122447
2. https://www.ncbi.nlm.nih.gov/pubmed/?term=19583962
3. https://www.ncbi.nlm.nih.gov/pubmed/?term=19709338
4. https://www.ncbi.nlm.nih.gov/pubmed/?term=19768221
5. https://www.ncbi.nlm.nih.gov/pubmed/?term=20492570
6. https://www.ncbi.nlm.nih.gov/pubmed/?term=21300019
7. https://www.ncbi.nlm.nih.gov/pubmed/?term=21451573
8. https://www.ncbi.nlm.nih.gov/pubmed/?term=21456254
9. https://www.ncbi.nlm.nih.gov/pubmed/?term=22009769
10. https://www.ncbi.nlm.nih.gov/pubmed/?term=22718031
11. https://www.ncbi.nlm.nih.gov/pubmed/?term=23426683
12. https://www.ncbi.nlm.nih.gov/pubmed/?term=23667843
13. https://www.ncbi.nlm.nih.gov/pubmed/?term=25515858
14. https://www.ncbi.nlm.nih.gov/pubmed/?term=25602940
15. https://www.ncbi.nlm.nih.gov/pubmed/?term=25703728
16. https://www.ncbi.nlm.nih.gov/pubmed/?term=27373998
17. https://www.ncbi.nlm.nih.gov/pubmed/?term=28972093
18. Barupal DK, Fiehn O: Generating the Blood Exposome Database Using a Comprehensive Text Mining and Database Fusion Approach. Environ Health Perspect. 2019 Sep;127(9):97008. doi: 10.1289/EHP4713. Epub 2019 Sep 26.