NP-MRD: Showing NP-Card for Vicenin III (NP0137586)

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Record Information

Version

2.0

Created at

2022-05-30 16:56:58 UTC

Updated at

2022-05-30 16:56:58 UTC

NP-MRD ID

NP0137586

Secondary Accession Numbers

None

Natural Product Identification

Common Name

Vicenin III

Description

Vicenin III is found in Artemisia herba-alba, Craspedolobium schochii, Ephedra chilensis, Gnetum africanum, Linum grandiflorum, Rhynchosia minima and Scleropyrum pentandrum.

Structure

MOL 3D MOL SDF PDB SMILES InChI


  Mrv1652307301920002D          

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M  END

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 19 30  1  1  0  0  0
 20 22  1  0  0  0  0
 20 23  1  1  0  0  0
 21 25  2  0  0  0  0
 21 27  1  0  0  0  0
 22 24  1  0  0  0  0
 23 25  1  0  0  0  0
 23 28  2  0  0  0  0
 24 26  1  0  0  0  0
 26 29  1  0  0  0  0
 27 31  2  0  0  0  0
 28 31  1  0  0  0  0
 31 32  1  0  0  0  0
 32 34  1  0  0  0  0
 33 34  2  0  0  0  0
 33 35  1  0  0  0  0
 35 36  2  0  0  0  0
 35 37  1  0  0  0  0
 36 38  1  0  0  0  0
 37 39  2  0  0  0  0
 38 40  2  0  0  0  0
 39 40  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0137586

> <DATABASE_NAME>
NP-MRD

> <SMILES>
OC[C@H]1O[C@H]([C@H](O)[C@@H](O)[C@@H]1O)C1=C(O)C([C@@H]2OC[C@@H](O)[C@H](O)[C@H]2O)=C2OC(=CC(=O)C2=C1O)C1=CC=C(O)C=C1

> <INCHI_IDENTIFIER>
InChI=1S/C26H28O14/c27-6-13-18(32)21(35)23(37)26(40-13)15-19(33)14-10(29)5-12(8-1-3-9(28)4-2-8)39-24(14)16(20(15)34)25-22(36)17(31)11(30)7-38-25/h1-5,11,13,17-18,21-23,25-28,30-37H,6-7H2/t11-,13-,17+,18-,21+,22-,23-,25+,26+/m1/s1

> <INCHI_KEY>
MMDUKUSNQNWVET-MCIQUCDDSA-N

> <FORMULA>
C26H28O14

> <MOLECULAR_WEIGHT>
564.496

> <EXACT_MASS>
564.147905582

> <JCHEM_ACCEPTOR_COUNT>
14

> <JCHEM_ATOM_COUNT>
68

> <JCHEM_AVERAGE_POLARIZABILITY>
54.914951401529834

> <JCHEM_BIOAVAILABILITY>
0

> <JCHEM_DONOR_COUNT>
10

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
5,7-dihydroxy-2-(4-hydroxyphenyl)-6-[(2S,3R,4R,5S,6R)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]-8-[(2S,3R,4S,5R)-3,4,5-trihydroxyoxan-2-yl]-4H-chromen-4-one

> <JCHEM_LOGP>
-2.1776177343333334

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
5

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-1

> <JCHEM_PKA>
7.630168354527644

> <JCHEM_PKA_STRONGEST_ACIDIC>
5.737643124492441

> <JCHEM_PKA_STRONGEST_BASIC>
-3.6431904735401384

> <JCHEM_POLAR_SURFACE_AREA>
247.05999999999995

> <JCHEM_REFRACTIVITY>
133.18799999999993

> <JCHEM_ROTATABLE_BOND_COUNT>
4

> <JCHEM_RULE_OF_FIVE>
0

> <JCHEM_TRADITIONAL_IUPAC>
5,7-dihydroxy-2-(4-hydroxyphenyl)-6-[(2S,3R,4R,5S,6R)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]-8-[(2S,3R,4S,5R)-3,4,5-trihydroxyoxan-2-yl]chromen-4-one

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 30-JUL-19   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   30-JUL-19         0                                  
HETATM    1  O   UNK     0      18.298 -12.408   0.000  0.00  0.00           O+0
HETATM    2  O   UNK     0      23.633  -7.788   0.000  0.00  0.00           O+0
HETATM    3  O   UNK     0      20.965 -15.488   0.000  0.00  0.00           O+0
HETATM    4  O   UNK     0      18.298 -17.028   0.000  0.00  0.00           O+0
HETATM    5  O   UNK     0      15.631 -15.488   0.000  0.00  0.00           O+0
HETATM    6  O   UNK     0      19.632  -8.558   0.000  0.00  0.00           O+0
HETATM    7  O   UNK     0      19.632  -5.478   0.000  0.00  0.00           O+0
HETATM    8  O   UNK     0      24.946 -10.088   0.000  0.00  0.00           O+0
HETATM    9  O   UNK     0      19.632 -10.098   0.000  0.00  0.00           O+0
HETATM   10  O   UNK     0      22.299  -3.938   0.000  0.00  0.00           O+0
HETATM   11  O   UNK     0      22.299 -14.718   0.000  0.00  0.00           O+0
HETATM   12  O   UNK     0      14.297 -13.178   0.000  0.00  0.00           O+0
HETATM   13  O   UNK     0      24.994 -14.771   0.000  0.00  0.00           O+0
HETATM   14  O   UNK     0      31.727  -7.735   0.000  0.00  0.00           O+0
HETATM   15  C   UNK     0      19.632 -13.178   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0      19.632 -14.718   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0      18.298 -15.488   0.000  0.00  0.00           C+0
HETATM   18  C   UNK     0      16.965 -14.718   0.000  0.00  0.00           C+0
HETATM   19  C   UNK     0      16.965 -13.178   0.000  0.00  0.00           C+0
HETATM   20  C   UNK     0      22.299  -8.558   0.000  0.00  0.00           C+0
HETATM   21  C   UNK     0      20.965 -12.397   0.000  0.00  0.00           C+0
HETATM   22  C   UNK     0      20.965  -7.788   0.000  0.00  0.00           C+0
HETATM   23  C   UNK     0      22.300 -10.099   0.000  0.00  0.00           C+0
HETATM   24  C   UNK     0      20.965  -6.248   0.000  0.00  0.00           C+0
HETATM   25  C   UNK     0      20.965 -10.868   0.000  0.00  0.00           C+0
HETATM   26  C   UNK     0      22.299  -5.478   0.000  0.00  0.00           C+0
HETATM   27  C   UNK     0      22.300 -13.166   0.000  0.00  0.00           C+0
HETATM   28  C   UNK     0      23.613 -10.868   0.000  0.00  0.00           C+0
HETATM   29  C   UNK     0      23.633  -6.248   0.000  0.00  0.00           C+0
HETATM   30  C   UNK     0      15.631 -12.408   0.000  0.00  0.00           C+0
HETATM   31  C   UNK     0      23.613 -12.387   0.000  0.00  0.00           C+0
HETATM   32  C   UNK     0      24.946 -13.156   0.000  0.00  0.00           C+0
HETATM   33  C   UNK     0      26.280 -10.858   0.000  0.00  0.00           C+0
HETATM   34  C   UNK     0      26.280 -12.387   0.000  0.00  0.00           C+0
HETATM   35  C   UNK     0      27.735 -10.061   0.000  0.00  0.00           C+0
HETATM   36  C   UNK     0      29.072 -10.826   0.000  0.00  0.00           C+0
HETATM   37  C   UNK     0      27.730  -8.521   0.000  0.00  0.00           C+0
HETATM   38  C   UNK     0      30.403 -10.051   0.000  0.00  0.00           C+0
HETATM   39  C   UNK     0      29.060  -7.746   0.000  0.00  0.00           C+0
HETATM   40  C   UNK     0      30.397  -8.511   0.000  0.00  0.00           C+0
CONECT    1   15   19                                                       
CONECT    2   20   29                                                       
CONECT    3   16                                                            
CONECT    4   17                                                            
CONECT    5   18                                                            
CONECT    6   22                                                            
CONECT    7   24                                                            
CONECT    8   28   33                                                       
CONECT    9   25                                                            
CONECT   10   26                                                            
CONECT   11   27                                                            
CONECT   12   30                                                            
CONECT   13   32                                                            
CONECT   14   40                                                            
CONECT   15    1   16   21                                                  
CONECT   16    3   15   17                                                  
CONECT   17    4   16   18                                                  
CONECT   18    5   17   19                                                  
CONECT   19    1   18   30                                                  
CONECT   20    2   22   23                                                  
CONECT   21   15   25   27                                                  
CONECT   22    6   20   24                                                  
CONECT   23   20   25   28                                                  
CONECT   24    7   22   26                                                  
CONECT   25    9   21   23                                                  
CONECT   26   10   24   29                                                  
CONECT   27   11   21   31                                                  
CONECT   28    8   23   31                                                  
CONECT   29    2   26                                                       
CONECT   30   12   19                                                       
CONECT   31   27   28   32                                                  
CONECT   32   13   31   34                                                  
CONECT   33    8   34   35                                                  
CONECT   34   32   33                                                       
CONECT   35   33   36   37                                                  
CONECT   36   35   38                                                       
CONECT   37   35   39                                                       
CONECT   38   36   40                                                       
CONECT   39   37   40                                                       
CONECT   40   14   38   39                                                  
MASTER        0    0    0    0    0    0    0    0   40    0   88    0
END

View in JSmol

Synonyms

Value	Source
2-(4-Hydroxyphenyl)-5,7-dihydroxy-6-beta-D-glucopyranosyl-8-beta-D-xylopyranosyl-4H-1-benzopyran-4-one	ChEBI
5,7-Dihydroxy-2-(4-hydroxyphenyl)-6-[(2S,3R,4R,5S,6R)-3,4,5-trihydroxy-6-(hydroxymethyl)tetrahydro-2H-pyran-2-yl]-8-[(2S,3R,4S,5R)-3,4,5-trihydroxytetrahydro-2H-pyran-2-yl]-4H-chromen-4-one	ChEBI
6-beta-D-Glucopyranosyl-8-beta-D-xylopyranosylapigenin	ChEBI
6-C-beta-D-Glucosyl-8-C-beta-D-xylosyl-4',5,7-trihydroxyflavone	ChEBI
6-C-Glucopyranosyl-8-C-beta-D-xylopyranosylapigenin	ChEBI
6-C-Glucosyl-8-C-xylosylapigenin	ChEBI
Apigenin 8-C-xyloside-6-C-glucoside	ChEBI
Vicenin III	ChEBI
2-(4-Hydroxyphenyl)-5,7-dihydroxy-6-b-D-glucopyranosyl-8-b-D-xylopyranosyl-4H-1-benzopyran-4-one	Generator
2-(4-Hydroxyphenyl)-5,7-dihydroxy-6-β-D-glucopyranosyl-8-β-D-xylopyranosyl-4H-1-benzopyran-4-one	Generator
6-b-D-Glucopyranosyl-8-b-D-xylopyranosylapigenin	Generator
6-Β-D-glucopyranosyl-8-β-D-xylopyranosylapigenin	Generator
6-C-b-D-Glucosyl-8-C-b-D-xylosyl-4',5,7-trihydroxyflavone	Generator
6-C-Β-D-glucosyl-8-C-β-D-xylosyl-4',5,7-trihydroxyflavone	Generator
6-C-Glucopyranosyl-8-C-b-D-xylopyranosylapigenin	Generator
6-C-Glucopyranosyl-8-C-β-D-xylopyranosylapigenin	Generator

Chemical Formula

C₂₆H₂₈O₁₄

Average Mass

564.4960 Da

Monoisotopic Mass

564.14791 Da

IUPAC Name

5,7-dihydroxy-2-(4-hydroxyphenyl)-6-[(2S,3R,4R,5S,6R)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]-8-[(2S,3R,4S,5R)-3,4,5-trihydroxyoxan-2-yl]-4H-chromen-4-one

Traditional Name

5,7-dihydroxy-2-(4-hydroxyphenyl)-6-[(2S,3R,4R,5S,6R)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]-8-[(2S,3R,4S,5R)-3,4,5-trihydroxyoxan-2-yl]chromen-4-one

CAS Registry Number

Not Available

SMILES

OC[C@H]1O[C@H]([C@H](O)[C@@H](O)[C@@H]1O)C1=C(O)C([C@@H]2OC[C@@H](O)[C@H](O)[C@H]2O)=C2OC(=CC(=O)C2=C1O)C1=CC=C(O)C=C1

InChI Identifier

InChI=1S/C26H28O14/c27-6-13-18(32)21(35)23(37)26(40-13)15-19(33)14-10(29)5-12(8-1-3-9(28)4-2-8)39-24(14)16(20(15)34)25-22(36)17(31)11(30)7-38-25/h1-5,11,13,17-18,21-23,25-28,30-37H,6-7H2/t11-,13-,17+,18-,21+,22-,23-,25+,26+/m1/s1

InChI Key

MMDUKUSNQNWVET-MCIQUCDDSA-N

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, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 100 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 252 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 1000 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 50 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 200 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 75 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 300 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 101 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 400 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 126 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 500 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 151 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 600 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 176 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 700 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 201 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 800 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 226 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 900 MHz, H₂O, 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
Artemisia herba-alba	LOTUS Database	35616633
Craspedolobium schochii	LOTUS Database	35616633
Ephedra chilensis	LOTUS Database	35616633
Gnetum africanum	LOTUS Database	35616633
Linum grandiflorum	LOTUS Database	35616633
Rhynchosia minima	LOTUS Database	35616633
Scleropyrum pentandrum	LOTUS Database	35616633

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as flavonoid 8-c-glycosides. Flavonoid 8-C-glycosides are compounds containing a carbohydrate moiety which is C-glycosidically linked to 8-position of a 2-phenylchromen-4-one flavonoid backbone.

Kingdom

Organic compounds

Super Class

Phenylpropanoids and polyketides

Class

Flavonoids

Sub Class

Flavonoid glycosides

Direct Parent

Flavonoid 8-C-glycosides

Alternative Parents

Substituents

Flavonoid-8-c-glycoside
4'-hydroxyflavonoid
5-hydroxyflavonoid
7-hydroxyflavonoid
Flavone
Hydroxyflavonoid
Phenolic glycoside
C-glycosyl compound
Chromone
Glycosyl compound
Benzopyran
1-benzopyran
1-hydroxy-2-unsubstituted benzenoid
Phenol
Pyranone
Pyran
Monocyclic benzene moiety
Oxane
Monosaccharide
Benzenoid
Heteroaromatic compound
Vinylogous acid
Secondary alcohol
Polyol
Oxacycle
Dialkyl ether
Ether
Organoheterocyclic compound
Hydrocarbon derivative
Organic oxygen compound
Organooxygen compound
Primary alcohol
Organic oxide
Alcohol
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	-2.2	ChemAxon
pKa (Strongest Acidic)	5.74	ChemAxon
pKa (Strongest Basic)	-3.6	ChemAxon
Physiological Charge	-1	ChemAxon
Hydrogen Acceptor Count	14	ChemAxon
Hydrogen Donor Count	10	ChemAxon
Polar Surface Area	247.06 Å²	ChemAxon
Rotatable Bond Count	4	ChemAxon
Refractivity	133.19 m³·mol⁻¹	ChemAxon
Polarizability	54.91 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	No	ChemAxon

External Links

HMDB ID

Not Available

DrugBank ID

Not Available

Phenol Explorer Compound ID

Not Available

FoodDB ID

FDB011642

KNApSAcK ID

C00006380

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

185958

PDB ID

Not Available

ChEBI ID

142905

Good Scents ID

Not Available

References

General References

Showing NP-Card for Vicenin III (NP0137586)

MOL for NP0137586 (Vicenin III)

3D MOL for NP0137586 (Vicenin III)

3D SDF for NP0137586 (Vicenin III)

3D-SDF for NP0137586 (Vicenin III)

PDB for NP0137586 (Vicenin III)

3D PDB for NP0137586 (Vicenin III)

SMILES for NP0137586 (Vicenin III)

INCHI for NP0137586 (Vicenin III)

Structure for NP0137586 (Vicenin III)

3D Structure for NP0137586 (Vicenin III)