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Record Information
StatusDetected and Quantified
Creation Date2006-05-22 15:12:05 UTC
Update Date2017-12-07 01:49:26 UTC
Secondary Accession Numbers
  • HMDB02708
Metabolite Identification
Common NameCyanidin
DescriptionCyanidin, or flavan-3-ol, is a natural organic compound which is classified as a flavonoid and an anthocyanin. It is a pigment found in many redberries including but not limited to bilberry, blackberry, blueberry, cherry, cranberry, elderberry, hawthorn, loganberry and raspberry. It can also be found in other fruits such as apples and plums. The highest concentrations of cyanidin are found in the skin of the fruit. Recently, the biosynthesis of cyanidin 3-O-glucoside in Escherichia coli was demonstrated. -- Wikipedia.
2-(3,4-Dihydroxyphenyl)-3,5,7-trihydroxy-1-benzopyrylium chlorideHMDB
3,3',4',5,7-Pentahydroxy-2-phenylbenzopyrylium chlorideHMDB
3,3',4',5,7-Pentahydroxyflavylium chlorideHMDB
Cyanidin chlorideHMDB
Cyanidol chlorideHMDB
IdB 1027HMDB
Chemical FormulaC15H11ClO6
Average Molecular Weight322.697
Monoisotopic Molecular Weight322.024415791
IUPAC Name2-(3,4-dihydroxyphenyl)-3,5,7-trihydroxy-1λ⁴-chromen-1-ylium chloride
Traditional Namecyanidin chloride
CAS Registry Number528-58-5
InChI Identifier
Chemical Taxonomy
DescriptionThis compound belongs to the class of organic compounds known as 7-hydroxyflavonoids. These are flavonoids that bear one hydroxyl group at the C-7 position of the flavonoid skeleton.
KingdomOrganic compounds
Super ClassPhenylpropanoids and polyketides
Sub ClassHydroxyflavonoids
Direct Parent7-hydroxyflavonoids
Alternative Parents
  • 3'-hydroxyflavonoid
  • 3-hydroxyflavonoid
  • 4'-hydroxyflavonoid
  • 7-hydroxyflavonoid
  • 5-hydroxyflavonoid
  • Anthocyanidin
  • Benzopyran
  • 1-benzopyran
  • Catechol
  • 1-hydroxy-4-unsubstituted benzenoid
  • 1-hydroxy-2-unsubstituted benzenoid
  • Phenol
  • Monocyclic benzene moiety
  • Benzenoid
  • Heteroaromatic compound
  • Polyol
  • Oxacycle
  • Organoheterocyclic compound
  • Organic oxygen compound
  • Organooxygen compound
  • Organic zwitterion
  • Organic salt
  • Organic chloride salt
  • Hydrocarbon derivative
  • Aromatic heteropolycyclic compound
Molecular FrameworkAromatic heteropolycyclic compounds
External DescriptorsNot Available

Biological location:


  Biofluid and excreta:

  Cell and elements:


  Organ and components:



Route of exposure:



Physical Properties
Experimental Properties
Melting Point> 300 °CNot Available
Boiling PointNot AvailableNot Available
Water SolubilityNot AvailableNot Available
LogPNot AvailableNot Available
Predicted Properties
Water Solubility0.049 g/LALOGPS
pKa (Strongest Acidic)6.01ChemAxon
pKa (Strongest Basic)-5.9ChemAxon
Physiological Charge-1ChemAxon
Hydrogen Acceptor Count5ChemAxon
Hydrogen Donor Count5ChemAxon
Polar Surface Area114.29 ŲChemAxon
Rotatable Bond Count1ChemAxon
Refractivity84.11 m³·mol⁻¹ChemAxon
Polarizability28.11 ųChemAxon
Number of Rings3ChemAxon
Rule of FiveYesChemAxon
Ghose FilterYesChemAxon
Veber's RuleYesChemAxon
MDDR-like RuleYesChemAxon
Spectrum TypeDescriptionSplash Key
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (Non-derivatized) - 70eV, Positivesplash10-0ab9-0981000000-b03145f35dffd7b73034View in MoNA
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (5 TMS) - 70eV, Positivesplash10-001i-2062095000-78127582ff2f81e09993View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Positivesplash10-00di-0009000000-f9880830ba79067d96b6View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Positivesplash10-00di-0009000000-f9880830ba79067d96b6View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Positivesplash10-00di-0009000000-f9880830ba79067d96b6View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Negativesplash10-00di-0009000000-eee166fbbcec693fd35dView in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Negativesplash10-00di-0009000000-eee166fbbcec693fd35dView in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Negativesplash10-00di-0009000000-eee166fbbcec693fd35dView in MoNA
Biological Properties
Cellular Locations
  • Membrane (predicted from logP)
Biofluid Locations
  • Blood
  • Urine
Tissue Location
  • Fibroblasts
  • Kidney
PathwaysNot Available
Normal Concentrations
BloodDetected and Quantified0.02 (0.03 +/- 0.01) uMAdult (>18 years old)Not SpecifiedNormal details
UrineExpected but not Quantified Not AvailableNot AvailableConsuming polyphenols described by Phenol-Explorer entry 19 details
UrineDetected and Quantified1.04 +/- 0.26 umol/mmol creatinineAdult (>18 years old)Not SpecifiedNormal details
Abnormal Concentrations
Not Available
Associated Disorders and Diseases
Disease ReferencesNone
Associated OMIM IDsNone
DrugBank IDNot Available
Phenol Explorer Compound IDNot Available
FoodDB IDFDB002602
KNApSAcK IDC00006614
Chemspider ID61546
KEGG Compound IDC05905
BioCyc IDCPD-7632
BiGG IDNot Available
Wikipedia LinkCyanidin
PubChem Compound68247
PDB IDNot Available
ChEBI ID604446
Synthesis ReferenceSaito, Norio; Yokoi, Masato; Yamaji, Minako; Honda, Toshio. Cyanidin 3-p-coumaroylglucoside in Camellia species and cultivars. Phytochemistry (1987), 26(10), 2761-2.
Material Safety Data Sheet (MSDS)Download (PDF)
General References
  1. Wu X, Cao G, Prior RL: Absorption and metabolism of anthocyanins in elderly women after consumption of elderberry or blueberry. J Nutr. 2002 Jul;132(7):1865-71. [PubMed:12097661 ]
  2. Russo A, La Fauci L, Acquaviva R, Campisi A, Raciti G, Scifo C, Renis M, Galvano G, Vanella A, Galvano F: Ochratoxin A-induced DNA damage in human fibroblast: protective effect of cyanidin 3-O-beta-d-glucoside. J Nutr Biochem. 2005 Jan;16(1):31-7. [PubMed:15629238 ]
  3. Talavera S, Felgines C, Texier O, Besson C, Gil-Izquierdo A, Lamaison JL, Remesy C: Anthocyanin metabolism in rats and their distribution to digestive area, kidney, and brain. J Agric Food Chem. 2005 May 18;53(10):3902-8. [PubMed:15884815 ]
  4. Miyazawa T, Nakagawa K, Kudo M, Muraishi K, Someya K: Direct intestinal absorption of red fruit anthocyanins, cyanidin-3-glucoside and cyanidin-3,5-diglucoside, into rats and humans. J Agric Food Chem. 1999 Mar;47(3):1083-91. [PubMed:10552420 ]
  5. He J, Magnuson BA, Lala G, Tian Q, Schwartz SJ, Giusti MM: Intact anthocyanins and metabolites in rat urine and plasma after 3 months of anthocyanin supplementation. Nutr Cancer. 2006;54(1):3-12. [PubMed:16800768 ]
  6. Stoner GD, Sardo C, Apseloff G, Mullet D, Wargo W, Pound V, Singh A, Sanders J, Aziz R, Casto B, Sun X: Pharmacokinetics of anthocyanins and ellagic acid in healthy volunteers fed freeze-dried black raspberries daily for 7 days. J Clin Pharmacol. 2005 Oct;45(10):1153-64. [PubMed:16172180 ]
  7. Lazze MC, Savio M, Pizzala R, Cazzalini O, Perucca P, Scovassi AI, Stivala LA, Bianchi L: Anthocyanins induce cell cycle perturbations and apoptosis in different human cell lines. Carcinogenesis. 2004 Aug;25(8):1427-33. Epub 2004 Mar 11. [PubMed:15016660 ]