NP-MRD: Showing NP-Card for physcion diglucoside (NP0244179)

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Record Information

Version

2.0

Created at

2022-09-07 04:54:35 UTC

Updated at

2022-09-07 04:54:36 UTC

NP-MRD ID

NP0244179

Secondary Accession Numbers

None

Natural Product Identification

Common Name

physcion diglucoside

Description

Physcion 8-gentiobioside, also known as physcion diglucoside, belongs to the class of organic compounds known as anthraquinones. These are organic compounds containing either anthracene-9,10-quinone, 1,4-anthraquinone, or 1,2-anthraquinone. Thus, physcion 8-gentiobioside is considered to be an aromatic polyketide. physcion diglucoside is found in Rhamnus virgata, Senna obtusifolia and Senna tora. Based on a literature review very few articles have been published on physcion 8-gentiobioside.

Structure

MOL 3D MOL SDF PDB SMILES InChI

  Mrv1652309072206542D          

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M  END

     RDKit          3D

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M  END

  Mrv1652309072206542D          

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    1.4289   -0.0000    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
   -0.7145   -0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    0.8250    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
    0.7145    2.0625    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289    0.8250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.1434    1.2375    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.1434    2.0625    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  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  1  0  0  0  0
  7  6  1  6  0  0  0
  7  8  1  0  0  0  0
  8  9  1  0  0  0  0
  9 10  1  6  0  0  0
 10 11  1  0  0  0  0
 12 11  1  6  0  0  0
 12 13  1  0  0  0  0
 13 14  1  0  0  0  0
 14 15  1  6  0  0  0
 15 16  1  0  0  0  0
 14 17  1  0  0  0  0
 17 18  1  1  0  0  0
 17 19  1  0  0  0  0
 19 20  1  6  0  0  0
 19 21  1  0  0  0  0
 12 21  1  0  0  0  0
 21 22  1  1  0  0  0
  9 23  1  0  0  0  0
 23 24  1  1  0  0  0
 23 25  1  0  0  0  0
 25 26  1  6  0  0  0
 25 27  1  0  0  0  0
  7 27  1  0  0  0  0
 27 28  1  1  0  0  0
  5 29  2  0  0  0  0
 29 30  1  0  0  0  0
 30 31  2  0  0  0  0
  3 31  1  0  0  0  0
 30 32  1  0  0  0  0
 32 33  2  0  0  0  0
 32 34  1  0  0  0  0
 34 35  2  0  0  0  0
 35 36  1  0  0  0  0
 36 37  1  0  0  0  0
 36 38  2  0  0  0  0
 38 39  1  0  0  0  0
 39 40  1  0  0  0  0
 39 41  2  0  0  0  0
 34 41  1  0  0  0  0
 41 42  1  0  0  0  0
 29 42  1  0  0  0  0
 42 43  2  0  0  0  0
M  END
> <DATABASE_ID>
NP0244179

> <DATABASE_NAME>
NP-MRD

> <SMILES>
COC1=CC(O[C@@H]2O[C@H](CO[C@@H]3O[C@H](CO)[C@@H](O)[C@H](O)[C@H]3O)[C@@H](O)[C@H](O)[C@H]2O)=C2C(=O)C3=C(O)C=C(C)C=C3C(=O)C2=C1

> <INCHI_IDENTIFIER>
InChI=1S/C28H32O15/c1-9-3-11-17(13(30)4-9)22(34)18-12(19(11)31)5-10(39-2)6-14(18)41-28-26(38)24(36)21(33)16(43-28)8-40-27-25(37)23(35)20(32)15(7-29)42-27/h3-6,15-16,20-21,23-30,32-33,35-38H,7-8H2,1-2H3/t15-,16-,20-,21-,23+,24+,25-,26-,27-,28-/m1/s1

> <INCHI_KEY>
YMXXCMGLMRYEQD-BFTLVBKUSA-N

> <FORMULA>
C28H32O15

> <MOLECULAR_WEIGHT>
608.549

> <EXACT_MASS>
608.17412033

> <JCHEM_ACCEPTOR_COUNT>
15

> <JCHEM_ATOM_COUNT>
75

> <JCHEM_AVERAGE_POLARIZABILITY>
59.57525450904831

> <JCHEM_BIOAVAILABILITY>
0

> <JCHEM_DONOR_COUNT>
8

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
1-hydroxy-6-methoxy-3-methyl-8-{[(2S,3R,4S,5S,6R)-3,4,5-trihydroxy-6-({[(2R,3R,4S,5S,6R)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}methyl)oxan-2-yl]oxy}-9,10-dihydroanthracene-9,10-dione

> <JCHEM_LOGP>
-0.7215781839999996

> <JCHEM_MDDR_LIKE_RULE>
1

> <JCHEM_NUMBER_OF_RINGS>
5

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
11.905356934352795

> <JCHEM_PKA_STRONGEST_ACIDIC>
8.296752566073323

> <JCHEM_PKA_STRONGEST_BASIC>
-2.981083422322401

> <JCHEM_POLAR_SURFACE_AREA>
242.12999999999997

> <JCHEM_REFRACTIVITY>
141.1749

> <JCHEM_ROTATABLE_BOND_COUNT>
7

> <JCHEM_RULE_OF_FIVE>
0

> <JCHEM_TRADITIONAL_IUPAC>
physcion diglucoside

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 07-SEP-22   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   07-SEP-22         0                                  
HETATM    1  C   UNK     0       9.336  -2.310   0.000  0.00  0.00           C+0
HETATM    2  O   UNK     0       9.336  -0.770   0.000  0.00  0.00           O+0
HETATM    3  C   UNK     0       8.002  -0.000   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       8.002   1.540   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       6.668   2.310   0.000  0.00  0.00           C+0
HETATM    6  O   UNK     0       6.668   3.850   0.000  0.00  0.00           O+0
HETATM    7  C   UNK     0       8.002   4.620   0.000  0.00  0.00           C+0
HETATM    8  O   UNK     0       8.002   6.160   0.000  0.00  0.00           O+0
HETATM    9  C   UNK     0       9.336   6.930   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0       9.336   8.470   0.000  0.00  0.00           C+0
HETATM   11  O   UNK     0      10.669   9.240   0.000  0.00  0.00           O+0
HETATM   12  C   UNK     0      10.669  10.780   0.000  0.00  0.00           C+0
HETATM   13  O   UNK     0       9.336  11.550   0.000  0.00  0.00           O+0
HETATM   14  C   UNK     0       9.336  13.090   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0       8.002  13.860   0.000  0.00  0.00           C+0
HETATM   16  O   UNK     0       8.002  15.400   0.000  0.00  0.00           O+0
HETATM   17  C   UNK     0      10.669  13.860   0.000  0.00  0.00           C+0
HETATM   18  O   UNK     0      10.669  15.400   0.000  0.00  0.00           O+0
HETATM   19  C   UNK     0      12.003  13.090   0.000  0.00  0.00           C+0
HETATM   20  O   UNK     0      13.337  13.860   0.000  0.00  0.00           O+0
HETATM   21  C   UNK     0      12.003  11.550   0.000  0.00  0.00           C+0
HETATM   22  O   UNK     0      13.337  10.780   0.000  0.00  0.00           O+0
HETATM   23  C   UNK     0      10.669   6.160   0.000  0.00  0.00           C+0
HETATM   24  O   UNK     0      12.003   6.930   0.000  0.00  0.00           O+0
HETATM   25  C   UNK     0      10.669   4.620   0.000  0.00  0.00           C+0
HETATM   26  O   UNK     0      12.003   3.850   0.000  0.00  0.00           O+0
HETATM   27  C   UNK     0       9.336   3.850   0.000  0.00  0.00           C+0
HETATM   28  O   UNK     0       9.336   2.310   0.000  0.00  0.00           O+0
HETATM   29  C   UNK     0       5.335   1.540   0.000  0.00  0.00           C+0
HETATM   30  C   UNK     0       5.335   0.000   0.000  0.00  0.00           C+0
HETATM   31  C   UNK     0       6.668  -0.770   0.000  0.00  0.00           C+0
HETATM   32  C   UNK     0       4.001  -0.770   0.000  0.00  0.00           C+0
HETATM   33  O   UNK     0       4.001  -2.310   0.000  0.00  0.00           O+0
HETATM   34  C   UNK     0       2.667  -0.000   0.000  0.00  0.00           C+0
HETATM   35  C   UNK     0       1.334  -0.770   0.000  0.00  0.00           C+0
HETATM   36  C   UNK     0      -0.000   0.000   0.000  0.00  0.00           C+0
HETATM   37  C   UNK     0      -1.334  -0.770   0.000  0.00  0.00           C+0
HETATM   38  C   UNK     0       0.000   1.540   0.000  0.00  0.00           C+0
HETATM   39  C   UNK     0       1.334   2.310   0.000  0.00  0.00           C+0
HETATM   40  O   UNK     0       1.334   3.850   0.000  0.00  0.00           O+0
HETATM   41  C   UNK     0       2.667   1.540   0.000  0.00  0.00           C+0
HETATM   42  C   UNK     0       4.001   2.310   0.000  0.00  0.00           C+0
HETATM   43  O   UNK     0       4.001   3.850   0.000  0.00  0.00           O+0
CONECT    1    2                                                            
CONECT    2    1    3                                                       
CONECT    3    2    4   31                                                  
CONECT    4    3    5                                                       
CONECT    5    4    6   29                                                  
CONECT    6    5    7                                                       
CONECT    7    6    8   27                                                  
CONECT    8    7    9                                                       
CONECT    9    8   10   23                                                  
CONECT   10    9   11                                                       
CONECT   11   10   12                                                       
CONECT   12   11   13   21                                                  
CONECT   13   12   14                                                       
CONECT   14   13   15   17                                                  
CONECT   15   14   16                                                       
CONECT   16   15                                                            
CONECT   17   14   18   19                                                  
CONECT   18   17                                                            
CONECT   19   17   20   21                                                  
CONECT   20   19                                                            
CONECT   21   19   12   22                                                  
CONECT   22   21                                                            
CONECT   23    9   24   25                                                  
CONECT   24   23                                                            
CONECT   25   23   26   27                                                  
CONECT   26   25                                                            
CONECT   27   25    7   28                                                  
CONECT   28   27                                                            
CONECT   29    5   30   42                                                  
CONECT   30   29   31   32                                                  
CONECT   31   30    3                                                       
CONECT   32   30   33   34                                                  
CONECT   33   32                                                            
CONECT   34   32   35   41                                                  
CONECT   35   34   36                                                       
CONECT   36   35   37   38                                                  
CONECT   37   36                                                            
CONECT   38   36   39                                                       
CONECT   39   38   40   41                                                  
CONECT   40   39                                                            
CONECT   41   39   34   42                                                  
CONECT   42   41   29   43                                                  
CONECT   43   42                                                            
MASTER        0    0    0    0    0    0    0    0   43    0   94    0
END

View in JSmol

Synonyms

Value	Source
Physcion 8-O-beta-D-gentiobioside	ChEBI
Physcion diglucoside	ChEBI
Physcion 8-O-b-D-gentiobioside	Generator
Physcion 8-O-β-D-gentiobioside	Generator

Chemical Formula

C₂₈H₃₂O₁₅

Average Mass

608.5490 Da

Monoisotopic Mass

608.17412 Da

IUPAC Name

1-hydroxy-6-methoxy-3-methyl-8-{[(2S,3R,4S,5S,6R)-3,4,5-trihydroxy-6-({[(2R,3R,4S,5S,6R)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}methyl)oxan-2-yl]oxy}-9,10-dihydroanthracene-9,10-dione

Traditional Name

physcion diglucoside

CAS Registry Number

Not Available

SMILES

COC1=CC(O[C@@H]2O[C@H](CO[C@@H]3O[C@H](CO)[C@@H](O)[C@H](O)[C@H]3O)[C@@H](O)[C@H](O)[C@H]2O)=C2C(=O)C3=C(O)C=C(C)C=C3C(=O)C2=C1

InChI Identifier

InChI=1S/C28H32O15/c1-9-3-11-17(13(30)4-9)22(34)18-12(19(11)31)5-10(39-2)6-14(18)41-28-26(38)24(36)21(33)16(43-28)8-40-27-25(37)23(35)20(32)15(7-29)42-27/h3-6,15-16,20-21,23-30,32-33,35-38H,7-8H2,1-2H3/t15-,16-,20-,21-,23+,24+,25-,26-,27-,28-/m1/s1

InChI Key

YMXXCMGLMRYEQD-BFTLVBKUSA-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
Rhamnus virgata	LOTUS Database	35616633
Senna obtusifolia	LOTUS Database	35616633
Senna tora	LOTUS Database	35616633

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as anthraquinones. These are organic compounds containing either anthracene-9,10-quinone, 1,4-anthraquinone, or 1,2-anthraquinone.

Kingdom

Super Class

Class

Sub Class

Direct Parent

Alternative Parents

Substituents

9,10-anthraquinone
Anthraquinone
Phenolic glycoside
Disaccharide
Glycosyl compound
O-glycosyl compound
Anisole
Aryl ketone
1-hydroxy-4-unsubstituted benzenoid
1-hydroxy-2-unsubstituted benzenoid
Alkyl aryl ether
Oxane
Vinylogous acid
Secondary alcohol
Ketone
Acetal
Oxacycle
Organoheterocyclic compound
Ether
Polyol
Alcohol
Organic oxygen compound
Organic oxide
Primary alcohol
Hydrocarbon derivative
Organooxygen compound
Aromatic heteropolycyclic compound

Molecular Framework

Aromatic heteropolycyclic compounds

External Descriptors

disaccharide derivative (CHEBI:27598 )
gentiobioside (CHEBI:27598 )
Anthracenes and phenanthrenes (C10382 )
Anthraquinone type (C10382 )
Anthracenes and phenanthrenes (LMPK13040012 )

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	-0.72	ChemAxon
pKa (Strongest Acidic)	8.3	ChemAxon
pKa (Strongest Basic)	-3	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	15	ChemAxon
Hydrogen Donor Count	8	ChemAxon
Polar Surface Area	242.13 Å²	ChemAxon
Rotatable Bond Count	7	ChemAxon
Refractivity	141.17 m³·mol⁻¹	ChemAxon
Polarizability	59.58 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

C00002849

Chemspider ID

391102

KEGG Compound ID

C10382

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

442762

PDB ID

Not Available

ChEBI ID

27598

Good Scents ID

Not Available

References

General References

LOTUS database [Link]

Showing NP-Card for physcion diglucoside (NP0244179)

MOL for NP0244179 (physcion diglucoside)

3D MOL for NP0244179 (physcion diglucoside)

3D SDF for NP0244179 (physcion diglucoside)

3D-SDF for NP0244179 (physcion diglucoside)

PDB for NP0244179 (physcion diglucoside)

3D PDB for NP0244179 (physcion diglucoside)

SMILES for NP0244179 (physcion diglucoside)

INCHI for NP0244179 (physcion diglucoside)

Structure for NP0244179 (physcion diglucoside)

3D Structure for NP0244179 (physcion diglucoside)