NP-MRD: Showing NP-Card for Delphinidin 3'-O-(2''-O-galloyl-beta-galactopyranoside) (NP0057851)

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Record Information

Version

2.0

Created at

2022-04-28 03:13:15 UTC

Updated at

2022-04-28 03:13:16 UTC

NP-MRD ID

NP0057851

Secondary Accession Numbers

None

Natural Product Identification

Common Name

Delphinidin 3'-O-(2''-O-galloyl-beta-galactopyranoside)

Description

[(2S,3R,4S,5R,6R)-2-[5-(3,7-dihydroxy-5-oxo-5H-chromen-2-yl)-2,3-dihydroxyphenoxy]-4,5-dihydroxy-6-(hydroxymethyl)oxan-3-yl][hydroxy(3,4,5-trihydroxyphenyl)methylidene]oxidanium belongs to the class of organic compounds known as anthocyanins. These are organic compounds containing a flavylium ion or 2-phenylchromenylium based skeleton bound to a sugar. Delphinidin 3'-O-(2''-O-galloyl-beta-galactopyranoside) is found in Nymphaea caerulea. Based on a literature review very few articles have been published on [(2S,3R,4S,5R,6R)-2-[5-(3,7-dihydroxy-5-oxo-5H-chromen-2-yl)-2,3-dihydroxyphenoxy]-4,5-dihydroxy-6-(hydroxymethyl)oxan-3-yl][hydroxy(3,4,5-trihydroxyphenyl)methylidene]oxidanium.

Structure

MOL 3D MOL SDF PDB SMILES InChI


  Mrv1652304282205132D          

 44 48  0  0  1  0            999 V2000
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 16 42  1  0  0  0  0
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  1 44  1  0  0  0  0
M  CHG  1   8   1
M  END

     RDKit          3D

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 34 63  1  1
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 32 61  1  6
 33 62  1  0
M  CHG  1  11   1
M  END


  Mrv1652304282205132D          

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    7.1447    0.8250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.8592    1.2375    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    8.5737    0.8250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    8.5737   -0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.8592   -0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    9.2881   -0.4125    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    9.2881    1.2375    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    7.8592    2.0625    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.0013    1.2375    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.5724    2.0625    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0000   -2.4750    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  2  0  0  0  0
  2  3  1  0  0  0  0
  3  4  2  0  0  0  0
  4  5  1  0  0  0  0
  5  6  2  0  0  0  0
  1  6  1  0  0  0  0
  5  7  1  0  0  0  0
  3  8  1  0  0  0  0
  8  9  2  0  0  0  0
  9 10  1  0  0  0  0
 10 11  2  0  0  0  0
  2 11  1  0  0  0  0
 10 12  1  0  0  0  0
  9 13  1  0  0  0  0
 13 14  2  0  0  0  0
 14 15  1  0  0  0  0
 15 16  2  0  0  0  0
 16 17  1  0  0  0  0
 17 18  2  0  0  0  0
 13 18  1  0  0  0  0
 17 19  1  0  0  0  0
 20 19  1  1  0  0  0
 20 21  1  0  0  0  0
 21 22  1  0  0  0  0
 22 23  1  0  0  0  0
 23 24  1  0  0  0  0
 24 25  1  0  0  0  0
 20 25  1  0  0  0  0
 24 26  1  1  0  0  0
 26 27  1  0  0  0  0
 23 28  1  1  0  0  0
 22 29  1  1  0  0  0
 21 30  1  6  0  0  0
 30 31  1  0  0  0  0
 31 32  2  0  0  0  0
 31 33  1  0  0  0  0
 33 34  2  0  0  0  0
 34 35  1  0  0  0  0
 35 36  2  0  0  0  0
 36 37  1  0  0  0  0
 37 38  2  0  0  0  0
 33 38  1  0  0  0  0
 37 39  1  0  0  0  0
 36 40  1  0  0  0  0
 35 41  1  0  0  0  0
 16 42  1  0  0  0  0
 15 43  1  0  0  0  0
  1 44  1  0  0  0  0
M  CHG  1   8   1
M  END
> <DATABASE_ID>
NP0057851

> <DATABASE_NAME>
NP-MRD

> <SMILES>
OC[C@H]1O[C@@H](OC2=CC(=CC(O)=C2O)C2=[O+]C3=CC(O)=CC(O)=C3C=C2O)[C@H](OC(=O)C2=CC(O)=C(O)C(O)=C2)[C@@H](O)[C@H]1O

> <INCHI_IDENTIFIER>
InChI=1S/C28H24O16/c29-8-20-23(38)24(39)26(44-27(40)10-2-14(32)21(36)15(33)3-10)28(43-20)42-19-4-9(1-16(34)22(19)37)25-17(35)7-12-13(31)5-11(30)6-18(12)41-25/h1-7,20,23-24,26,28-29,38-39H,8H2,(H7-,30,31,32,33,34,35,36,37,40)/p+1/t20-,23+,24+,26-,28-/m1/s1

> <INCHI_KEY>
UXXMDNQESOLZEI-JGSGXJSYSA-O

> <FORMULA>
C28H25O16

> <MOLECULAR_WEIGHT>
617.491

> <EXACT_MASS>
617.113711145

> <JCHEM_ACCEPTOR_COUNT>
15

> <JCHEM_ATOM_COUNT>
69

> <JCHEM_AVERAGE_POLARIZABILITY>
57.831149511243694

> <JCHEM_BIOAVAILABILITY>
0

> <JCHEM_DONOR_COUNT>
11

> <JCHEM_FORMAL_CHARGE>
1

> <JCHEM_GHOSE_FILTER>
0

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

> <ALOGPS_LOGP>
2.15

> <JCHEM_LOGP>
2.008899999999999

> <ALOGPS_LOGS>
-3.20

> <JCHEM_MDDR_LIKE_RULE>
1

> <JCHEM_NUMBER_OF_RINGS>
5

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-1

> <JCHEM_PKA>
6.793139135665314

> <JCHEM_PKA_STRONGEST_ACIDIC>
5.988382854700149

> <JCHEM_PKA_STRONGEST_BASIC>
-5.533617594062014

> <JCHEM_POLAR_SURFACE_AREA>
280.43

> <JCHEM_REFRACTIVITY>
154.00310000000002

> <JCHEM_ROTATABLE_BOND_COUNT>
7

> <JCHEM_RULE_OF_FIVE>
0

> <ALOGPS_SOLUBILITY>
4.07e-01 g/l

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

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 28-APR-22   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   28-APR-22         0                                  
HETATM    1  C   UNK     0      -0.000  -3.080   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       1.334  -2.310   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       1.334  -0.770   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       0.000  -0.000   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      -1.334  -2.310   0.000  0.00  0.00           C+0
HETATM    7  O   UNK     0      -2.667  -0.000   0.000  0.00  0.00           O+0
HETATM    8  O   UNK     0       2.667  -0.000   0.000  0.00  0.00           O+1
HETATM    9  C   UNK     0       4.001  -0.770   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0       4.001  -2.310   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0       2.667  -3.080   0.000  0.00  0.00           C+0
HETATM   12  O   UNK     0       5.335  -3.080   0.000  0.00  0.00           O+0
HETATM   13  C   UNK     0       5.335  -0.000   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0       5.335   1.540   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0       6.668   2.310   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0       8.002   1.540   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0       8.002  -0.000   0.000  0.00  0.00           C+0
HETATM   18  C   UNK     0       6.668  -0.770   0.000  0.00  0.00           C+0
HETATM   19  O   UNK     0       9.336  -0.770   0.000  0.00  0.00           O+0
HETATM   20  C   UNK     0       9.336  -2.310   0.000  0.00  0.00           C+0
HETATM   21  C   UNK     0      10.669  -3.080   0.000  0.00  0.00           C+0
HETATM   22  C   UNK     0      10.669  -4.620   0.000  0.00  0.00           C+0
HETATM   23  C   UNK     0       9.336  -5.390   0.000  0.00  0.00           C+0
HETATM   24  C   UNK     0       8.002  -4.620   0.000  0.00  0.00           C+0
HETATM   25  O   UNK     0       8.002  -3.080   0.000  0.00  0.00           O+0
HETATM   26  C   UNK     0       6.668  -5.390   0.000  0.00  0.00           C+0
HETATM   27  O   UNK     0       5.335  -4.620   0.000  0.00  0.00           O+0
HETATM   28  O   UNK     0       9.336  -6.930   0.000  0.00  0.00           O+0
HETATM   29  O   UNK     0      12.003  -5.390   0.000  0.00  0.00           O+0
HETATM   30  O   UNK     0      12.003  -2.310   0.000  0.00  0.00           O+0
HETATM   31  C   UNK     0      12.003  -0.770   0.000  0.00  0.00           C+0
HETATM   32  O   UNK     0      10.669  -0.000   0.000  0.00  0.00           O+0
HETATM   33  C   UNK     0      13.337  -0.000   0.000  0.00  0.00           C+0
HETATM   34  C   UNK     0      13.337   1.540   0.000  0.00  0.00           C+0
HETATM   35  C   UNK     0      14.670   2.310   0.000  0.00  0.00           C+0
HETATM   36  C   UNK     0      16.004   1.540   0.000  0.00  0.00           C+0
HETATM   37  C   UNK     0      16.004  -0.000   0.000  0.00  0.00           C+0
HETATM   38  C   UNK     0      14.670  -0.770   0.000  0.00  0.00           C+0
HETATM   39  O   UNK     0      17.338  -0.770   0.000  0.00  0.00           O+0
HETATM   40  O   UNK     0      17.338   2.310   0.000  0.00  0.00           O+0
HETATM   41  O   UNK     0      14.670   3.850   0.000  0.00  0.00           O+0
HETATM   42  O   UNK     0       9.336   2.310   0.000  0.00  0.00           O+0
HETATM   43  O   UNK     0       6.668   3.850   0.000  0.00  0.00           O+0
HETATM   44  O   UNK     0      -0.000  -4.620   0.000  0.00  0.00           O+0
CONECT    1    2    6   44                                                  
CONECT    2    1    3   11                                                  
CONECT    3    2    4    8                                                  
CONECT    4    3    5                                                       
CONECT    5    4    6    7                                                  
CONECT    6    5    1                                                       
CONECT    7    5                                                            
CONECT    8    3    9                                                       
CONECT    9    8   10   13                                                  
CONECT   10    9   11   12                                                  
CONECT   11   10    2                                                       
CONECT   12   10                                                            
CONECT   13    9   14   18                                                  
CONECT   14   13   15                                                       
CONECT   15   14   16   43                                                  
CONECT   16   15   17   42                                                  
CONECT   17   16   18   19                                                  
CONECT   18   17   13                                                       
CONECT   19   17   20                                                       
CONECT   20   19   21   25                                                  
CONECT   21   20   22   30                                                  
CONECT   22   21   23   29                                                  
CONECT   23   22   24   28                                                  
CONECT   24   23   25   26                                                  
CONECT   25   24   20                                                       
CONECT   26   24   27                                                       
CONECT   27   26                                                            
CONECT   28   23                                                            
CONECT   29   22                                                            
CONECT   30   21   31                                                       
CONECT   31   30   32   33                                                  
CONECT   32   31                                                            
CONECT   33   31   34   38                                                  
CONECT   34   33   35                                                       
CONECT   35   34   36   41                                                  
CONECT   36   35   37   40                                                  
CONECT   37   36   38   39                                                  
CONECT   38   37   33                                                       
CONECT   39   37                                                            
CONECT   40   36                                                            
CONECT   41   35                                                            
CONECT   42   16                                                            
CONECT   43   15                                                            
CONECT   44    1                                                            
MASTER        0    0    0    0    0    0    0    0   44    0   96    0
END

View in JSmol

Synonyms

Not Available

Chemical Formula

C₂₈H₂₅O₁₆

Average Mass

617.4910 Da

Monoisotopic Mass

617.11371 Da

IUPAC Name

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

Traditional Name

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

CAS Registry Number

Not Available

SMILES

OC[C@H]1O[C@@H](OC2=CC(=CC(O)=C2O)C2=[O+]C3=CC(O)=CC(O)=C3C=C2O)[C@H](OC(=O)C2=CC(O)=C(O)C(O)=C2)[C@@H](O)[C@H]1O

InChI Identifier

InChI=1S/C28H24O16/c29-8-20-23(38)24(39)26(44-27(40)10-2-14(32)21(36)15(33)3-10)28(43-20)42-19-4-9(1-16(34)22(19)37)25-17(35)7-12-13(31)5-11(30)6-18(12)41-25/h1-7,20,23-24,26,28-29,38-39H,8H2,(H7-,30,31,32,33,34,35,36,37,40)/p+1/t20-,23+,24+,26-,28-/m1/s1

InChI Key

UXXMDNQESOLZEI-JGSGXJSYSA-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 caerulea	Plant	KNApSAcK

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as anthocyanins. These are organic compounds containing a flavylium ion or 2-phenylchromenylium based skeleton bound to a sugar.

Kingdom

Organic compounds

Super Class

Phenylpropanoids and polyketides

Class

Flavonoids

Sub Class

Flavonoid glycosides

Direct Parent

Anthocyanins

Alternative Parents

Substituents

Anthocyanin
Anthocyanidin-3p-o-glycoside
Hydroxyflavonoid
3'-hydroxyflavonoid
7-hydroxyflavonoid
5-hydroxyflavonoid
4'-hydroxyflavonoid
3-hydroxyflavonoid
Anthocyanidin
Phenolic glycoside
Galloyl ester
Gallic acid or derivatives
Hexose monosaccharide
P-hydroxybenzoic acid alkyl ester
O-glycosyl compound
Glycosyl compound
P-hydroxybenzoic acid ester
M-hydroxybenzoic acid ester
Benzoate ester
Benzopyran
1-benzopyran
Benzenetriol
Benzoic acid or derivatives
Pyrogallol derivative
Phenol ether
Catechol
Phenoxy compound
Benzoyl
Phenol
1-hydroxy-2-unsubstituted benzenoid
1-hydroxy-4-unsubstituted benzenoid
Monosaccharide
Oxane
Monocyclic benzene moiety
Benzenoid
Heteroaromatic compound
Secondary alcohol
Carboxylic acid ester
Polyol
Monocarboxylic acid or derivatives
Acetal
Oxacycle
Carboxylic acid derivative
Organoheterocyclic compound
Hydrocarbon derivative
Alcohol
Primary alcohol
Organic oxygen compound
Organic oxide
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	2.15	ALOGPS
logP	2.01	ChemAxon
logS	-3.2	ALOGPS
pKa (Strongest Acidic)	5.99	ChemAxon
pKa (Strongest Basic)	-5.5	ChemAxon
Physiological Charge	-1	ChemAxon
Hydrogen Acceptor Count	15	ChemAxon
Hydrogen Donor Count	11	ChemAxon
Polar Surface Area	280.43 Å²	ChemAxon
Rotatable Bond Count	7	ChemAxon
Refractivity	154 m³·mol⁻¹	ChemAxon
Polarizability	57.83 Å³	ChemAxon
Number of Rings	5	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

Not Available

DrugBank ID

Not Available

Phenol Explorer Compound ID

Not Available

FoodDB ID

Not Available

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

5316500

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

Not Available

Showing NP-Card for Delphinidin 3'-O-(2''-O-galloyl-beta-galactopyranoside) (NP0057851)

MOL for NP0057851 (Delphinidin 3'-O-(2''-O-galloyl-beta-galactopyranoside))

3D MOL for NP0057851 (Delphinidin 3'-O-(2''-O-galloyl-beta-galactopyranoside))

3D SDF for NP0057851 (Delphinidin 3'-O-(2''-O-galloyl-beta-galactopyranoside))

3D-SDF for NP0057851 (Delphinidin 3'-O-(2''-O-galloyl-beta-galactopyranoside))

PDB for NP0057851 (Delphinidin 3'-O-(2''-O-galloyl-beta-galactopyranoside))

3D PDB for NP0057851 (Delphinidin 3'-O-(2''-O-galloyl-beta-galactopyranoside))

SMILES for NP0057851 (Delphinidin 3'-O-(2''-O-galloyl-beta-galactopyranoside))

INCHI for NP0057851 (Delphinidin 3'-O-(2''-O-galloyl-beta-galactopyranoside))

Structure for NP0057851 (Delphinidin 3'-O-(2''-O-galloyl-beta-galactopyranoside))

3D Structure for NP0057851 (Delphinidin 3'-O-(2''-O-galloyl-beta-galactopyranoside))