NP-MRD: Showing NP-Card for Cyanidin 3-(6''-acetyl-galactoside) (NP0045232)

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Record Information

Version

2.0

Created at

2022-03-17 19:09:44 UTC

Updated at

2022-03-17 19:09:44 UTC

NP-MRD ID

NP0045232

Secondary Accession Numbers

None

Natural Product Identification

Common Name

Cyanidin 3-(6''-acetyl-galactoside)

Description

Cyanidin 3-(6''-acetyl-galactoside) belongs to the class of organic compounds known as anthocyanidin-3-o-glycosides. These are phenolic compounds containing one anthocyanidin moiety which is O-glycosidically linked to a carbohydrate moiety at the C3-position. Cyanidin 3-(6''-acetyl-galactoside) is an extremely weak basic (essentially neutral) compound (based on its pKa). Outside of the human body, Cyanidin 3-(6''-acetyl-galactoside) is found, on average, in the highest concentration within lowbush blueberries and highbush blueberries. Cyanidin 3-(6''-acetyl-galactoside) is found in Nymphaea alba . This could make cyanidin 3-(6''-acetyl-galactoside) a potential biomarker for the consumption of these foods.

Structure

MOL 3D MOL SDF PDB SMILES InChI

  Mrv1652305231900012D          

 40 43  0  0  1  0            999 V2000
    2.1434    4.5375    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.2868   -2.4750    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.0013   -2.8875    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.0013   -1.2375    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145   -0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289   -1.6500    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8579    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8579    2.4750    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.1434    3.7125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.2868   -1.6500    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
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  3  2  2  0  0  0  0
  9  1  1  0  0  0  0
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 33 22  1  0  0  0  0
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 35 18  1  0  0  0  0
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 18 36  1  1  0  0  0
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 23 40  1  1  0  0  0
M  CHG  1  33   1
M  END

     RDKit          3D

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 21 22  1  0
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 25 24  1  0
 24 23  2  0
  8 30  1  0
 30 31  1  0
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 32 34  1  0
 34 35  1  0
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 11 10  2  0
 23 22  1  0
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  6 41  1  6
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 35 58  1  0
M  CHG  1  20   1
M  END

  Mrv1652305231900012D          

 40 43  0  0  1  0            999 V2000
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 23 40  1  1  0  0  0
M  CHG  1  33   1
M  END
> <DATABASE_ID>
NP0045232

> <DATABASE_NAME>
NP-MRD

> <SMILES>
[H][C@]1(COC(C)=O)O[C@@]([H])(OC2=C([O+]=C3C=C(O)C=C(O)C3=C2)C2=CC(O)=C(O)C=C2)[C@]([H])(O)[C@@]([H])(O)[C@@]1([H])O

> <INCHI_IDENTIFIER>
InChI=1S/C23H22O12/c1-9(24)32-8-18-19(29)20(30)21(31)23(35-18)34-17-7-12-14(27)5-11(25)6-16(12)33-22(17)10-2-3-13(26)15(28)4-10/h2-7,18-21,23,29-31H,8H2,1H3,(H3-,25,26,27,28)/p+1/t18-,19+,20+,21-,23-/m1/s1

> <INCHI_KEY>
HBXXDBKJLPLXPR-DLBZZEGUSA-O

> <FORMULA>
C23H23O12

> <MOLECULAR_WEIGHT>
491.4215

> <EXACT_MASS>
491.1189512

> <JCHEM_ACCEPTOR_COUNT>
11

> <JCHEM_ATOM_COUNT>
58

> <JCHEM_AVERAGE_POLARIZABILITY>
47.40196525223719

> <JCHEM_BIOAVAILABILITY>
0

> <JCHEM_DONOR_COUNT>
7

> <JCHEM_FORMAL_CHARGE>
1

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
3-{[(2S,3R,4S,5R,6R)-6-[(acetyloxy)methyl]-3,4,5-trihydroxyoxan-2-yl]oxy}-2-(3,4-dihydroxyphenyl)-5,7-dihydroxy-1lambda4-chromen-1-ylium

> <ALOGPS_LOGP>
1.14

> <JCHEM_LOGP>
0.8160999999999996

> <ALOGPS_LOGS>
-3.11

> <JCHEM_MDDR_LIKE_RULE>
1

> <JCHEM_NUMBER_OF_RINGS>
4

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
7.4579610956641815

> <JCHEM_PKA_STRONGEST_ACIDIC>
6.388329618750466

> <JCHEM_PKA_STRONGEST_BASIC>
-3.649102880226849

> <JCHEM_POLAR_SURFACE_AREA>
199.50999999999996

> <JCHEM_REFRACTIVITY>
125.40899999999998

> <JCHEM_ROTATABLE_BOND_COUNT>
6

> <JCHEM_RULE_OF_FIVE>
0

> <ALOGPS_SOLUBILITY>
4.12e-01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
3-{[(2S,3R,4S,5R,6R)-6-[(acetyloxy)methyl]-3,4,5-trihydroxyoxan-2-yl]oxy}-2-(3,4-dihydroxyphenyl)-5,7-dihydroxy-1lambda4-chromen-1-ylium

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 23-MAY-19   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   23-MAY-19         0                                  
HETATM    1  C   UNK     0       4.001   8.470   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       8.002  -4.620   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       9.336  -5.390   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       9.336  -2.310   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       1.334  -0.770   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       2.667  -3.080   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       5.335   0.000   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0       5.335   4.620   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0       4.001   6.930   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0       8.002  -3.080   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0       1.334  -2.310   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0       4.001  -0.770   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0      10.669  -4.620   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0       2.667   0.000   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0      10.669  -3.080   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0       4.001  -2.310   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0       6.668  -0.770   0.000  0.00  0.00           C+0
HETATM   18  C   UNK     0       6.668   3.850   0.000  0.00  0.00           C+0
HETATM   19  C   UNK     0       8.002   4.620   0.000  0.00  0.00           C+0
HETATM   20  C   UNK     0       9.336   3.850   0.000  0.00  0.00           C+0
HETATM   21  C   UNK     0       9.336   2.310   0.000  0.00  0.00           C+0
HETATM   22  C   UNK     0       6.668  -2.310   0.000  0.00  0.00           C+0
HETATM   23  C   UNK     0       8.002   1.540   0.000  0.00  0.00           C+0
HETATM   24  O   UNK     0       2.667   6.160   0.000  0.00  0.00           O+0
HETATM   25  O   UNK     0       0.000  -3.080   0.000  0.00  0.00           O+0
HETATM   26  O   UNK     0      12.003  -5.390   0.000  0.00  0.00           O+0
HETATM   27  O   UNK     0       2.667   1.540   0.000  0.00  0.00           O+0
HETATM   28  O   UNK     0      12.003  -2.310   0.000  0.00  0.00           O+0
HETATM   29  O   UNK     0       8.002   6.160   0.000  0.00  0.00           O+0
HETATM   30  O   UNK     0      10.669   4.620   0.000  0.00  0.00           O+0
HETATM   31  O   UNK     0      10.669   1.540   0.000  0.00  0.00           O+0
HETATM   32  O   UNK     0       5.335   6.160   0.000  0.00  0.00           O+0
HETATM   33  O   UNK     0       5.335  -3.080   0.000  0.00  0.00           O+1
HETATM   34  O   UNK     0       8.002  -0.000   0.000  0.00  0.00           O+0
HETATM   35  O   UNK     0       6.668   2.310   0.000  0.00  0.00           O+0
HETATM   36  H   UNK     0       6.668   5.390   0.000  0.00  0.00           H+0
HETATM   37  H   UNK     0       9.336   5.390   0.000  0.00  0.00           H+0
HETATM   38  H   UNK     0      10.669   3.080   0.000  0.00  0.00           H+0
HETATM   39  H   UNK     0       8.002   3.080   0.000  0.00  0.00           H+0
HETATM   40  H   UNK     0       9.336   0.770   0.000  0.00  0.00           H+0
CONECT    1    9                                                            
CONECT    2    3   10                                                       
CONECT    3    2   13                                                       
CONECT    4   10   15                                                       
CONECT    5   11   14                                                       
CONECT    6   11   16                                                       
CONECT    7   12   17                                                       
CONECT    8   18   32                                                       
CONECT    9    1   24   32                                                  
CONECT   10    2    4   22                                                  
CONECT   11    5    6   25                                                  
CONECT   12    7   14   16                                                  
CONECT   13    3   15   26                                                  
CONECT   14    5   12   27                                                  
CONECT   15    4   13   28                                                  
CONECT   16    6   12   33                                                  
CONECT   17    7   22   34                                                  
CONECT   18    8   19   35   36                                             
CONECT   19   18   20   29   37                                             
CONECT   20   19   21   30   38                                             
CONECT   21   20   23   31   39                                             
CONECT   22   10   17   33                                                  
CONECT   23   21   34   35   40                                             
CONECT   24    9                                                            
CONECT   25   11                                                            
CONECT   26   13                                                            
CONECT   27   14                                                            
CONECT   28   15                                                            
CONECT   29   19                                                            
CONECT   30   20                                                            
CONECT   31   21                                                            
CONECT   32    8    9                                                       
CONECT   33   16   22                                                       
CONECT   34   17   23                                                       
CONECT   35   18   23                                                       
CONECT   36   18                                                            
CONECT   37   19                                                            
CONECT   38   20                                                            
CONECT   39   21                                                            
CONECT   40   23                                                            
MASTER        0    0    0    0    0    0    0    0   40    0   86    0
END

View in JSmol

Synonyms

Value	Source
Cyanidin 3-(6-acetylgalactoside)	HMDB
Cyanidin 3-O-(6''-acetyl-galactoside)	HMDB

Chemical Formula

C₂₃H₂₃O₁₂

Average Mass

491.4215 Da

Monoisotopic Mass

491.11895 Da

IUPAC Name

3-{[(2S,3R,4S,5R,6R)-6-[(acetyloxy)methyl]-3,4,5-trihydroxyoxan-2-yl]oxy}-2-(3,4-dihydroxyphenyl)-5,7-dihydroxy-1lambda4-chromen-1-ylium

Traditional Name

3-{[(2S,3R,4S,5R,6R)-6-[(acetyloxy)methyl]-3,4,5-trihydroxyoxan-2-yl]oxy}-2-(3,4-dihydroxyphenyl)-5,7-dihydroxy-1lambda4-chromen-1-ylium

CAS Registry Number

350602-26-5

SMILES

[H][C@]1(COC(C)=O)O[C@@]([H])(OC2=C([O+]=C3C=C(O)C=C(O)C3=C2)C2=CC(O)=C(O)C=C2)[C@]([H])(O)[C@@]([H])(O)[C@@]1([H])O

InChI Identifier

InChI=1S/C23H22O12/c1-9(24)32-8-18-19(29)20(30)21(31)23(35-18)34-17-7-12-14(27)5-11(25)6-16(12)33-22(17)10-2-3-13(26)15(28)4-10/h2-7,18-21,23,29-31H,8H2,1H3,(H3-,25,26,27,28)/p+1/t18-,19+,20+,21-,23-/m1/s1

InChI Key

HBXXDBKJLPLXPR-DLBZZEGUSA-O

Experimental Spectra

Not Available

Predicted Spectra

Spectrum Type	Description	Depositor ID	Depositor Organization	Depositor	Deposition Date	View
1D NMR	¹³C NMR Spectrum (1D, 25 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 100 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 252 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 1000 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 50 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 200 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 75 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 300 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 101 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 400 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 126 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 500 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 151 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 600 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 176 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 700 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 201 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 800 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 226 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 900 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum

Chemical Shift Submissions

Not Available

Species

Species of Origin

Species Name	Source	Reference
Nymphaea alba	Plant	KNApSAcK
Vaccinium angustifolium	FooDB	PHENOL EXPLORER
Vaccinium corymbosum	FooDB	PHENOL EXPLORER

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as anthocyanidin-3-o-glycosides. These are phenolic compounds containing one anthocyanidin moiety which is O-glycosidically linked to a carbohydrate moiety at the C3-position.

Kingdom

Organic compounds

Super Class

Phenylpropanoids and polyketides

Class

Flavonoids

Sub Class

Flavonoid glycosides

Direct Parent

Anthocyanidin-3-O-glycosides

Alternative Parents

Substituents

Anthocyanidin-3-o-glycoside
Flavonoid-3-o-glycoside
3'-hydroxyflavonoid
4'-hydroxyflavonoid
5-hydroxyflavonoid
7-hydroxyflavonoid
Hydroxyflavonoid
Anthocyanidin
Glycosyl compound
O-glycosyl compound
Benzopyran
1-benzopyran
Catechol
1-hydroxy-4-unsubstituted benzenoid
1-hydroxy-2-unsubstituted benzenoid
Phenol
Monocyclic benzene moiety
Benzenoid
Monosaccharide
Oxane
Heteroaromatic compound
Secondary alcohol
Carboxylic acid ester
Polyol
Monocarboxylic acid or derivatives
Acetal
Oxacycle
Organoheterocyclic compound
Carboxylic acid derivative
Hydrocarbon derivative
Organooxygen compound
Organic oxygen compound
Organic oxide
Carbonyl group
Alcohol
Organic cation
Aromatic heteropolycyclic compound

Molecular Framework

Aromatic heteropolycyclic compounds

External Descriptors

Not Available

Physical Properties

State

Not Available

Experimental Properties

Property	Value	Reference
Melting Point	Not Available	Not Available
Boiling Point	Not Available	Not Available
Water Solubility	Not Available	Not Available
LogP	Not Available	Not Available

Predicted Properties

Property	Value	Source
logP	1.14	ALOGPS
logP	0.82	ChemAxon
logS	-3.1	ALOGPS
pKa (Strongest Acidic)	6.39	ChemAxon
pKa (Strongest Basic)	-3.6	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	11	ChemAxon
Hydrogen Donor Count	7	ChemAxon
Polar Surface Area	199.51 Å²	ChemAxon
Rotatable Bond Count	6	ChemAxon
Refractivity	125.41 m³·mol⁻¹	ChemAxon
Polarizability	47.4 Å³	ChemAxon
Number of Rings	4	ChemAxon
Bioavailability	No	ChemAxon
Rule of Five	No	ChemAxon
Ghose Filter	No	ChemAxon
Veber's Rule	No	ChemAxon
MDDR-like Rule	Yes	ChemAxon

External Links

HMDB ID

HMDB0029236

DrugBank ID

Not Available

Phenol Explorer Compound ID

FoodDB ID

FDB000004

KNApSAcK ID

Not Available

Chemspider ID

30776739

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

122396785

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

Not Available

Showing NP-Card for Cyanidin 3-(6''-acetyl-galactoside) (NP0045232)

MOL for NP0045232 (Cyanidin 3-(6''-acetyl-galactoside))

3D MOL for NP0045232 (Cyanidin 3-(6''-acetyl-galactoside))

3D SDF for NP0045232 (Cyanidin 3-(6''-acetyl-galactoside))

3D-SDF for NP0045232 (Cyanidin 3-(6''-acetyl-galactoside))

PDB for NP0045232 (Cyanidin 3-(6''-acetyl-galactoside))

3D PDB for NP0045232 (Cyanidin 3-(6''-acetyl-galactoside))

SMILES for NP0045232 (Cyanidin 3-(6''-acetyl-galactoside))

INCHI for NP0045232 (Cyanidin 3-(6''-acetyl-galactoside))

Structure for NP0045232 (Cyanidin 3-(6''-acetyl-galactoside))

3D Structure for NP0045232 (Cyanidin 3-(6''-acetyl-galactoside))