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Record Information
StatusDetected and Quantified
Creation Date2006-05-22 15:12:05 UTC
Update Date2020-06-15 17:04:52 UTC
Secondary Accession Numbers
  • HMDB0125127
  • HMDB02708
Metabolite Identification
Common NameCyanidin
DescriptionCyanidin, also known as cyanidin chloride (CAS: 528-58-5), 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. Thus, cyanidin is considered to be a flavonoid lipid molecule. Cyanidin is a very hydrophobic molecule, practically insoluble (in water), and relatively neutral. Cyanidin (and its glycosides) is the most commonly occurring of the anthocyanins, a widespread group of pigments responsible for the red-blue colour of many fruits and vegetables (PMID: 14711454 ). BioTransformer predicts that cyanidin is a product of cyanidin 3-​glucoside metabolism via a glycoside-hydrolysis reaction occurring in human gut microbiota and catalyzed by the EC.3.2.1.X enzyme (PMID: 30612223 ).
3,3',4',5,7-Pentahydroxyflavylium chlorideKEGG
Chlorure de 3,3',4',5,7-pentahydroxyflavyliumKEGG
2-(3,4-Dihydroxyphenyl)-3,5,7-trihydroxy-1-benzopyrylium chlorideKEGG
3,3',4',5,7-Pentahydroxy-2-phenylbenzopyrylium chlorideKEGG
Cyanidin chlorideKEGG
Cyanidol chlorideKEGG
IdB 1027KEGG
Cyanidin ionMeSH
1-Benzopyrylium, 2-(3,4-dihydroxyphenyl)-3,5,7-trihydroxy-, chlorideMeSH
2-(3,4-Dihydroxyphenyl) chromenylium-3,5,7-triolMeSH
Flavylium, 3,3',4',5,7-pentahydroxy-, chlorideMeSH
1-Benzopyrylium, 2-(3,4-dihydroxyphenyl)-3,5,7-trihydroxy-, chloride (1:1)MeSH
Cyanidin cationMeSH
Chemical FormulaC15H11O6
Average Molecular Weight287.2442
Monoisotopic Molecular Weight287.055563084
IUPAC Name2-(3,4-dihydroxyphenyl)-3,5,7-trihydroxy-2H-chromen-2-ylium
Traditional Name2-(3,4-dihydroxyphenyl)-3,5,7-trihydroxy-2H-chromen-2-ylium
CAS Registry Number13306-05-3
InChI Identifier
Chemical Taxonomy
Description 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
  • 5-hydroxyflavonoid
  • 7-hydroxyflavonoid
  • Anthocyanidin
  • Benzopyran
  • 1-benzopyran
  • Catechol
  • 1-hydroxy-4-unsubstituted benzenoid
  • 1-hydroxy-2-unsubstituted benzenoid
  • Phenol
  • Benzenoid
  • Monocyclic benzene moiety
  • Heteroaromatic compound
  • Organoheterocyclic compound
  • Oxacycle
  • Polyol
  • Organooxygen compound
  • Hydrocarbon derivative
  • Organic oxygen compound
  • Organic cation
  • Aromatic heteropolycyclic compound
Molecular FrameworkAromatic heteropolycyclic compounds
External Descriptors

Route of exposure:


Biological location:

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)6.47ChemAxon
pKa (Strongest Basic)-2.9ChemAxon
Physiological Charge0ChemAxon
Hydrogen Acceptor Count5ChemAxon
Hydrogen Donor Count5ChemAxon
Polar Surface Area114.29 ŲChemAxon
Rotatable Bond Count1ChemAxon
Refractivity74.16 m³·mol⁻¹ChemAxon
Polarizability28.09 ųChemAxon
Number of Rings3ChemAxon
Rule of FiveYesChemAxon
Ghose FilterNoChemAxon
Veber's RuleNoChemAxon
MDDR-like RuleNoChemAxon
Spectrum TypeDescriptionSplash KeyView
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (Non-derivatized) - 70eV, Positivesplash10-0abi-0690000000-173d2265dcd29fa12c94Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS ( TMS) - 70eV, Positivesplash10-001i-2062095000-78127582ff2f81e09993Spectrum
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-QFT 20V, positivesplash10-000i-0190000000-5ab24abbf0384667d604Spectrum
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-IT 20V, positivesplash10-000i-0390000000-cb44415a595e007f6f39Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Positivesplash10-000i-0090000000-0a9fc784dd803d3a889eSpectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Positivesplash10-000i-0090000000-3284da347edb43bf4585Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Positivesplash10-01ti-0970000000-ffb2d72fad14ec3d596aSpectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Negativesplash10-000i-0090000000-b5bd359053422415d91aSpectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Negativesplash10-000i-0090000000-c2b4878a408c4329c697Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Negativesplash10-057i-4950000000-95db0e67894990e7b23aSpectrum
Biological Properties
Cellular Locations
  • Membrane (predicted from logP)
Biospecimen Locations
  • Blood
  • Urine
Tissue Locations
  • Fibroblasts
  • Kidney
Normal Concentrations
BloodDetected and Quantified0.02 (0.03 +/- 0.01) uMAdult (>18 years old)Not SpecifiedNormal details
UrineExpected but not QuantifiedNot QuantifiedNot 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
FooDB IDFDB002602
KNApSAcK IDC00006614
Chemspider ID114193
KEGG Compound IDC05905
BioCyc IDCPD-591
BiGG IDNot Available
Wikipedia LinkCyanidin
METLIN IDNot Available
PubChem Compound128861
PDB IDNot Available
ChEBI ID27843
Food Biomarker OntologyNot Available
VMH IDNot Available
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 ]
  8. Galvano F, La Fauci L, Lazzarino G, Fogliano V, Ritieni A, Ciappellano S, Battistini NC, Tavazzi B, Galvano G: Cyanidins: metabolism and biological properties. J Nutr Biochem. 2004 Jan;15(1):2-11. doi: 10.1016/j.jnutbio.2003.07.004. [PubMed:14711454 ]
  9. Djoumbou-Feunang Y, Fiamoncini J, Gil-de-la-Fuente A, Greiner R, Manach C, Wishart DS: BioTransformer: a comprehensive computational tool for small molecule metabolism prediction and metabolite identification. J Cheminform. 2019 Jan 5;11(1):2. doi: 10.1186/s13321-018-0324-5. [PubMed:30612223 ]
  10. Djoumbou Feunang, Yannick (2017). Cheminformatics Tools for Enabling Metabolomics, 2017 (PhD thesis). University of Alberta.


General function:
Involved in magnesium ion binding
Specific function:
Catalyzes the O-methylation, and thereby the inactivation, of catecholamine neurotransmitters and catechol hormones. Also shortens the biological half-lives of certain neuroactive drugs, like L-DOPA, alpha-methyl DOPA and isoproterenol.
Gene Name:
Uniprot ID:
Molecular weight:
Cyanidin → 3,5,7-trihydroxy-2-(4-hydroxy-3-methoxyphenyl)-1λ⁴-chromen-1-yliumdetails
General function:
Involved in transferase activity, transferring hexosyl groups
Specific function:
UDPGT is of major importance in the conjugation and subsequent elimination of potentially toxic xenobiotics and endogenous compounds. This isoform glucuronidates bilirubin IX-alpha to form both the IX-alpha-C8 and IX-alpha-C12 monoconjugates and diconjugate. Is also able to catalyze the glucuronidation of 17beta-estradiol, 17alpha-ethinylestradiol, 1-hydroxypyrene, 4-methylumbelliferone, 1-naphthol, paranitrophenol, scopoletin, and umbelliferone.
Gene Name:
Uniprot ID:
Molecular weight:
Cyanidin → 3-[(6-carboxy-3,4,5-trihydroxyoxan-2-yl)oxy]-2-(3,4-dihydroxyphenyl)-5,7-dihydroxy-1λ⁴-chromen-1-yliumdetails
Cyanidin → 2-{4-[(6-carboxy-3,4,5-trihydroxyoxan-2-yl)oxy]-3-hydroxyphenyl}-3,5,7-trihydroxy-1λ⁴-chromen-1-yliumdetails
Cyanidin → 2-{3-[(6-carboxy-3,4,5-trihydroxyoxan-2-yl)oxy]-4-hydroxyphenyl}-3,5,7-trihydroxy-1λ⁴-chromen-1-yliumdetails
Cyanidin → 5-[(6-carboxy-3,4,5-trihydroxyoxan-2-yl)oxy]-2-(3,4-dihydroxyphenyl)-3,7-dihydroxy-1λ⁴-chromen-1-yliumdetails
Cyanidin → (6-carboxy-3,4,5-trihydroxyoxan-2-yl)[2-(3,4-dihydroxyphenyl)-3,5-dihydroxy-7H-chromen-7-ylidene]oxidaniumdetails