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Showing NP-Card for Cyanidin 3-(2G-glucosylrutinoside) (NP0048968)

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Record Information
Version2.0
Created at2022-03-17 21:05:01 UTC
Updated at2022-03-17 21:05:01 UTC
NP-MRD IDNP0048968
Secondary Accession NumbersNone
Natural Product Identification
Common NameCyanidin 3-(2G-glucosylrutinoside)
DescriptionCyanidin 3-(2G-glucosylrutinoside) 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-(2G-glucosylrutinoside) is an extremely weak basic (essentially neutral) compound (based on its pKa). Outside of the human body, Cyanidin 3-(2G-glucosylrutinoside) is found, on average, in the highest concentration within a few different foods, such as sour cherries, red raspberries, and redcurrants and in a lower concentration in cloudberries. Cyanidin 3-(2G-glucosylrutinoside) has also been detected, but not quantified in, several different foods, such as fruits, purple mangosteens, blackcurrants, gooseberries, and strawberries. Cyanidin 3-(2G-glucosylrutinoside) is found in Acer buergerianum, Acer circumlobatum, Acer ornatum, Acer palmatum, Acer sieboldianum, Cornus suecica , Dipteronia sinensis, Garcinia mangostana L. and Viburnum lantana L. . This could make cyanidin 3-(2g-glucosylrutinoside) a potential biomarker for the consumption of these foods.
Structure
Thumb
MOLSDFPDBSMILESInChI

MOL for NP0048968 (Cyanidin 3-(2G-glucosylrutinoside))

Cyanidine 3-o-glucosyl-rutinoside
  Mrv1652309231718022D          

 53 58  0  0  0  0            999 V2000
    2.8579    5.7750    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8579    4.9499    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.1434    4.5375    0.0000 O   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
    1.4289    3.3000    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289    2.4749    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145    2.0625    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145    1.2374    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    0.8250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    0.0000    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
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    3.5724   -0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
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    1.4289   -1.6500    0.0000 O   0  3  0  0  0  0  0  0  0  0  0  0
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    0.0000   -1.6500    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000   -2.4749    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
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  2 52  1  0  0  0  0
 52 53  1  0  0  0  0
M  CHG  1  21   1
M  END
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3D MOL for NP0048968 (Cyanidin 3-(2G-glucosylrutinoside))

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3D SDF for NP0048968 (Cyanidin 3-(2G-glucosylrutinoside))
Cyanidine 3-o-glucosyl-rutinoside
  Mrv1652309231718022D          

 53 58  0  0  0  0            999 V2000
    2.8579    5.7750    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8579    4.9499    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.1434    4.5375    0.0000 O   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
    1.4289    3.3000    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
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    0.7145   -0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
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M  CHG  1  21   1
M  END
> <DATABASE_ID>
NP0048968

> <DATABASE_NAME>
NP-MRD

> <SMILES>
CC1OC(OCC2OC(OC3=CC4=C(O)C=C(O)C=C4[O+]=C3C3=CC=C(O)C(O)=C3)C(OC3OC(CO)C(O)C(O)C3O)C(O)C2O)C(O)C(O)C1O

> <INCHI_IDENTIFIER>
InChI=1S/C33H40O20/c1-10-21(39)24(42)27(45)31(48-10)47-9-20-23(41)26(44)30(53-32-28(46)25(43)22(40)19(8-34)51-32)33(52-20)50-18-7-13-15(37)5-12(35)6-17(13)49-29(18)11-2-3-14(36)16(38)4-11/h2-7,10,19-28,30-34,39-46H,8-9H2,1H3,(H3-,35,36,37,38)/p+1

> <INCHI_KEY>
MSUVUDCULKNUJL-UHFFFAOYSA-O

> <FORMULA>
C33H41O20

> <MOLECULAR_WEIGHT>
757.6666

> <EXACT_MASS>
757.219118752

> <JCHEM_ACCEPTOR_COUNT>
20

> <JCHEM_ATOM_COUNT>
94

> <JCHEM_AVERAGE_POLARIZABILITY>
72.6612982494116

> <JCHEM_BIOAVAILABILITY>
0

> <JCHEM_DONOR_COUNT>
13

> <JCHEM_FORMAL_CHARGE>
1

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
3-[(4,5-dihydroxy-3-{[3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}-6-{[(3,4,5-trihydroxy-6-methyloxan-2-yl)oxy]methyl}oxan-2-yl)oxy]-2-(3,4-dihydroxyphenyl)-5,7-dihydroxy-1lambda4-chromen-1-ylium

> <ALOGPS_LOGP>
-0.05

> <JCHEM_LOGP>
-2.7608000000000024

> <ALOGPS_LOGS>
-2.28

> <JCHEM_MDDR_LIKE_RULE>
1

> <JCHEM_NUMBER_OF_RINGS>
6

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-1

> <JCHEM_PKA>
7.457953116791116

> <JCHEM_PKA_STRONGEST_ACIDIC>
6.388326300212073

> <JCHEM_PKA_STRONGEST_BASIC>
-3.678622844118399

> <JCHEM_POLAR_SURFACE_AREA>
331.51000000000005

> <JCHEM_REFRACTIVITY>
179.54040000000015

> <JCHEM_ROTATABLE_BOND_COUNT>
9

> <JCHEM_RULE_OF_FIVE>
0

> <ALOGPS_SOLUBILITY>
4.16e+00 g/l

> <JCHEM_TRADITIONAL_IUPAC>
3-[(4,5-dihydroxy-3-{[3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}-6-{[(3,4,5-trihydroxy-6-methyloxan-2-yl)oxy]methyl}oxan-2-yl)oxy]-2-(3,4-dihydroxyphenyl)-5,7-dihydroxy-1lambda4-chromen-1-ylium

> <JCHEM_VEBER_RULE>
0

$$$$

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3D-SDF for NP0048968 (Cyanidin 3-(2G-glucosylrutinoside))
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PDB for NP0048968 (Cyanidin 3-(2G-glucosylrutinoside))
HEADER    PROTEIN                                 23-SEP-17   NONE
TITLE     NULL                                                        
COMPND    MOLECULE: Cyanidine 3-o-glucosyl-rutinoside                 
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   23-SEP-17         0                                  
HETATM    1  C   UNK     0       5.335  10.780   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       5.335   9.240   0.000  0.00  0.00           C+0
HETATM    3  O   UNK     0       4.001   8.470   0.000  0.00  0.00           O+0
HETATM    4  C   UNK     0       4.001   6.930   0.000  0.00  0.00           C+0
HETATM    5  O   UNK     0       2.667   6.160   0.000  0.00  0.00           O+0
HETATM    6  C   UNK     0       2.667   4.620   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       1.334   3.850   0.000  0.00  0.00           C+0
HETATM    8  O   UNK     0       1.334   2.310   0.000  0.00  0.00           O+0
HETATM    9  C   UNK     0       0.000   1.540   0.000  0.00  0.00           C+0
HETATM   10  O   UNK     0       0.000   0.000   0.000  0.00  0.00           O+0
HETATM   11  C   UNK     0       1.334  -0.770   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0       2.667   0.000   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0       4.001  -0.770   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0       5.335   0.000   0.000  0.00  0.00           C+0
HETATM   15  O   UNK     0       5.335   1.540   0.000  0.00  0.00           O+0
HETATM   16  C   UNK     0       6.668  -0.770   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0       6.668  -2.310   0.000  0.00  0.00           C+0
HETATM   18  O   UNK     0       8.002  -3.080   0.000  0.00  0.00           O+0
HETATM   19  C   UNK     0       5.335  -3.080   0.000  0.00  0.00           C+0
HETATM   20  C   UNK     0       4.001  -2.310   0.000  0.00  0.00           C+0
HETATM   21  O   UNK     0       2.667  -3.080   0.000  0.00  0.00           O+1
HETATM   22  C   UNK     0       1.334  -2.310   0.000  0.00  0.00           C+0
HETATM   23  C   UNK     0       0.000  -3.080   0.000  0.00  0.00           C+0
HETATM   24  C   UNK     0       0.000  -4.620   0.000  0.00  0.00           C+0
HETATM   25  C   UNK     0      -1.334  -5.390   0.000  0.00  0.00           C+0
HETATM   26  C   UNK     0      -2.667  -4.620   0.000  0.00  0.00           C+0
HETATM   27  O   UNK     0      -4.001  -5.390   0.000  0.00  0.00           O+0
HETATM   28  C   UNK     0      -2.667  -3.080   0.000  0.00  0.00           C+0
HETATM   29  O   UNK     0      -4.001  -2.310   0.000  0.00  0.00           O+0
HETATM   30  C   UNK     0      -1.334  -2.310   0.000  0.00  0.00           C+0
HETATM   31  C   UNK     0      -1.334   2.310   0.000  0.00  0.00           C+0
HETATM   32  O   UNK     0      -2.667   1.540   0.000  0.00  0.00           O+0
HETATM   33  C   UNK     0      -4.001   2.310   0.000  0.00  0.00           C+0
HETATM   34  O   UNK     0      -4.001   3.850   0.000  0.00  0.00           O+0
HETATM   35  C   UNK     0      -5.335   4.620   0.000  0.00  0.00           C+0
HETATM   36  C   UNK     0      -5.335   6.160   0.000  0.00  0.00           C+0
HETATM   37  O   UNK     0      -6.668   6.930   0.000  0.00  0.00           O+0
HETATM   38  C   UNK     0      -6.668   3.850   0.000  0.00  0.00           C+0
HETATM   39  O   UNK     0      -8.002   4.620   0.000  0.00  0.00           O+0
HETATM   40  C   UNK     0      -6.668   2.310   0.000  0.00  0.00           C+0
HETATM   41  O   UNK     0      -8.002   1.540   0.000  0.00  0.00           O+0
HETATM   42  C   UNK     0      -5.335   1.540   0.000  0.00  0.00           C+0
HETATM   43  O   UNK     0      -5.335   0.000   0.000  0.00  0.00           O+0
HETATM   44  C   UNK     0      -1.334   3.850   0.000  0.00  0.00           C+0
HETATM   45  O   UNK     0      -2.667   4.620   0.000  0.00  0.00           O+0
HETATM   46  C   UNK     0       0.000   4.620   0.000  0.00  0.00           C+0
HETATM   47  O   UNK     0       0.000   6.160   0.000  0.00  0.00           O+0
HETATM   48  C   UNK     0       5.335   6.160   0.000  0.00  0.00           C+0
HETATM   49  O   UNK     0       5.335   4.620   0.000  0.00  0.00           O+0
HETATM   50  C   UNK     0       6.668   6.930   0.000  0.00  0.00           C+0
HETATM   51  O   UNK     0       8.002   6.160   0.000  0.00  0.00           O+0
HETATM   52  C   UNK     0       6.668   8.470   0.000  0.00  0.00           C+0
HETATM   53  O   UNK     0       8.002   9.240   0.000  0.00  0.00           O+0
CONECT    1    2                                                            
CONECT    2    1    3   52                                                  
CONECT    3    2    4                                                       
CONECT    4    3    5   48                                                  
CONECT    5    4    6                                                       
CONECT    6    5    7                                                       
CONECT    7    6    8   46                                                  
CONECT    8    7    9                                                       
CONECT    9    8   10   31                                                  
CONECT   10    9   11                                                       
CONECT   11   10   12   22                                                  
CONECT   12   11   13                                                       
CONECT   13   12   14   20                                                  
CONECT   14   13   15   16                                                  
CONECT   15   14                                                            
CONECT   16   14   17                                                       
CONECT   17   16   18   19                                                  
CONECT   18   17                                                            
CONECT   19   17   20                                                       
CONECT   20   19   13   21                                                  
CONECT   21   20   22                                                       
CONECT   22   21   11   23                                                  
CONECT   23   22   24   30                                                  
CONECT   24   23   25                                                       
CONECT   25   24   26                                                       
CONECT   26   25   27   28                                                  
CONECT   27   26                                                            
CONECT   28   26   29   30                                                  
CONECT   29   28                                                            
CONECT   30   28   23                                                       
CONECT   31    9   32   44                                                  
CONECT   32   31   33                                                       
CONECT   33   32   34   42                                                  
CONECT   34   33   35                                                       
CONECT   35   34   36   38                                                  
CONECT   36   35   37                                                       
CONECT   37   36                                                            
CONECT   38   35   39   40                                                  
CONECT   39   38                                                            
CONECT   40   38   41   42                                                  
CONECT   41   40                                                            
CONECT   42   40   33   43                                                  
CONECT   43   42                                                            
CONECT   44   31   45   46                                                  
CONECT   45   44                                                            
CONECT   46   44    7   47                                                  
CONECT   47   46                                                            
CONECT   48    4   49   50                                                  
CONECT   49   48                                                            
CONECT   50   48   51   52                                                  
CONECT   51   50                                                            
CONECT   52   50    2   53                                                  
CONECT   53   52                                                            
MASTER        0    0    0    0    0    0    0    0   53    0  116    0
END

Download
3D PDB for NP0048968 (Cyanidin 3-(2G-glucosylrutinoside))
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SMILES for NP0048968 (Cyanidin 3-(2G-glucosylrutinoside))
CC1OC(OCC2OC(OC3=CC4=C(O)C=C(O)C=C4[O+]=C3C3=CC=C(O)C(O)=C3)C(OC3OC(CO)C(O)C(O)C3O)C(O)C2O)C(O)C(O)C1O
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INCHI for NP0048968 (Cyanidin 3-(2G-glucosylrutinoside))
InChI=1S/C33H40O20/c1-10-21(39)24(42)27(45)31(48-10)47-9-20-23(41)26(44)30(53-32-28(46)25(43)22(40)19(8-34)51-32)33(52-20)50-18-7-13-15(37)5-12(35)6-17(13)49-29(18)11-2-3-14(36)16(38)4-11/h2-7,10,19-28,30-34,39-46H,8-9H2,1H3,(H3-,35,36,37,38)/p+1
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View in JSmol
Synonyms
ValueSource
Cyanidin 3-O-glucosyl-rutinosideHMDB
Chemical FormulaC33H41O20
Average Mass757.6666 Da
Monoisotopic Mass757.21912 Da
IUPAC Name3-[(4,5-dihydroxy-3-{[3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}-6-{[(3,4,5-trihydroxy-6-methyloxan-2-yl)oxy]methyl}oxan-2-yl)oxy]-2-(3,4-dihydroxyphenyl)-5,7-dihydroxy-1lambda4-chromen-1-ylium
Traditional Name3-[(4,5-dihydroxy-3-{[3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}-6-{[(3,4,5-trihydroxy-6-methyloxan-2-yl)oxy]methyl}oxan-2-yl)oxy]-2-(3,4-dihydroxyphenyl)-5,7-dihydroxy-1lambda4-chromen-1-ylium
CAS Registry Number55028-57-4
SMILES
CC1OC(OCC2OC(OC3=CC4=C(O)C=C(O)C=C4[O+]=C3C3=CC=C(O)C(O)=C3)C(OC3OC(CO)C(O)C(O)C3O)C(O)C2O)C(O)C(O)C1O
InChI Identifier
InChI=1S/C33H40O20/c1-10-21(39)24(42)27(45)31(48-10)47-9-20-23(41)26(44)30(53-32-28(46)25(43)22(40)19(8-34)51-32)33(52-20)50-18-7-13-15(37)5-12(35)6-17(13)49-29(18)11-2-3-14(36)16(38)4-11/h2-7,10,19-28,30-34,39-46H,8-9H2,1H3,(H3-,35,36,37,38)/p+1
InChI KeyMSUVUDCULKNUJL-UHFFFAOYSA-O
Experimental Spectra
Not Available
Predicted Spectra
Not Available
Chemical Shift Submissions
Not Available
Species
Species of Origin
Species NameSourceReference
Acer buergerianumPlant
Acer circumlobatumPlant
Acer ornatumPlant
Acer palmatumPlant
Acer sieboldianumPlant
Cornus suecicaPlant
Dipteronia sinensisPlant
Fragaria x ananassaFooDB
Garcinia mangostanaFooDB
Garcinia mangostana L.Plant
Photinia melanocarpaFooDB
Prunus aviumFooDB
Prunus cerasusFooDB
Ribes nigrumFooDB
Ribes rubrumFooDB
Ribes uva-crispaFooDB
Rubus chamaemorusFooDB
Rubus idaeusFooDB
Sambucus nigraFooDB
Vaccinium angustifoliumFooDB
Viburnum lantana L.Plant
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.
KingdomOrganic compounds  
Super ClassPhenylpropanoids and polyketides  
ClassFlavonoids  
Sub ClassFlavonoid glycosides  
Direct ParentAnthocyanidin-3-O-glycosides  
Alternative Parents
Substituents
  • Oligosaccharide
    • 

  • Anthocyanidin-3-o-glycoside
    • 

  • Flavonoid-3-o-glycoside
    • 

  • Hydroxyflavonoid
    • 

  • 3'-hydroxyflavonoid
    • 

  • 4'-hydroxyflavonoid
    • 

  • 5-hydroxyflavonoid
    • 

  • 7-hydroxyflavonoid
    • 

  • Anthocyanidin
    • 

  • O-glycosyl compound
    • 

  • Glycosyl compound
    • 

  • 1-benzopyran
    • 

  • Benzopyran
    • 

  • Catechol
    • 

  • 1-hydroxy-2-unsubstituted benzenoid
    • 

  • Phenol
    • 

  • 1-hydroxy-4-unsubstituted benzenoid
    • 

  • Monocyclic benzene moiety
    • 

  • Benzenoid
    • 

  • Oxane
    • 

  • Heteroaromatic compound
    • 

  • Secondary alcohol
    • 

  • Organoheterocyclic compound
    • 

  • Oxacycle
    • 

  • Polyol
    • 

  • Acetal
    • 

  • Primary alcohol
    • 

  • Hydrocarbon derivative
    • 

  • Organic oxygen compound
    • 

  • Alcohol
    • 

  • Organooxygen compound
    • 

  • Organic cation
    • 

  • Aromatic heteropolycyclic compound
Molecular FrameworkAromatic heteropolycyclic compounds
External DescriptorsNot Available
Physical Properties
StateNot Available
Experimental Properties
PropertyValueReference
Melting PointNot AvailableNot Available
Boiling PointNot AvailableNot Available
Water SolubilityNot AvailableNot Available
LogPNot AvailableNot Available
Predicted Properties
PropertyValueSource
logP-0.05ALOGPS
logP-2.8ChemAxon
logS-2.3ALOGPS
pKa (Strongest Acidic)6.39ChemAxon
pKa (Strongest Basic)-3.7ChemAxon
Physiological Charge-1ChemAxon
Hydrogen Acceptor Count20ChemAxon
Hydrogen Donor Count13ChemAxon
Polar Surface Area331.51 ŲChemAxon
Rotatable Bond Count9ChemAxon
Refractivity179.54 m³·mol⁻¹ChemAxon
Polarizability72.66 ųChemAxon
Number of Rings6ChemAxon
BioavailabilityNoChemAxon
Rule of FiveNoChemAxon
Ghose FilterNoChemAxon
Veber's RuleNoChemAxon
MDDR-like RuleYesChemAxon
HMDB IDHMDB0037988  
DrugBank IDNot Available
Phenol Explorer Compound ID21  
FoodDB IDFDB017177  
KNApSAcK IDC00006672  
Chemspider IDNot Available
KEGG Compound IDNot Available
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkNot Available
METLIN IDNot Available
PubChem Compound56671053  
PDB IDNot Available
ChEBI IDNot Available
Good Scents IDNot Available
References
General ReferencesNot Available