NP-MRD: Showing NP-Card for rhodionidin (NP0266518)

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Record Information

Version

2.0

Created at

2022-09-08 10:53:00 UTC

Updated at

2022-09-08 10:53:00 UTC

NP-MRD ID

NP0266518

Secondary Accession Numbers

None

Natural Product Identification

Common Name

rhodionidin

Description

Herbacetin 7-rhamnoside-8-glucoside 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. Thus, herbacetin 7-rhamnoside-8-glucoside is considered to be a flavonoid. rhodionidin is found in Rhodiola rosea. Based on a literature review very few articles have been published on Herbacetin 7-rhamnoside-8-glucoside.

Structure

MOL 3D MOL SDF PDB SMILES InChI


  Mrv1652309082212532D          

 43 47  0  0  1  0            999 V2000
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M  END

     RDKit          3D

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M  END


  Mrv1652309082212532D          

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    0.0000   -4.1250    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    0.0000   -4.9500    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145   -3.7125    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    1.4289   -4.1250    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7145   -0.4125    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    0.0000   -0.0000    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4289   -0.0000    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   -1.4289    0.8250    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1434   -0.4125    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   -2.8579   -0.0000    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  2  1  1  1  0  0  0
  2  3  1  0  0  0  0
  3  4  1  0  0  0  0
  4  5  1  6  0  0  0
  5  6  1  0  0  0  0
  6  7  2  0  0  0  0
  7  8  1  0  0  0  0
  8  9  1  0  0  0  0
  8 10  2  0  0  0  0
 10 11  1  0  0  0  0
 11 12  2  0  0  0  0
 11 13  1  0  0  0  0
 13 14  1  0  0  0  0
 13 15  2  0  0  0  0
 15 16  1  0  0  0  0
 16 17  2  0  0  0  0
 17 18  1  0  0  0  0
 18 19  2  0  0  0  0
 19 20  1  0  0  0  0
 19 21  1  0  0  0  0
 21 22  2  0  0  0  0
 16 22  1  0  0  0  0
 15 23  1  0  0  0  0
 23 24  1  0  0  0  0
 10 24  1  0  0  0  0
 24 25  2  0  0  0  0
  6 25  1  0  0  0  0
 25 26  1  0  0  0  0
 27 26  1  1  0  0  0
 27 28  1  0  0  0  0
 28 29  1  0  0  0  0
 29 30  1  1  0  0  0
 30 31  1  0  0  0  0
 29 32  1  0  0  0  0
 32 33  1  6  0  0  0
 32 34  1  0  0  0  0
 34 35  1  1  0  0  0
 34 36  1  0  0  0  0
 27 36  1  0  0  0  0
 36 37  1  6  0  0  0
  4 38  1  0  0  0  0
 38 39  1  1  0  0  0
 38 40  1  0  0  0  0
 40 41  1  1  0  0  0
 40 42  1  0  0  0  0
  2 42  1  0  0  0  0
 42 43  1  6  0  0  0
M  END
> <DATABASE_ID>
NP0266518

> <DATABASE_NAME>
NP-MRD

> <SMILES>
C[C@@H]1O[C@@H](OC2=CC(O)=C3C(=O)C(O)=C(OC3=C2O[C@@H]2O[C@H](CO)[C@@H](O)[C@H](O)[C@H]2O)C2=CC=C(O)C=C2)[C@H](O)[C@H](O)[C@H]1O

> <INCHI_IDENTIFIER>
InChI=1S/C27H30O16/c1-8-15(31)18(34)21(37)26(39-8)40-12-6-11(30)14-17(33)20(36)23(9-2-4-10(29)5-3-9)42-25(14)24(12)43-27-22(38)19(35)16(32)13(7-28)41-27/h2-6,8,13,15-16,18-19,21-22,26-32,34-38H,7H2,1H3/t8-,13+,15-,16+,18+,19-,21+,22+,26-,27-/m0/s1

> <INCHI_KEY>
CQFZDNWCTZWQSH-UCPCOQSFSA-N

> <FORMULA>
C27H30O16

> <MOLECULAR_WEIGHT>
610.521

> <EXACT_MASS>
610.153384886

> <JCHEM_ACCEPTOR_COUNT>
16

> <JCHEM_ATOM_COUNT>
73

> <JCHEM_AVERAGE_POLARIZABILITY>
57.41129782896472

> <JCHEM_BIOAVAILABILITY>
0

> <JCHEM_DONOR_COUNT>
10

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

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

> <JCHEM_LOGP>
-1.332926756

> <JCHEM_MDDR_LIKE_RULE>
1

> <JCHEM_NUMBER_OF_RINGS>
5

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
8.496132713964812

> <JCHEM_PKA_STRONGEST_ACIDIC>
7.444760240827467

> <JCHEM_PKA_STRONGEST_BASIC>
-3.6483953863024583

> <JCHEM_POLAR_SURFACE_AREA>
265.52

> <JCHEM_REFRACTIVITY>
139.60730000000004

> <JCHEM_ROTATABLE_BOND_COUNT>
6

> <JCHEM_RULE_OF_FIVE>
0

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

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 08-SEP-22   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   08-SEP-22         0                                  
HETATM    1  C   UNK     0      -5.335  -3.080   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0      -4.001  -2.310   0.000  0.00  0.00           C+0
HETATM    3  O   UNK     0      -2.667  -3.080   0.000  0.00  0.00           O+0
HETATM    4  C   UNK     0      -1.334  -2.310   0.000  0.00  0.00           C+0
HETATM    5  O   UNK     0       0.000  -3.080   0.000  0.00  0.00           O+0
HETATM    6  C   UNK     0       1.334  -2.310   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       1.334  -0.770   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0       2.667   0.000   0.000  0.00  0.00           C+0
HETATM    9  O   UNK     0       2.667   1.540   0.000  0.00  0.00           O+0
HETATM   10  C   UNK     0       4.001  -0.770   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0       5.335   0.000   0.000  0.00  0.00           C+0
HETATM   12  O   UNK     0       5.335   1.540   0.000  0.00  0.00           O+0
HETATM   13  C   UNK     0       6.668  -0.770   0.000  0.00  0.00           C+0
HETATM   14  O   UNK     0       8.002  -0.000   0.000  0.00  0.00           O+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  -3.080   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0       9.336  -2.310   0.000  0.00  0.00           C+0
HETATM   18  C   UNK     0      10.669  -3.080   0.000  0.00  0.00           C+0
HETATM   19  C   UNK     0      10.669  -4.620   0.000  0.00  0.00           C+0
HETATM   20  O   UNK     0      12.003  -5.390   0.000  0.00  0.00           O+0
HETATM   21  C   UNK     0       9.336  -5.390   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  O   UNK     0       5.335  -3.080   0.000  0.00  0.00           O+0
HETATM   24  C   UNK     0       4.001  -2.310   0.000  0.00  0.00           C+0
HETATM   25  C   UNK     0       2.667  -3.080   0.000  0.00  0.00           C+0
HETATM   26  O   UNK     0       2.667  -4.620   0.000  0.00  0.00           O+0
HETATM   27  C   UNK     0       1.334  -5.390   0.000  0.00  0.00           C+0
HETATM   28  O   UNK     0       0.000  -4.620   0.000  0.00  0.00           O+0
HETATM   29  C   UNK     0      -1.334  -5.390   0.000  0.00  0.00           C+0
HETATM   30  C   UNK     0      -2.667  -4.620   0.000  0.00  0.00           C+0
HETATM   31  O   UNK     0      -4.001  -5.390   0.000  0.00  0.00           O+0
HETATM   32  C   UNK     0      -1.334  -6.930   0.000  0.00  0.00           C+0
HETATM   33  O   UNK     0      -2.667  -7.700   0.000  0.00  0.00           O+0
HETATM   34  C   UNK     0       0.000  -7.700   0.000  0.00  0.00           C+0
HETATM   35  O   UNK     0       0.000  -9.240   0.000  0.00  0.00           O+0
HETATM   36  C   UNK     0       1.334  -6.930   0.000  0.00  0.00           C+0
HETATM   37  O   UNK     0       2.667  -7.700   0.000  0.00  0.00           O+0
HETATM   38  C   UNK     0      -1.334  -0.770   0.000  0.00  0.00           C+0
HETATM   39  O   UNK     0       0.000  -0.000   0.000  0.00  0.00           O+0
HETATM   40  C   UNK     0      -2.667  -0.000   0.000  0.00  0.00           C+0
HETATM   41  O   UNK     0      -2.667   1.540   0.000  0.00  0.00           O+0
HETATM   42  C   UNK     0      -4.001  -0.770   0.000  0.00  0.00           C+0
HETATM   43  O   UNK     0      -5.335  -0.000   0.000  0.00  0.00           O+0
CONECT    1    2                                                            
CONECT    2    1    3   42                                                  
CONECT    3    2    4                                                       
CONECT    4    3    5   38                                                  
CONECT    5    4    6                                                       
CONECT    6    5    7   25                                                  
CONECT    7    6    8                                                       
CONECT    8    7    9   10                                                  
CONECT    9    8                                                            
CONECT   10    8   11   24                                                  
CONECT   11   10   12   13                                                  
CONECT   12   11                                                            
CONECT   13   11   14   15                                                  
CONECT   14   13                                                            
CONECT   15   13   16   23                                                  
CONECT   16   15   17   22                                                  
CONECT   17   16   18                                                       
CONECT   18   17   19                                                       
CONECT   19   18   20   21                                                  
CONECT   20   19                                                            
CONECT   21   19   22                                                       
CONECT   22   21   16                                                       
CONECT   23   15   24                                                       
CONECT   24   23   10   25                                                  
CONECT   25   24    6   26                                                  
CONECT   26   25   27                                                       
CONECT   27   26   28   36                                                  
CONECT   28   27   29                                                       
CONECT   29   28   30   32                                                  
CONECT   30   29   31                                                       
CONECT   31   30                                                            
CONECT   32   29   33   34                                                  
CONECT   33   32                                                            
CONECT   34   32   35   36                                                  
CONECT   35   34                                                            
CONECT   36   34   27   37                                                  
CONECT   37   36                                                            
CONECT   38    4   39   40                                                  
CONECT   39   38                                                            
CONECT   40   38   41   42                                                  
CONECT   41   40                                                            
CONECT   42   40    2   43                                                  
CONECT   43   42                                                            
MASTER        0    0    0    0    0    0    0    0   43    0   94    0
END

View in JSmol

Synonyms

Not Available

Chemical Formula

C₂₇H₃₀O₁₆

Average Mass

610.5210 Da

Monoisotopic Mass

610.15338 Da

IUPAC Name

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

Traditional Name

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

CAS Registry Number

Not Available

SMILES

C[C@@H]1O[C@@H](OC2=CC(O)=C3C(=O)C(O)=C(OC3=C2O[C@@H]2O[C@H](CO)[C@@H](O)[C@H](O)[C@H]2O)C2=CC=C(O)C=C2)[C@H](O)[C@H](O)[C@H]1O

InChI Identifier

InChI=1S/C27H30O16/c1-8-15(31)18(34)21(37)26(39-8)40-12-6-11(30)14-17(33)20(36)23(9-2-4-10(29)5-3-9)42-25(14)24(12)43-27-22(38)19(35)16(32)13(7-28)41-27/h2-6,8,13,15-16,18-19,21-22,26-32,34-38H,7H2,1H3/t8-,13+,15-,16+,18+,19-,21+,22+,26-,27-/m0/s1

InChI Key

CQFZDNWCTZWQSH-UCPCOQSFSA-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
Rhodiola rosea	LOTUS Database	35616633

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-7-o-glycoside
Flavonoid-8-o-glycoside
3-hydroxyflavone
Hydroxyflavonoid
3-hydroxyflavonoid
4'-hydroxyflavonoid
5-hydroxyflavonoid
Flavone
Phenolic glycoside
O-glycosyl compound
Glycosyl compound
Chromone
1-benzopyran
Benzopyran
Pyranone
1-hydroxy-2-unsubstituted benzenoid
Phenol
Monocyclic benzene moiety
Pyran
Monosaccharide
Oxane
Benzenoid
Heteroaromatic compound
Vinylogous acid
Secondary alcohol
Organoheterocyclic compound
Oxacycle
Acetal
Polyol
Primary alcohol
Organic oxide
Organic oxygen compound
Alcohol
Hydrocarbon derivative
Organooxygen compound
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	-1.3	ChemAxon
pKa (Strongest Acidic)	7.44	ChemAxon
pKa (Strongest Basic)	-3.6	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	16	ChemAxon
Hydrogen Donor Count	10	ChemAxon
Polar Surface Area	265.52 Å²	ChemAxon
Rotatable Bond Count	6	ChemAxon
Refractivity	139.61 m³·mol⁻¹	ChemAxon
Polarizability	57.41 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

C00005348

Chemspider ID

52083507

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

91864469

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

LOTUS database [Link]

Showing NP-Card for rhodionidin (NP0266518)

MOL for NP0266518 (rhodionidin)

3D MOL for NP0266518 (rhodionidin)

3D SDF for NP0266518 (rhodionidin)

3D-SDF for NP0266518 (rhodionidin)

PDB for NP0266518 (rhodionidin)

3D PDB for NP0266518 (rhodionidin)

SMILES for NP0266518 (rhodionidin)

INCHI for NP0266518 (rhodionidin)

Structure for NP0266518 (rhodionidin)

3D Structure for NP0266518 (rhodionidin)