NP-MRD: Showing NP-Card for Peonidin 3-arabinoside (NP0049008)

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Record Information

Version

2.0

Created at

2022-03-17 21:05:40 UTC

Updated at

2022-03-17 21:05:40 UTC

NP-MRD ID

NP0049008

Secondary Accession Numbers

None

Natural Product Identification

Common Name

Peonidin 3-arabinoside

Description

3-Caffeoylpelargonidin 5-glucoside belongs to the class of organic compounds known as anthocyanidin-5-o-glycosides. These are phenolic compounds containing one anthocyanidin moiety which is O-glycosidically linked to a carbohydrate moiety at the C5-position. 3-Caffeoylpelargonidin 5-glucoside is an extremely weak basic (essentially neutral) compound (based on its pKa). Outside of the human body, 3-Caffeoylpelargonidin 5-glucoside has been detected, but not quantified in, root vegetables. Peonidin 3-arabinoside is found in Gaylussacia spp., Phalaris arundinacea, Prunus laurocerasus and Vaccinium padifolium. This could make 3-caffeoylpelargonidin 5-glucoside a potential biomarker for the consumption of these foods.

Structure

MOL SDF PDB SMILES InChI


  Mrv0541 02241210252D          

 31 34  0  0  0  0            999 V2000
    1.2533   -0.5602    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.6820    3.5649    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.9670    3.1523    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.9670    2.3273    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.2533    1.9148    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.2533    1.0898    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.9670    0.6773    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.6820    1.0898    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.6820    1.9148    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.3970    2.3273    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6053   -1.3866    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6053   -0.5616    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3190   -0.1491    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3190    0.6759    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.0340    1.0884    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6053    1.0884    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8903    0.6759    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8903   -0.1477    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1767   -0.5602    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.5383   -0.1477    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.5383    0.6773    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1767    1.0884    0.0000 O   0  3  0  0  0  0  0  0  0  0  0  0
    0.5859   -1.8701    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.8408   -2.6547    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    1.6658   -2.6547    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    1.9207   -1.8700    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    1.2533   -1.3852    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    2.7053   -1.6151    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.1507   -3.3221    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.3559   -3.3221    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.6915   -4.0758    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  1 20  1  0  0  0  0
  2  3  1  0  0  0  0
  3  4  1  0  0  0  0
  4  5  1  0  0  0  0
  4  9  2  0  0  0  0
  5  6  2  0  0  0  0
  6  7  1  0  0  0  0
  6 21  1  0  0  0  0
  7  8  2  0  0  0  0
  8  9  1  0  0  0  0
  9 10  1  0  0  0  0
 11 12  1  0  0  0  0
 12 13  2  0  0  0  0
 12 18  1  0  0  0  0
 13 14  1  0  0  0  0
 14 15  1  0  0  0  0
 14 16  2  0  0  0  0
 16 17  1  0  0  0  0
 17 18  2  0  0  0  0
 17 22  1  0  0  0  0
 18 19  1  0  0  0  0
 19 20  2  0  0  0  0
 20 21  1  0  0  0  0
 21 22  2  0  0  0  0
 27  1  1  6  0  0  0
 23 24  1  0  0  0  0
 24 25  1  0  0  0  0
 25 26  1  0  0  0  0
 26 27  1  0  0  0  0
 23 27  1  0  0  0  0
 26 28  1  1  0  0  0
 25 29  1  6  0  0  0
 24 30  1  1  0  0  0
 30 31  1  0  0  0  0
M  CHG  1  22   1
M  END


  Mrv0541 02241210252D          

 31 34  0  0  0  0            999 V2000
    1.2533   -0.5602    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.6820    3.5649    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.9670    3.1523    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.9670    2.3273    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.2533    1.9148    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.2533    1.0898    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.9670    0.6773    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.6820    1.0898    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.6820    1.9148    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.3970    2.3273    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6053   -1.3866    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6053   -0.5616    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3190   -0.1491    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3190    0.6759    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.0340    1.0884    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6053    1.0884    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8903    0.6759    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8903   -0.1477    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1767   -0.5602    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.5383   -0.1477    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.5383    0.6773    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1767    1.0884    0.0000 O   0  3  0  0  0  0  0  0  0  0  0  0
    0.5859   -1.8701    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.8408   -2.6547    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    1.6658   -2.6547    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    1.9207   -1.8700    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    1.2533   -1.3852    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    2.7053   -1.6151    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.1507   -3.3221    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.3559   -3.3221    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.6915   -4.0758    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  1 20  1  0  0  0  0
  2  3  1  0  0  0  0
  3  4  1  0  0  0  0
  4  5  1  0  0  0  0
  4  9  2  0  0  0  0
  5  6  2  0  0  0  0
  6  7  1  0  0  0  0
  6 21  1  0  0  0  0
  7  8  2  0  0  0  0
  8  9  1  0  0  0  0
  9 10  1  0  0  0  0
 11 12  1  0  0  0  0
 12 13  2  0  0  0  0
 12 18  1  0  0  0  0
 13 14  1  0  0  0  0
 14 15  1  0  0  0  0
 14 16  2  0  0  0  0
 16 17  1  0  0  0  0
 17 18  2  0  0  0  0
 17 22  1  0  0  0  0
 18 19  1  0  0  0  0
 19 20  2  0  0  0  0
 20 21  1  0  0  0  0
 21 22  2  0  0  0  0
 27  1  1  6  0  0  0
 23 24  1  0  0  0  0
 24 25  1  0  0  0  0
 25 26  1  0  0  0  0
 26 27  1  0  0  0  0
 23 27  1  0  0  0  0
 26 28  1  1  0  0  0
 25 29  1  6  0  0  0
 24 30  1  1  0  0  0
 30 31  1  0  0  0  0
M  CHG  1  22   1
M  END
> <DATABASE_ID>
NP0049008

> <DATABASE_NAME>
NP-MRD

> <SMILES>
COC1=C(O)C=CC(=C1)C1=[O+]C2=C(C=C1O[C@H]1O[C@H](CO)[C@@H](O)[C@@H]1O)C(O)=CC(O)=C2

> <INCHI_IDENTIFIER>
InChI=1S/C21H20O10/c1-28-15-4-9(2-3-12(15)24)20-16(30-21-19(27)18(26)17(8-22)31-21)7-11-13(25)5-10(23)6-14(11)29-20/h2-7,17-19,21-22,26-27H,8H2,1H3,(H2-,23,24,25)/p+1/t17-,18-,19+,21+/m1/s1

> <INCHI_KEY>
KGHFAKPGOXLHAB-BNDYYXHWSA-O

> <FORMULA>
C21H21O10

> <MOLECULAR_WEIGHT>
433.3854

> <EXACT_MASS>
433.113471892

> <JCHEM_ACCEPTOR_COUNT>
9

> <JCHEM_AVERAGE_POLARIZABILITY>
42.33865484929726

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
6

> <JCHEM_FORMAL_CHARGE>
1

> <JCHEM_GHOSE_FILTER>
1

> <JCHEM_IUPAC>
3-{[(2R,3S,4S,5R)-3,4-dihydroxy-5-(hydroxymethyl)oxolan-2-yl]oxy}-5,7-dihydroxy-2-(4-hydroxy-3-methoxyphenyl)-1λ⁴-chromen-1-ylium

> <ALOGPS_LOGP>
1.62

> <JCHEM_LOGP>
1.0912000000000002

> <ALOGPS_LOGS>
-3.31

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
4

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
7.538795589957727

> <JCHEM_PKA_STRONGEST_ACIDIC>
6.3955253035299835

> <JCHEM_PKA_STRONGEST_BASIC>
-2.9811524252368704

> <JCHEM_POLAR_SURFACE_AREA>
162.21

> <JCHEM_REFRACTIVITY>
114.77729999999997

> <JCHEM_ROTATABLE_BOND_COUNT>
5

> <JCHEM_RULE_OF_FIVE>
0

> <ALOGPS_SOLUBILITY>
2.29e-01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
3-{[(2R,3S,4S,5R)-3,4-dihydroxy-5-(hydroxymethyl)oxolan-2-yl]oxy}-5,7-dihydroxy-2-(4-hydroxy-3-methoxyphenyl)-1λ⁴-chromen-1-ylium

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 24-FEB-12   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   24-FEB-12         0                                  
HETATM    1  O   UNK     0       2.339  -1.046   0.000  0.00  0.00           O+0
HETATM    2  C   UNK     0       5.006   6.654   0.000  0.00  0.00           C+0
HETATM    3  O   UNK     0       3.672   5.884   0.000  0.00  0.00           O+0
HETATM    4  C   UNK     0       3.672   4.344   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       2.339   3.574   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       2.339   2.034   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       3.672   1.264   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0       5.006   2.034   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0       5.006   3.574   0.000  0.00  0.00           C+0
HETATM   10  O   UNK     0       6.341   4.344   0.000  0.00  0.00           O+0
HETATM   11  O   UNK     0      -2.997  -2.588   0.000  0.00  0.00           O+0
HETATM   12  C   UNK     0      -2.997  -1.048   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0      -4.329  -0.278   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0      -4.329   1.262   0.000  0.00  0.00           C+0
HETATM   15  O   UNK     0      -5.663   2.032   0.000  0.00  0.00           O+0
HETATM   16  C   UNK     0      -2.997   2.032   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0      -1.662   1.262   0.000  0.00  0.00           C+0
HETATM   18  C   UNK     0      -1.662  -0.276   0.000  0.00  0.00           C+0
HETATM   19  C   UNK     0      -0.330  -1.046   0.000  0.00  0.00           C+0
HETATM   20  C   UNK     0       1.005  -0.276   0.000  0.00  0.00           C+0
HETATM   21  C   UNK     0       1.005   1.264   0.000  0.00  0.00           C+0
HETATM   22  O   UNK     0      -0.330   2.032   0.000  0.00  0.00           O+1
HETATM   23  O   UNK     0       1.094  -3.491   0.000  0.00  0.00           O+0
HETATM   24  C   UNK     0       1.569  -4.955   0.000  0.00  0.00           C+0
HETATM   25  C   UNK     0       3.109  -4.955   0.000  0.00  0.00           C+0
HETATM   26  C   UNK     0       3.585  -3.491   0.000  0.00  0.00           C+0
HETATM   27  C   UNK     0       2.339  -2.586   0.000  0.00  0.00           C+0
HETATM   28  O   UNK     0       5.050  -3.015   0.000  0.00  0.00           O+0
HETATM   29  O   UNK     0       4.015  -6.201   0.000  0.00  0.00           O+0
HETATM   30  C   UNK     0       0.664  -6.201   0.000  0.00  0.00           C+0
HETATM   31  O   UNK     0       1.291  -7.608   0.000  0.00  0.00           O+0
CONECT    1   20   27                                                       
CONECT    2    3                                                            
CONECT    3    2    4                                                       
CONECT    4    3    5    9                                                  
CONECT    5    4    6                                                       
CONECT    6    5    7   21                                                  
CONECT    7    6    8                                                       
CONECT    8    7    9                                                       
CONECT    9    4    8   10                                                  
CONECT   10    9                                                            
CONECT   11   12                                                            
CONECT   12   11   13   18                                                  
CONECT   13   12   14                                                       
CONECT   14   13   15   16                                                  
CONECT   15   14                                                            
CONECT   16   14   17                                                       
CONECT   17   16   18   22                                                  
CONECT   18   12   17   19                                                  
CONECT   19   18   20                                                       
CONECT   20    1   19   21                                                  
CONECT   21    6   20   22                                                  
CONECT   22   17   21                                                       
CONECT   23   24   27                                                       
CONECT   24   23   25   30                                                  
CONECT   25   24   26   29                                                  
CONECT   26   25   27   28                                                  
CONECT   27    1   26   23                                                  
CONECT   28   26                                                            
CONECT   29   25                                                            
CONECT   30   24   31                                                       
CONECT   31   30                                                            
MASTER        0    0    0    0    0    0    0    0   31    0   68    0
END

View in JSmol

Synonyms

Value	Source
Peonidin 3-O-arabinoside	HMDB

Chemical Formula

C₂₁H₂₁O₁₀

Average Mass

433.3854 Da

Monoisotopic Mass

433.11347 Da

IUPAC Name

3-{[(2R,3S,4S,5R)-3,4-dihydroxy-5-(hydroxymethyl)oxolan-2-yl]oxy}-5,7-dihydroxy-2-(4-hydroxy-3-methoxyphenyl)-1λ⁴-chromen-1-ylium

Traditional Name

3-{[(2R,3S,4S,5R)-3,4-dihydroxy-5-(hydroxymethyl)oxolan-2-yl]oxy}-5,7-dihydroxy-2-(4-hydroxy-3-methoxyphenyl)-1λ⁴-chromen-1-ylium

CAS Registry Number

27214-74-0

SMILES

COC1=C(O)C=CC(=C1)C1=[O+]C2=C(C=C1O[C@H]1O[C@H](CO)[C@@H](O)[C@@H]1O)C(O)=CC(O)=C2

InChI Identifier

InChI=1S/C21H20O10/c1-28-15-4-9(2-3-12(15)24)20-16(30-21-19(27)18(26)17(8-22)31-21)7-11-13(25)5-10(23)6-14(11)29-20/h2-7,17-19,21-22,26-27H,8H2,1H3,(H2-,23,24,25)/p+1/t17-,18-,19+,21+/m1/s1

InChI Key

KGHFAKPGOXLHAB-BNDYYXHWSA-O

Experimental Spectra

Not Available

Predicted Spectra

Not Available

Chemical Shift Submissions

Not Available

Species

Species of Origin

Species Name	Source	Reference
Allium cepa	FooDB	KNAPSACK
Empetrum nigrum	FooDB	KNAPSACK
Gaylussacia spp.	Plant	KNApSAcK
Phalaris arundinacea	Plant	KNApSAcK
Photinia melanocarpa	FooDB	PHENOL EXPLORER
Prunus laurocerasus	Plant	KNApSAcK
Vaccinium angustifolium	FooDB	11312849
Vaccinium corymbosum	FooDB	Kader, F., Rove, B., Girardin, M., and Metche, M. (1996). Fractionation and identification of the...
Vaccinium macrocarpon	FooDB	11312849
Vaccinium myrtillus	FooDB	Dr. Duke's Phytochemical and Ethnobotanical Databases
Vaccinium padifolium	Plant	KNApSAcK
Vaccinium vitis-idaea	FooDB	PHENOL EXPLORER
Vitis aestivalis	FooDB	PHENOL EXPLORER
Vitis vinifera L.	FooDB	PHENOL EXPLORER

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as anthocyanidin-5-o-glycosides. These are phenolic compounds containing one anthocyanidin moiety which is O-glycosidically linked to a carbohydrate moiety at the C5-position.

Kingdom

Organic compounds

Super Class

Phenylpropanoids and polyketides

Class

Flavonoids

Sub Class

Flavonoid glycosides

Direct Parent

Anthocyanidin-5-O-glycosides

Alternative Parents

Substituents

Anthocyanidin-5-o-glycoside
Hydroxyflavonoid
4'-hydroxyflavonoid
7-hydroxyflavonoid
Anthocyanidin
Phenolic glycoside
Hexose monosaccharide
Hydroxycinnamic acid or derivatives
Coumaric acid or derivatives
Cinnamic acid or derivatives
Cinnamic acid ester
O-glycosyl compound
Glycosyl compound
Benzopyran
1-benzopyran
Catechol
Styrene
1-hydroxy-2-unsubstituted benzenoid
Fatty acid ester
Phenol
1-hydroxy-4-unsubstituted benzenoid
Oxane
Benzenoid
Fatty acyl
Monocyclic benzene moiety
Monosaccharide
Heteroaromatic compound
Alpha,beta-unsaturated carboxylic ester
Enoate ester
Carboxylic acid ester
Secondary alcohol
Polyol
Carboxylic acid derivative
Organoheterocyclic compound
Oxacycle
Acetal
Monocarboxylic acid or derivatives
Primary alcohol
Organic oxide
Organic oxygen compound
Carbonyl group
Hydrocarbon derivative
Alcohol
Organooxygen compound
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	1.62	ALOGPS
logP	1.09	ChemAxon
logS	-3.3	ALOGPS
pKa (Strongest Acidic)	6.4	ChemAxon
pKa (Strongest Basic)	-3	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	9	ChemAxon
Hydrogen Donor Count	6	ChemAxon
Polar Surface Area	162.21 Å²	ChemAxon
Rotatable Bond Count	5	ChemAxon
Refractivity	114.78 m³·mol⁻¹	ChemAxon
Polarizability	42.34 Å³	ChemAxon
Number of Rings	4	ChemAxon
Bioavailability	Yes	ChemAxon
Rule of Five	No	ChemAxon
Ghose Filter	Yes	ChemAxon
Veber's Rule	No	ChemAxon
MDDR-like Rule	No	ChemAxon

External Links

HMDB ID

HMDB0038087

DrugBank ID

Not Available

Phenol Explorer Compound ID

Not Available

FoodDB ID

FDB017301

KNApSAcK ID

Not Available

Chemspider ID

Not Available

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

131752292

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

Not Available

Showing NP-Card for Peonidin 3-arabinoside (NP0049008)

MOL for NP0049008 (Peonidin 3-arabinoside)

3D MOL for NP0049008 (Peonidin 3-arabinoside)

3D SDF for NP0049008 (Peonidin 3-arabinoside)

3D-SDF for NP0049008 (Peonidin 3-arabinoside)

PDB for NP0049008 (Peonidin 3-arabinoside)

3D PDB for NP0049008 (Peonidin 3-arabinoside)

SMILES for NP0049008 (Peonidin 3-arabinoside)

INCHI for NP0049008 (Peonidin 3-arabinoside)

Structure for NP0049008 (Peonidin 3-arabinoside)

3D Structure for NP0049008 (Peonidin 3-arabinoside)