NP-MRD: Showing NP-Card for Herbacetin 8-(2'',3''-diacetylxyloside) (NP0053917)

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Record Information

Version

2.0

Created at

2022-04-28 00:25:40 UTC

Updated at

2022-04-28 00:25:40 UTC

NP-MRD ID

NP0053917

Secondary Accession Numbers

None

Natural Product Identification

Common Name

Herbacetin 8-(2'',3''-diacetylxyloside)

Description

(2R,3R,4S,5S)-4-(acetyloxy)-5-hydroxy-2-{[3,5,7-trihydroxy-2-(4-hydroxyphenyl)-4-oxo-4H-chromen-8-yl]oxy}oxan-3-yl acetate belongs to the class of organic compounds known as flavonoid-8-o-glycosides. These are phenolic compounds containing a flavonoid moiety which is O-glycosidically linked to carbohydrate moiety at the C8-position. Herbacetin 8-(2'',3''-diacetylxyloside) is found in Rhodiola algida and Rhodiola gelida. Based on a literature review very few articles have been published on (2R,3R,4S,5S)-4-(acetyloxy)-5-hydroxy-2-{[3,5,7-trihydroxy-2-(4-hydroxyphenyl)-4-oxo-4H-chromen-8-yl]oxy}oxan-3-yl acetate.

Structure

MOL 3D MOL SDF PDB SMILES InChI


  Mrv1652304282202252D          

 37 40  0  0  1  0            999 V2000
   -0.7145   -0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7145   -1.2375    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
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    0.7145   -1.2375    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145   -0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000   -0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    0.8250    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
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   -0.7145    2.0625    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
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M  END

     RDKit          3D

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M  END


  Mrv1652304282202252D          

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M  END
> <DATABASE_ID>
NP0053917

> <DATABASE_NAME>
NP-MRD

> <SMILES>
CC(=O)O[C@H]1[C@@H](O)CO[C@H](OC2=C3OC(=C(O)C(=O)C3=C(O)C=C2O)C2=CC=C(O)C=C2)[C@@H]1OC(C)=O

> <INCHI_IDENTIFIER>
InChI=1S/C24H22O13/c1-9(25)34-21-15(30)8-33-24(23(21)35-10(2)26)37-20-14(29)7-13(28)16-17(31)18(32)19(36-22(16)20)11-3-5-12(27)6-4-11/h3-7,15,21,23-24,27-30,32H,8H2,1-2H3/t15-,21-,23+,24+/m0/s1

> <INCHI_KEY>
XISTWCWMRYYNJX-VZQIUVLXSA-N

> <FORMULA>
C24H22O13

> <MOLECULAR_WEIGHT>
518.427

> <EXACT_MASS>
518.106040768

> <JCHEM_ACCEPTOR_COUNT>
11

> <JCHEM_ATOM_COUNT>
59

> <JCHEM_AVERAGE_POLARIZABILITY>
48.44857804141782

> <JCHEM_BIOAVAILABILITY>
0

> <JCHEM_DONOR_COUNT>
5

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(2R,3R,4S,5S)-4-(acetyloxy)-5-hydroxy-2-{[3,5,7-trihydroxy-2-(4-hydroxyphenyl)-4-oxo-4H-chromen-8-yl]oxy}oxan-3-yl acetate

> <ALOGPS_LOGP>
2.31

> <JCHEM_LOGP>
1.400817133333334

> <ALOGPS_LOGS>
-2.90

> <JCHEM_MDDR_LIKE_RULE>
1

> <JCHEM_NUMBER_OF_RINGS>
4

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-1

> <JCHEM_PKA>
8.11594972292615

> <JCHEM_PKA_STRONGEST_ACIDIC>
6.762703001363498

> <JCHEM_PKA_STRONGEST_BASIC>
-3.5421079363998533

> <JCHEM_POLAR_SURFACE_AREA>
198.51

> <JCHEM_REFRACTIVITY>
121.3471

> <JCHEM_ROTATABLE_BOND_COUNT>
7

> <JCHEM_RULE_OF_FIVE>
0

> <ALOGPS_SOLUBILITY>
6.48e-01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
(2R,3R,4S,5S)-4-(acetyloxy)-5-hydroxy-2-{[3,5,7-trihydroxy-2-(4-hydroxyphenyl)-4-oxochromen-8-yl]oxy}oxan-3-yl acetate

> <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      -1.334  -0.770   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       0.000  -3.080   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       1.334  -2.310   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       0.000  -0.000   0.000  0.00  0.00           C+0
HETATM    7  O   UNK     0       0.000   1.540   0.000  0.00  0.00           O+0
HETATM    8  C   UNK     0      -1.334   2.310   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0      -1.334   3.850   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0      -2.667   4.620   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0      -4.001   3.850   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0      -4.001   2.310   0.000  0.00  0.00           C+0
HETATM   13  O   UNK     0      -2.667   1.540   0.000  0.00  0.00           O+0
HETATM   14  O   UNK     0      -5.335   4.620   0.000  0.00  0.00           O+0
HETATM   15  O   UNK     0      -2.667   6.160   0.000  0.00  0.00           O+0
HETATM   16  C   UNK     0      -4.001   6.930   0.000  0.00  0.00           C+0
HETATM   17  O   UNK     0      -4.001   8.470   0.000  0.00  0.00           O+0
HETATM   18  C   UNK     0      -5.335   6.160   0.000  0.00  0.00           C+0
HETATM   19  O   UNK     0       0.000   4.620   0.000  0.00  0.00           O+0
HETATM   20  C   UNK     0       1.334   3.850   0.000  0.00  0.00           C+0
HETATM   21  O   UNK     0       1.334   2.310   0.000  0.00  0.00           O+0
HETATM   22  C   UNK     0       2.667   4.620   0.000  0.00  0.00           C+0
HETATM   23  O   UNK     0       2.667  -0.000   0.000  0.00  0.00           O+0
HETATM   24  C   UNK     0       4.001  -0.770   0.000  0.00  0.00           C+0
HETATM   25  C   UNK     0       4.001  -2.310   0.000  0.00  0.00           C+0
HETATM   26  C   UNK     0       2.667  -3.080   0.000  0.00  0.00           C+0
HETATM   27  O   UNK     0       2.667  -4.620   0.000  0.00  0.00           O+0
HETATM   28  O   UNK     0       5.335  -3.080   0.000  0.00  0.00           O+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  C   UNK     0       6.668   2.310   0.000  0.00  0.00           C+0
HETATM   32  C   UNK     0       8.002   1.540   0.000  0.00  0.00           C+0
HETATM   33  C   UNK     0       8.002  -0.000   0.000  0.00  0.00           C+0
HETATM   34  C   UNK     0       6.668  -0.770   0.000  0.00  0.00           C+0
HETATM   35  O   UNK     0       9.336   2.310   0.000  0.00  0.00           O+0
HETATM   36  O   UNK     0       0.000  -4.620   0.000  0.00  0.00           O+0
HETATM   37  O   UNK     0      -2.667   0.000   0.000  0.00  0.00           O+0
CONECT    1    2    6   37                                                  
CONECT    2    1    3                                                       
CONECT    3    2    4   36                                                  
CONECT    4    3    5   26                                                  
CONECT    5    4    6   23                                                  
CONECT    6    5    1    7                                                  
CONECT    7    6    8                                                       
CONECT    8    7    9   13                                                  
CONECT    9    8   10   19                                                  
CONECT   10    9   11   15                                                  
CONECT   11   10   12   14                                                  
CONECT   12   11   13                                                       
CONECT   13   12    8                                                       
CONECT   14   11                                                            
CONECT   15   10   16                                                       
CONECT   16   15   17   18                                                  
CONECT   17   16                                                            
CONECT   18   16                                                            
CONECT   19    9   20                                                       
CONECT   20   19   21   22                                                  
CONECT   21   20                                                            
CONECT   22   20                                                            
CONECT   23    5   24                                                       
CONECT   24   23   25   29                                                  
CONECT   25   24   26   28                                                  
CONECT   26   25    4   27                                                  
CONECT   27   26                                                            
CONECT   28   25                                                            
CONECT   29   24   30   34                                                  
CONECT   30   29   31                                                       
CONECT   31   30   32                                                       
CONECT   32   31   33   35                                                  
CONECT   33   32   34                                                       
CONECT   34   33   29                                                       
CONECT   35   32                                                            
CONECT   36    3                                                            
CONECT   37    1                                                            
MASTER        0    0    0    0    0    0    0    0   37    0   80    0
END

View in JSmol

Synonyms

Value	Source
(2R,3R,4S,5S)-4-(Acetyloxy)-5-hydroxy-2-{[3,5,7-trihydroxy-2-(4-hydroxyphenyl)-4-oxo-4H-chromen-8-yl]oxy}oxan-3-yl acetic acid	Generator

Chemical Formula

C₂₄H₂₂O₁₃

Average Mass

518.4270 Da

Monoisotopic Mass

518.10604 Da

IUPAC Name

(2R,3R,4S,5S)-4-(acetyloxy)-5-hydroxy-2-{[3,5,7-trihydroxy-2-(4-hydroxyphenyl)-4-oxo-4H-chromen-8-yl]oxy}oxan-3-yl acetate

Traditional Name

(2R,3R,4S,5S)-4-(acetyloxy)-5-hydroxy-2-{[3,5,7-trihydroxy-2-(4-hydroxyphenyl)-4-oxochromen-8-yl]oxy}oxan-3-yl acetate

CAS Registry Number

Not Available

SMILES

CC(=O)O[C@H]1[C@@H](O)CO[C@H](OC2=C3OC(=C(O)C(=O)C3=C(O)C=C2O)C2=CC=C(O)C=C2)[C@@H]1OC(C)=O

InChI Identifier

InChI=1S/C24H22O13/c1-9(25)34-21-15(30)8-33-24(23(21)35-10(2)26)37-20-14(29)7-13(28)16-17(31)18(32)19(36-22(16)20)11-3-5-12(27)6-4-11/h3-7,15,21,23-24,27-30,32H,8H2,1-2H3/t15-,21-,23+,24+/m0/s1

InChI Key

XISTWCWMRYYNJX-VZQIUVLXSA-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, 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
Rhodiola algida	Plant	KNApSAcK
Rhodiola gelida	Plant	KNApSAcK

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as flavonoid-8-o-glycosides. These are phenolic compounds containing a flavonoid moiety which is O-glycosidically linked to carbohydrate moiety at the C8-position.

Kingdom

Organic compounds

Super Class

Phenylpropanoids and polyketides

Class

Flavonoids

Sub Class

Flavonoid glycosides

Direct Parent

Flavonoid-8-O-glycosides

Alternative Parents

Substituents

Flavonoid-8-o-glycoside
3-hydroxyflavone
Hydroxyflavonoid
Flavone
7-hydroxyflavonoid
5-hydroxyflavonoid
4'-hydroxyflavonoid
3-hydroxyflavonoid
Phenolic glycoside
O-glycosyl compound
Glycosyl compound
Chromone
1-benzopyran
Benzopyran
1-hydroxy-2-unsubstituted benzenoid
Pyranone
Phenol
Benzenoid
Pyran
Oxane
Monosaccharide
Dicarboxylic acid or derivatives
Monocyclic benzene moiety
Heteroaromatic compound
Vinylogous acid
Secondary alcohol
Carboxylic acid ester
Oxacycle
Organoheterocyclic compound
Polyol
Carboxylic acid derivative
Acetal
Organic oxygen compound
Organic oxide
Hydrocarbon derivative
Organooxygen compound
Carbonyl group
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	2.31	ALOGPS
logP	1.4	ChemAxon
logS	-2.9	ALOGPS
pKa (Strongest Acidic)	6.76	ChemAxon
pKa (Strongest Basic)	-3.5	ChemAxon
Physiological Charge	-1	ChemAxon
Hydrogen Acceptor Count	11	ChemAxon
Hydrogen Donor Count	5	ChemAxon
Polar Surface Area	198.51 Å²	ChemAxon
Rotatable Bond Count	7	ChemAxon
Refractivity	121.35 m³·mol⁻¹	ChemAxon
Polarizability	48.45 Å³	ChemAxon
Number of Rings	4	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

162875730

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

Showing NP-Card for Herbacetin 8-(2'',3''-diacetylxyloside) (NP0053917)

MOL for NP0053917 (Herbacetin 8-(2'',3''-diacetylxyloside))

3D MOL for NP0053917 (Herbacetin 8-(2'',3''-diacetylxyloside))

3D SDF for NP0053917 (Herbacetin 8-(2'',3''-diacetylxyloside))

3D-SDF for NP0053917 (Herbacetin 8-(2'',3''-diacetylxyloside))

PDB for NP0053917 (Herbacetin 8-(2'',3''-diacetylxyloside))

3D PDB for NP0053917 (Herbacetin 8-(2'',3''-diacetylxyloside))

SMILES for NP0053917 (Herbacetin 8-(2'',3''-diacetylxyloside))

INCHI for NP0053917 (Herbacetin 8-(2'',3''-diacetylxyloside))

Structure for NP0053917 (Herbacetin 8-(2'',3''-diacetylxyloside))

3D Structure for NP0053917 (Herbacetin 8-(2'',3''-diacetylxyloside))