NP-MRD: Showing NP-Card for Vicenin -1 (NP0140281)

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Record Information

Version

2.0

Created at

2022-06-29 21:21:14 UTC

Updated at

2022-06-29 21:21:14 UTC

NP-MRD ID

NP0140281

Secondary Accession Numbers

None

Natural Product Identification

Common Name

Vicenin -1

Description

Vicenin 1 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. Thus, vicenin 1 is considered to be a flavonoid. Vicenin -1 is found in Linum grandiflorum. Vicenin -1 was first documented in 2018 (PMID: 30223921). Based on a literature review a small amount of articles have been published on Vicenin 1 (PMID: 33475054) (PMID: 35671519) (PMID: 33486798) (PMID: 30961965).

Structure

MOL 3D MOL SDF PDB SMILES InChI


  Mrv1652306292223212D          

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  7 12  1  0  0  0  0
 12 13  1  0  0  0  0
 11 14  1  0  0  0  0
 14 15  2  0  0  0  0
 14 16  1  0  0  0  0
 16 17  2  0  0  0  0
 17 18  1  0  0  0  0
 10 18  1  0  0  0  0
 17 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
 22 23  1  0  0  0  0
 23 24  2  0  0  0  0
 19 24  1  0  0  0  0
 22 25  1  0  0  0  0
 26  9  1  1  0  0  0
 26 27  1  0  0  0  0
 27 28  1  0  0  0  0
 28 29  1  0  0  0  0
 29 30  1  0  0  0  0
 30 31  1  0  0  0  0
 26 31  1  0  0  0  0
 30 32  1  1  0  0  0
 32 33  1  0  0  0  0
 29 34  1  6  0  0  0
 28 35  1  1  0  0  0
 27 36  1  6  0  0  0
  8 37  1  0  0  0  0
  4 38  1  1  0  0  0
  3 39  1  6  0  0  0
  2 40  1  1  0  0  0
M  END
> <DATABASE_ID>
NP0140281

> <DATABASE_NAME>
NP-MRD

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

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

> <FORMULA>
C26H28O14

> <MOLECULAR_WEIGHT>
564.496

> <EXACT_MASS>
564.147905582

> <JCHEM_ACCEPTOR_COUNT>
14

> <JCHEM_ATOM_COUNT>
68

> <JCHEM_AVERAGE_POLARIZABILITY>
53.91316653457515

> <JCHEM_BIOAVAILABILITY>
0

> <JCHEM_DONOR_COUNT>
10

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

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

> <ALOGPS_LOGP>
-0.81

> <JCHEM_LOGP>
-2.1776177343333334

> <ALOGPS_LOGS>
-1.91

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
5

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-1

> <JCHEM_PKA>
7.630283837008169

> <JCHEM_PKA_STRONGEST_ACIDIC>
5.737651672484763

> <JCHEM_PKA_STRONGEST_BASIC>
-3.643190217937482

> <JCHEM_POLAR_SURFACE_AREA>
247.05999999999997

> <JCHEM_REFRACTIVITY>
133.18800000000002

> <JCHEM_ROTATABLE_BOND_COUNT>
4

> <JCHEM_RULE_OF_FIVE>
0

> <ALOGPS_SOLUBILITY>
6.94e+00 g/l

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

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 29-JUN-22   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   29-JUN-22         0                                  
HETATM    1  C   UNK     0      -5.335   0.000   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0      -5.335   1.540   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0      -4.001   2.310   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0      -2.667   1.540   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0      -2.667   0.000   0.000  0.00  0.00           C+0
HETATM    6  O   UNK     0      -4.001  -0.770   0.000  0.00  0.00           O+0
HETATM    7  C   UNK     0      -1.334  -0.770   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0      -1.334  -2.310   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0       0.000  -3.080   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0       1.334  -2.310   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0       1.334  -0.770   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0       0.000  -0.000   0.000  0.00  0.00           C+0
HETATM   13  O   UNK     0       0.000   1.540   0.000  0.00  0.00           O+0
HETATM   14  C   UNK     0       2.667  -0.000   0.000  0.00  0.00           C+0
HETATM   15  O   UNK     0       2.667   1.540   0.000  0.00  0.00           O+0
HETATM   16  C   UNK     0       4.001  -0.770   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0       4.001  -2.310   0.000  0.00  0.00           C+0
HETATM   18  O   UNK     0       2.667  -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       6.668  -2.310   0.000  0.00  0.00           C+0
HETATM   21  C   UNK     0       8.002  -3.080   0.000  0.00  0.00           C+0
HETATM   22  C   UNK     0       8.002  -4.620   0.000  0.00  0.00           C+0
HETATM   23  C   UNK     0       6.668  -5.390   0.000  0.00  0.00           C+0
HETATM   24  C   UNK     0       5.335  -4.620   0.000  0.00  0.00           C+0
HETATM   25  O   UNK     0       9.336  -5.390   0.000  0.00  0.00           O+0
HETATM   26  C   UNK     0       0.000  -4.620   0.000  0.00  0.00           C+0
HETATM   27  C   UNK     0       1.334  -5.390   0.000  0.00  0.00           C+0
HETATM   28  C   UNK     0       1.334  -6.930   0.000  0.00  0.00           C+0
HETATM   29  C   UNK     0       0.000  -7.700   0.000  0.00  0.00           C+0
HETATM   30  C   UNK     0      -1.334  -6.930   0.000  0.00  0.00           C+0
HETATM   31  O   UNK     0      -1.334  -5.390   0.000  0.00  0.00           O+0
HETATM   32  C   UNK     0      -2.667  -7.700   0.000  0.00  0.00           C+0
HETATM   33  O   UNK     0      -4.001  -6.930   0.000  0.00  0.00           O+0
HETATM   34  O   UNK     0       0.000  -9.240   0.000  0.00  0.00           O+0
HETATM   35  O   UNK     0       2.667  -7.700   0.000  0.00  0.00           O+0
HETATM   36  O   UNK     0       2.667  -4.620   0.000  0.00  0.00           O+0
HETATM   37  O   UNK     0      -2.667  -3.080   0.000  0.00  0.00           O+0
HETATM   38  O   UNK     0      -1.334   2.310   0.000  0.00  0.00           O+0
HETATM   39  O   UNK     0      -4.001   3.850   0.000  0.00  0.00           O+0
HETATM   40  O   UNK     0      -6.668   2.310   0.000  0.00  0.00           O+0
CONECT    1    2    6                                                       
CONECT    2    1    3   40                                                  
CONECT    3    2    4   39                                                  
CONECT    4    3    5   38                                                  
CONECT    5    4    6    7                                                  
CONECT    6    5    1                                                       
CONECT    7    5    8   12                                                  
CONECT    8    7    9   37                                                  
CONECT    9    8   10   26                                                  
CONECT   10    9   11   18                                                  
CONECT   11   10   12   14                                                  
CONECT   12   11    7   13                                                  
CONECT   13   12                                                            
CONECT   14   11   15   16                                                  
CONECT   15   14                                                            
CONECT   16   14   17                                                       
CONECT   17   16   18   19                                                  
CONECT   18   17   10                                                       
CONECT   19   17   20   24                                                  
CONECT   20   19   21                                                       
CONECT   21   20   22                                                       
CONECT   22   21   23   25                                                  
CONECT   23   22   24                                                       
CONECT   24   23   19                                                       
CONECT   25   22                                                            
CONECT   26    9   27   31                                                  
CONECT   27   26   28   36                                                  
CONECT   28   27   29   35                                                  
CONECT   29   28   30   34                                                  
CONECT   30   29   31   32                                                  
CONECT   31   30   26                                                       
CONECT   32   30   33                                                       
CONECT   33   32                                                            
CONECT   34   29                                                            
CONECT   35   28                                                            
CONECT   36   27                                                            
CONECT   37    8                                                            
CONECT   38    4                                                            
CONECT   39    3                                                            
CONECT   40    2                                                            
MASTER        0    0    0    0    0    0    0    0   40    0   88    0
END

View in JSmol

Synonyms

Value	Source
Vicenin	MeSH
6-C-beta-D-Xylopyranosyl-8-C-beta-D-glucopyranosyl apigenin	MeSH
Vicenin-1	MeSH

Chemical Formula

C₂₆H₂₈O₁₄

Average Mass

564.4960 Da

Monoisotopic Mass

564.14791 Da

IUPAC Name

Not Available

Traditional Name

Not Available

CAS Registry Number

Not Available

SMILES

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

InChI Identifier

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

OVMFOVNOXASTPA-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
Linum grandiflorum	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

External Links

HMDB ID

Not Available

DrugBank ID

Not Available

Phenol Explorer Compound ID

Not Available

FoodDB ID

Not Available

KNApSAcK ID

C00006176

Chemspider ID

57257122

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

13644663

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

Sun X, Tang X, Yang Q: An effective quantitative fingerprint method for evaluating the quality consistency of Desmodium styracifolium. Pharmazie. 2018 Oct 1;73(10):579-584. doi: 10.1691/ph.2018.8590. [PubMed:30223921 ]
Aumeeruddy MZ, Mahomoodally MF: Ethnomedicinal Plants for the Management of Diabetes Worldwide: A Systematic Review. Curr Med Chem. 2021;28(23):4670-4693. doi: 10.2174/0929867328666210121123037. [PubMed:33475054 ]
Li X, Chen C, Zhang T, Ding N, Zheng P, Yang M: Comparative pharmacokinetic studies of five C-glycosylflavones in normal and urolithiasis model rats following administration of total flavonoids from Desmodium styracifolium by liquid chromatography-tandem mass spectrometry. J Sep Sci. 2022 Aug;45(15):2901-2913. doi: 10.1002/jssc.202200010. Epub 2022 Jun 25. [PubMed:35671519 ]
Feng CY, Li SS, Taguchi G, Wu Q, Yin DD, Gu ZY, Wu J, Xu WZ, Liu C, Wang LS: Enzymatic basis for stepwise C-glycosylation in the formation of flavonoid di-C-glycosides in sacred lotus (Nelumbo nucifera Gaertn.). Plant J. 2021 Apr;106(2):351-365. doi: 10.1111/tpj.15168. Epub 2021 Apr 5. [PubMed:33486798 ]
Chen Y, Yan X, Lu F, Jiang X, Friesen JB, Pauli GF, Chen SN, Li DP: Preparation of flavone di-C-glycoside isomers from Jian-Gu injection (Premna fulva Craib.) using recycling counter-current chromatography. J Chromatogr A. 2019 Aug 16;1599:180-186. doi: 10.1016/j.chroma.2019.03.030. Epub 2019 Mar 21. [PubMed:30961965 ]

Showing NP-Card for Vicenin -1 (NP0140281)

MOL for NP0140281 (Vicenin -1)

3D MOL for NP0140281 (Vicenin -1)

3D SDF for NP0140281 (Vicenin -1)

3D-SDF for NP0140281 (Vicenin -1)

PDB for NP0140281 (Vicenin -1)

3D PDB for NP0140281 (Vicenin -1)

SMILES for NP0140281 (Vicenin -1)

INCHI for NP0140281 (Vicenin -1)

Structure for NP0140281 (Vicenin -1)

3D Structure for NP0140281 (Vicenin -1)