NP-MRD: Showing NP-Card for Pelargonidin 3-(2gluglucosylrutinoside) (NP0047704)

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Record Information

Version

2.0

Created at

2022-03-17 20:44:34 UTC

Updated at

2022-03-17 20:44:34 UTC

NP-MRD ID

NP0047704

Secondary Accession Numbers

None

Natural Product Identification

Common Name

Pelargonidin 3-(2gluglucosylrutinoside)

Description

Pelargonidin 3-(2glu 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. Pelargonidin 3-(2glu glucosylrutinoside) is an extremely weak basic (essentially neutral) compound (based on its pKa). Outside of the human body, Pelargonidin 3-(2glu glucosylrutinoside) is found, on average, in the highest concentration within red raspberries. Pelargonidin 3-(2glu glucosylrutinoside) has also been detected, but not quantified in, fruits. Pelargonidin 3-(2gluglucosylrutinoside) is found in Callistephus chinensis and Rubus spp. . This could make pelargonidin 3-(2glu glucosylrutinoside) a potential biomarker for the consumption of these foods.

Structure

MOL SDF PDB SMILES InChI

Pelargonidin 3-O-glucosyl-rutinoside
  Mrv1652309231721052D          

 66 71  0  0  1  0            999 V2000
    2.8579   -5.7750    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.1434   -5.3625    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    2.1434   -6.1875    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289   -4.9499    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289   -4.1250    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    1.4289   -3.3000    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145   -3.7125    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
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  2 64  1  0  0  0  0
 64 65  1  6  0  0  0
 64 66  1  6  0  0  0
M  CHG  1  25   1
M  END

Pelargonidin 3-O-glucosyl-rutinoside
  Mrv1652309231721052D          

 66 71  0  0  1  0            999 V2000
    2.8579   -5.7750    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.1434   -5.3625    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    2.1434   -6.1875    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289   -4.9499    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289   -4.1250    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
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    0.7145   -3.7125    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
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   -4.2868   -1.6500    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
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    2.8579   -3.3000    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
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 61 64  1  0  0  0  0
  2 64  1  0  0  0  0
 64 65  1  6  0  0  0
 64 66  1  6  0  0  0
M  CHG  1  25   1
M  END
> <DATABASE_ID>
NP0047704

> <DATABASE_NAME>
NP-MRD

> <SMILES>
[H][C@@]1(C)O[C@@]([H])(OC[C@@]2([H])O[C@@]([H])(OC3=CC4=C(C=C(O)C=C4O)[O+]=C3C3=CC=C(O)C=C3)[C@]([H])(O[C@]3([H])OC(CO)[C@@]([H])(O)[C@]([H])(O)[C@@]3([H])O)[C@@]([H])(O)[C@]2([H])O)[C@]([H])(O)[C@]([H])(O)[C@@]1([H])O

> <INCHI_IDENTIFIER>
InChI=1S/C33H40O19/c1-11-21(38)24(41)27(44)31(47-11)46-10-20-23(40)26(43)30(52-32-28(45)25(42)22(39)19(9-34)50-32)33(51-20)49-18-8-15-16(37)6-14(36)7-17(15)48-29(18)12-2-4-13(35)5-3-12/h2-8,11,19-28,30-34,38-45H,9-10H2,1H3,(H2-,35,36,37)/p+1/t11-,19?,20+,21-,22+,23+,24+,25-,26-,27+,28+,30+,31+,32-,33+/m0/s1

> <INCHI_KEY>
YGSWCXGIDLPEGH-HVZHPKBVSA-O

> <FORMULA>
C33H41O19

> <MOLECULAR_WEIGHT>
741.6672

> <EXACT_MASS>
741.22420413

> <JCHEM_ACCEPTOR_COUNT>
19

> <JCHEM_ATOM_COUNT>
93

> <JCHEM_AVERAGE_POLARIZABILITY>
71.63093487563879

> <JCHEM_BIOAVAILABILITY>
0

> <JCHEM_DONOR_COUNT>
12

> <JCHEM_FORMAL_CHARGE>
1

> <JCHEM_GHOSE_FILTER>
0

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

> <ALOGPS_LOGP>
-0.08

> <JCHEM_LOGP>
-2.4764000000000026

> <ALOGPS_LOGS>
-2.33

> <JCHEM_MDDR_LIKE_RULE>
1

> <JCHEM_NUMBER_OF_RINGS>
6

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
7.535843045578907

> <JCHEM_PKA_STRONGEST_ACIDIC>
6.3968149460864385

> <JCHEM_PKA_STRONGEST_BASIC>
-3.6764969324490426

> <JCHEM_POLAR_SURFACE_AREA>
311.28000000000003

> <JCHEM_REFRACTIVITY>
177.5595

> <JCHEM_ROTATABLE_BOND_COUNT>
9

> <JCHEM_RULE_OF_FIVE>
0

> <ALOGPS_SOLUBILITY>
3.62e+00 g/l

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

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 23-SEP-17   NONE
TITLE     NULL                                                        
COMPND    MOLECULE: Pelargonidin 3-O-glucosyl-rutinoside              
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   23-SEP-17         0                                  
HETATM    1  H   UNK     0       5.335 -10.780   0.000  0.00  0.00           H+0
HETATM    2  C   UNK     0       4.001 -10.010   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       4.001 -11.550   0.000  0.00  0.00           C+0
HETATM    4  O   UNK     0       2.667  -9.240   0.000  0.00  0.00           O+0
HETATM    5  C   UNK     0       2.667  -7.700   0.000  0.00  0.00           C+0
HETATM    6  H   UNK     0       2.667  -6.160   0.000  0.00  0.00           H+0
HETATM    7  O   UNK     0       1.334  -6.930   0.000  0.00  0.00           O+0
HETATM    8  C   UNK     0       0.000  -7.700   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0      -1.334  -6.930   0.000  0.00  0.00           C+0
HETATM   10  H   UNK     0      -1.334  -8.470   0.000  0.00  0.00           H+0
HETATM   11  O   UNK     0      -1.334  -5.390   0.000  0.00  0.00           O+0
HETATM   12  C   UNK     0      -2.667  -4.620   0.000  0.00  0.00           C+0
HETATM   13  H   UNK     0      -4.001  -3.850   0.000  0.00  0.00           H+0
HETATM   14  O   UNK     0      -2.667  -3.080   0.000  0.00  0.00           O+0
HETATM   15  C   UNK     0      -1.334  -2.310   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0       0.000  -3.080   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0       1.334  -2.310   0.000  0.00  0.00           C+0
HETATM   18  C   UNK     0       1.334  -0.770   0.000  0.00  0.00           C+0
HETATM   19  C   UNK     0       2.667   0.000   0.000  0.00  0.00           C+0
HETATM   20  C   UNK     0       4.001  -0.770   0.000  0.00  0.00           C+0
HETATM   21  O   UNK     0       5.335   0.000   0.000  0.00  0.00           O+0
HETATM   22  C   UNK     0       4.001  -2.310   0.000  0.00  0.00           C+0
HETATM   23  C   UNK     0       2.667  -3.080   0.000  0.00  0.00           C+0
HETATM   24  O   UNK     0       2.667  -4.620   0.000  0.00  0.00           O+0
HETATM   25  O   UNK     0       0.000   0.000   0.000  0.00  0.00           O+1
HETATM   26  C   UNK     0      -1.334  -0.770   0.000  0.00  0.00           C+0
HETATM   27  C   UNK     0      -2.667   0.000   0.000  0.00  0.00           C+0
HETATM   28  C   UNK     0      -4.001  -0.770   0.000  0.00  0.00           C+0
HETATM   29  C   UNK     0      -5.335   0.000   0.000  0.00  0.00           C+0
HETATM   30  C   UNK     0      -5.335   1.540   0.000  0.00  0.00           C+0
HETATM   31  O   UNK     0      -6.668   2.310   0.000  0.00  0.00           O+0
HETATM   32  C   UNK     0      -4.001   2.310   0.000  0.00  0.00           C+0
HETATM   33  C   UNK     0      -2.667   1.540   0.000  0.00  0.00           C+0
HETATM   34  C   UNK     0      -4.001  -5.390   0.000  0.00  0.00           C+0
HETATM   35  H   UNK     0      -5.335  -6.160   0.000  0.00  0.00           H+0
HETATM   36  O   UNK     0      -5.335  -4.620   0.000  0.00  0.00           O+0
HETATM   37  C   UNK     0      -6.668  -5.390   0.000  0.00  0.00           C+0
HETATM   38  H   UNK     0      -6.668  -3.850   0.000  0.00  0.00           H+0
HETATM   39  O   UNK     0      -6.668  -6.930   0.000  0.00  0.00           O+0
HETATM   40  C   UNK     0      -8.002  -7.700   0.000  0.00  0.00           C+0
HETATM   41  C   UNK     0      -8.002  -9.240   0.000  0.00  0.00           C+0
HETATM   42  O   UNK     0      -9.336 -10.010   0.000  0.00  0.00           O+0
HETATM   43  C   UNK     0      -9.336  -6.930   0.000  0.00  0.00           C+0
HETATM   44  H   UNK     0     -10.669  -6.160   0.000  0.00  0.00           H+0
HETATM   45  O   UNK     0     -10.669  -7.700   0.000  0.00  0.00           O+0
HETATM   46  C   UNK     0      -9.336  -5.390   0.000  0.00  0.00           C+0
HETATM   47  H   UNK     0      -9.336  -3.850   0.000  0.00  0.00           H+0
HETATM   48  O   UNK     0     -10.669  -4.620   0.000  0.00  0.00           O+0
HETATM   49  C   UNK     0      -8.002  -4.620   0.000  0.00  0.00           C+0
HETATM   50  H   UNK     0      -8.002  -6.160   0.000  0.00  0.00           H+0
HETATM   51  O   UNK     0      -8.002  -3.080   0.000  0.00  0.00           O+0
HETATM   52  C   UNK     0      -4.001  -6.930   0.000  0.00  0.00           C+0
HETATM   53  H   UNK     0      -4.001  -8.470   0.000  0.00  0.00           H+0
HETATM   54  O   UNK     0      -5.335  -7.700   0.000  0.00  0.00           O+0
HETATM   55  C   UNK     0      -2.667  -7.700   0.000  0.00  0.00           C+0
HETATM   56  H   UNK     0      -2.667  -6.160   0.000  0.00  0.00           H+0
HETATM   57  O   UNK     0      -2.667  -9.240   0.000  0.00  0.00           O+0
HETATM   58  C   UNK     0       4.001  -6.930   0.000  0.00  0.00           C+0
HETATM   59  H   UNK     0       5.335  -6.160   0.000  0.00  0.00           H+0
HETATM   60  O   UNK     0       4.001  -5.390   0.000  0.00  0.00           O+0
HETATM   61  C   UNK     0       5.335  -7.700   0.000  0.00  0.00           C+0
HETATM   62  H   UNK     0       6.668  -8.470   0.000  0.00  0.00           H+0
HETATM   63  O   UNK     0       6.668  -6.930   0.000  0.00  0.00           O+0
HETATM   64  C   UNK     0       5.335  -9.240   0.000  0.00  0.00           C+0
HETATM   65  H   UNK     0       4.001  -8.470   0.000  0.00  0.00           H+0
HETATM   66  O   UNK     0       6.668 -10.010   0.000  0.00  0.00           O+0
CONECT    1    2                                                            
CONECT    2    1    3    4   64                                             
CONECT    3    2                                                            
CONECT    4    2    5                                                       
CONECT    5    4    6    7   58                                             
CONECT    6    5                                                            
CONECT    7    5    8                                                       
CONECT    8    7    9                                                       
CONECT    9    8   10   11   55                                             
CONECT   10    9                                                            
CONECT   11    9   12                                                       
CONECT   12   11   13   14   34                                             
CONECT   13   12                                                            
CONECT   14   12   15                                                       
CONECT   15   14   16   26                                                  
CONECT   16   15   17                                                       
CONECT   17   16   18   23                                                  
CONECT   18   17   19   25                                                  
CONECT   19   18   20                                                       
CONECT   20   19   21   22                                                  
CONECT   21   20                                                            
CONECT   22   20   23                                                       
CONECT   23   22   17   24                                                  
CONECT   24   23                                                            
CONECT   25   18   26                                                       
CONECT   26   25   15   27                                                  
CONECT   27   26   28   33                                                  
CONECT   28   27   29                                                       
CONECT   29   28   30                                                       
CONECT   30   29   31   32                                                  
CONECT   31   30                                                            
CONECT   32   30   33                                                       
CONECT   33   32   27                                                       
CONECT   34   12   35   36   52                                             
CONECT   35   34                                                            
CONECT   36   34   37                                                       
CONECT   37   36   38   39   49                                             
CONECT   38   37                                                            
CONECT   39   37   40                                                       
CONECT   40   39   41   43                                                  
CONECT   41   40   42                                                       
CONECT   42   41                                                            
CONECT   43   40   44   45   46                                             
CONECT   44   43                                                            
CONECT   45   43                                                            
CONECT   46   43   47   48   49                                             
CONECT   47   46                                                            
CONECT   48   46                                                            
CONECT   49   46   37   50   51                                             
CONECT   50   49                                                            
CONECT   51   49                                                            
CONECT   52   34   53   54   55                                             
CONECT   53   52                                                            
CONECT   54   52                                                            
CONECT   55   52    9   56   57                                             
CONECT   56   55                                                            
CONECT   57   55                                                            
CONECT   58    5   59   60   61                                             
CONECT   59   58                                                            
CONECT   60   58                                                            
CONECT   61   58   62   63   64                                             
CONECT   62   61                                                            
CONECT   63   61                                                            
CONECT   64   61    2   65   66                                             
CONECT   65   64                                                            
CONECT   66   64                                                            
MASTER        0    0    0    0    0    0    0    0   66    0  142    0
END

View in JSmol

Synonyms

Value	Source
Pelargonidin 3-glucosyl-rutinoside	HMDB
Pelargonidin 3-O-glucosyl-rutinoside	HMDB

Chemical Formula

C₃₃H₄₁O₁₉

Average Mass

741.6672 Da

Monoisotopic Mass

741.22420 Da

IUPAC Name

3-{[(2S,3R,4S,5S,6R)-4,5-dihydroxy-3-{[(2S,3R,4S,5S)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}-6-({[(2R,3R,4R,5R,6S)-3,4,5-trihydroxy-6-methyloxan-2-yl]oxy}methyl)oxan-2-yl]oxy}-5,7-dihydroxy-2-(4-hydroxyphenyl)-1lambda4-chromen-1-ylium

Traditional Name

CAS Registry Number

Not Available

SMILES

[H][C@@]1(C)O[C@@]([H])(OC[C@@]2([H])O[C@@]([H])(OC3=CC4=C(C=C(O)C=C4O)[O+]=C3C3=CC=C(O)C=C3)[C@]([H])(O[C@]3([H])OC(CO)[C@@]([H])(O)[C@]([H])(O)[C@@]3([H])O)[C@@]([H])(O)[C@]2([H])O)[C@]([H])(O)[C@]([H])(O)[C@@]1([H])O

InChI Identifier

InChI=1S/C33H40O19/c1-11-21(38)24(41)27(44)31(47-11)46-10-20-23(40)26(43)30(52-32-28(45)25(42)22(39)19(9-34)50-32)33(51-20)49-18-8-15-16(37)6-14(36)7-17(15)48-29(18)12-2-4-13(35)5-3-12/h2-8,11,19-28,30-34,38-45H,9-10H2,1H3,(H2-,35,36,37)/p+1/t11-,19?,20+,21-,22+,23+,24+,25-,26-,27+,28+,30+,31+,32-,33+/m0/s1

InChI Key

YGSWCXGIDLPEGH-HVZHPKBVSA-O

Experimental Spectra

Not Available

Predicted Spectra

Not Available

Chemical Shift Submissions

Not Available

Species

Species of Origin

Species Name	Source	Reference
Callistephus chinensis	Plant	KNApSAcK
Rubus idaeus	FooDB	PHENOL EXPLORER
Rubus spp.	Plant	KNApSAcK

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

Oligosaccharide
Anthocyanidin-3-o-glycoside
Flavonoid-3-o-glycoside
7-hydroxyflavonoid
5-hydroxyflavonoid
Hydroxyflavonoid
4'-hydroxyflavonoid
Anthocyanidin
Glycosyl compound
O-glycosyl compound
Benzopyran
1-benzopyran
1-hydroxy-4-unsubstituted benzenoid
1-hydroxy-2-unsubstituted benzenoid
Phenol
Oxane
Benzenoid
Monocyclic benzene moiety
Heteroaromatic compound
Secondary alcohol
Organoheterocyclic compound
Oxacycle
Acetal
Polyol
Organooxygen compound
Hydrocarbon derivative
Organic oxygen compound
Alcohol
Primary 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	-0.08	ALOGPS
logP	-2.5	ChemAxon
logS	-2.3	ALOGPS
pKa (Strongest Acidic)	6.4	ChemAxon
pKa (Strongest Basic)	-3.7	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	19	ChemAxon
Hydrogen Donor Count	12	ChemAxon
Polar Surface Area	311.28 Å²	ChemAxon
Rotatable Bond Count	9	ChemAxon
Refractivity	177.56 m³·mol⁻¹	ChemAxon
Polarizability	71.63 Å³	ChemAxon
Number of Rings	6	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

HMDB0033689

DrugBank ID

Not Available

Phenol Explorer Compound ID

FoodDB ID

FDB011792

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

131751479

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

Not Available

Showing NP-Card for Pelargonidin 3-(2gluglucosylrutinoside) (NP0047704)

MOL for NP0047704 (Pelargonidin 3-(2gluglucosylrutinoside))

3D MOL for NP0047704 (Pelargonidin 3-(2gluglucosylrutinoside))

3D SDF for NP0047704 (Pelargonidin 3-(2gluglucosylrutinoside))

3D-SDF for NP0047704 (Pelargonidin 3-(2gluglucosylrutinoside))

PDB for NP0047704 (Pelargonidin 3-(2gluglucosylrutinoside))

3D PDB for NP0047704 (Pelargonidin 3-(2gluglucosylrutinoside))

SMILES for NP0047704 (Pelargonidin 3-(2gluglucosylrutinoside))

INCHI for NP0047704 (Pelargonidin 3-(2gluglucosylrutinoside))

Structure for NP0047704 (Pelargonidin 3-(2gluglucosylrutinoside))

3D Structure for NP0047704 (Pelargonidin 3-(2gluglucosylrutinoside))