NP-MRD: Showing NP-Card for Physcion 8-gentiobioside (NP0051630)

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Record Information

Version

2.0

Created at

2022-04-27 22:55:39 UTC

Updated at

2022-04-27 22:55:39 UTC

NP-MRD ID

NP0051630

Secondary Accession Numbers

None

Natural Product Identification

Common Name

Physcion 8-gentiobioside

Description

1-Hydroxy-6-methoxy-3-methyl-8-{[(2S,3R,4S,5S,6R)-3,4,5-trihydroxy-6-({[(2R,3S,4S,5S,6R)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}methyl)oxan-2-yl]oxy}-9,10-dihydroanthracene-9,10-dione 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. Physcion 8-gentiobioside is found in Cassia torosa, Rhamnus virgata and Rheum palmatum . Based on a literature review very few articles have been published on 1-hydroxy-6-methoxy-3-methyl-8-{[(2S,3R,4S,5S,6R)-3,4,5-trihydroxy-6-({[(2R,3S,4S,5S,6R)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}methyl)oxan-2-yl]oxy}-9,10-dihydroanthracene-9,10-dione.

Structure

MOL 3D MOL SDF PDB SMILES InChI


  Mrv1652304282200552D          

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M  END

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M  END


  Mrv1652304282200552D          

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    3.5724    3.7125    0.0000 O   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
    1.4289    0.8250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.1434   -0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.1434   -1.2375    0.0000 O   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 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
   -0.7145   -0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.0013   -0.4125    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.0013   -1.2375    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  2  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  2  0  0  0  0
  1  6  1  0  0  0  0
  6  7  1  0  0  0  0
  8  7  1  1  0  0  0
  8  9  1  0  0  0  0
  9 10  1  0  0  0  0
 10 11  1  0  0  0  0
 11 12  1  0  0  0  0
 12 13  1  0  0  0  0
  8 13  1  0  0  0  0
 12 14  1  1  0  0  0
 14 15  1  0  0  0  0
 16 15  1  1  0  0  0
 16 17  1  0  0  0  0
 17 18  1  0  0  0  0
 18 19  1  0  0  0  0
 19 20  1  0  0  0  0
 20 21  1  0  0  0  0
 16 21  1  0  0  0  0
 20 22  1  1  0  0  0
 22 23  1  0  0  0  0
 19 24  1  6  0  0  0
 18 25  1  1  0  0  0
 17 26  1  1  0  0  0
 11 27  1  6  0  0  0
 10 28  1  1  0  0  0
  9 29  1  6  0  0  0
  5 30  1  0  0  0  0
 30 31  2  0  0  0  0
 30 32  1  0  0  0  0
 32 33  2  0  0  0  0
 33 34  1  0  0  0  0
  4 34  1  0  0  0  0
 34 35  2  0  0  0  0
 33 36  1  0  0  0  0
 36 37  2  0  0  0  0
 37 38  1  0  0  0  0
 38 39  2  0  0  0  0
 32 39  1  0  0  0  0
 39 40  1  0  0  0  0
 37 41  1  0  0  0  0
  2 42  1  0  0  0  0
 42 43  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0051630

> <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(C=C(C)C=C3O)C(=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-WDNHTQQASA-N

> <FORMULA>
C28H32O15

> <MOLECULAR_WEIGHT>
608.549

> <EXACT_MASS>
608.17412033

> <JCHEM_ACCEPTOR_COUNT>
15

> <JCHEM_ATOM_COUNT>
75

> <JCHEM_AVERAGE_POLARIZABILITY>
59.581659130834396

> <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,3S,4S,5S,6R)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}methyl)oxan-2-yl]oxy}-9,10-dihydroanthracene-9,10-dione

> <ALOGPS_LOGP>
-0.30

> <JCHEM_LOGP>
-0.7215781839999996

> <ALOGPS_LOGS>
-2.19

> <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>
141.17489999999998

> <JCHEM_ROTATABLE_BOND_COUNT>
7

> <JCHEM_RULE_OF_FIVE>
0

> <ALOGPS_SOLUBILITY>
3.93e+00 g/l

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

> <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       8.002   1.540   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       8.002  -0.000   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       6.668  -0.770   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       5.335  -0.000   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       5.335   1.540   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       6.668   2.310   0.000  0.00  0.00           C+0
HETATM    7  O   UNK     0       6.668   3.850   0.000  0.00  0.00           O+0
HETATM    8  C   UNK     0       8.002   4.620   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0       8.002   6.160   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0       9.336   6.930   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0      10.669   6.160   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0      10.669   4.620   0.000  0.00  0.00           C+0
HETATM   13  O   UNK     0       9.336   3.850   0.000  0.00  0.00           O+0
HETATM   14  C   UNK     0      12.003   3.850   0.000  0.00  0.00           C+0
HETATM   15  O   UNK     0      13.337   4.620   0.000  0.00  0.00           O+0
HETATM   16  C   UNK     0      14.670   3.850   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0      16.004   4.620   0.000  0.00  0.00           C+0
HETATM   18  C   UNK     0      17.338   3.850   0.000  0.00  0.00           C+0
HETATM   19  C   UNK     0      17.338   2.310   0.000  0.00  0.00           C+0
HETATM   20  C   UNK     0      16.004   1.540   0.000  0.00  0.00           C+0
HETATM   21  O   UNK     0      14.670   2.310   0.000  0.00  0.00           O+0
HETATM   22  C   UNK     0      16.004   0.000   0.000  0.00  0.00           C+0
HETATM   23  O   UNK     0      17.338  -0.770   0.000  0.00  0.00           O+0
HETATM   24  O   UNK     0      18.672   1.540   0.000  0.00  0.00           O+0
HETATM   25  O   UNK     0      18.672   4.620   0.000  0.00  0.00           O+0
HETATM   26  O   UNK     0      16.004   6.160   0.000  0.00  0.00           O+0
HETATM   27  O   UNK     0      12.003   6.930   0.000  0.00  0.00           O+0
HETATM   28  O   UNK     0       9.336   8.470   0.000  0.00  0.00           O+0
HETATM   29  O   UNK     0       6.668   6.930   0.000  0.00  0.00           O+0
HETATM   30  C   UNK     0       4.001   2.310   0.000  0.00  0.00           C+0
HETATM   31  O   UNK     0       4.001   3.850   0.000  0.00  0.00           O+0
HETATM   32  C   UNK     0       2.667   1.540   0.000  0.00  0.00           C+0
HETATM   33  C   UNK     0       2.667   0.000   0.000  0.00  0.00           C+0
HETATM   34  C   UNK     0       4.001  -0.770   0.000  0.00  0.00           C+0
HETATM   35  O   UNK     0       4.001  -2.310   0.000  0.00  0.00           O+0
HETATM   36  C   UNK     0       1.334  -0.770   0.000  0.00  0.00           C+0
HETATM   37  C   UNK     0       0.000  -0.000   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      -1.334  -0.770   0.000  0.00  0.00           C+0
HETATM   42  O   UNK     0       9.336  -0.770   0.000  0.00  0.00           O+0
HETATM   43  C   UNK     0       9.336  -2.310   0.000  0.00  0.00           C+0
CONECT    1    2    6                                                       
CONECT    2    1    3   42                                                  
CONECT    3    2    4                                                       
CONECT    4    3    5   34                                                  
CONECT    5    4    6   30                                                  
CONECT    6    5    1    7                                                  
CONECT    7    6    8                                                       
CONECT    8    7    9   13                                                  
CONECT    9    8   10   29                                                  
CONECT   10    9   11   28                                                  
CONECT   11   10   12   27                                                  
CONECT   12   11   13   14                                                  
CONECT   13   12    8                                                       
CONECT   14   12   15                                                       
CONECT   15   14   16                                                       
CONECT   16   15   17   21                                                  
CONECT   17   16   18   26                                                  
CONECT   18   17   19   25                                                  
CONECT   19   18   20   24                                                  
CONECT   20   19   21   22                                                  
CONECT   21   20   16                                                       
CONECT   22   20   23                                                       
CONECT   23   22                                                            
CONECT   24   19                                                            
CONECT   25   18                                                            
CONECT   26   17                                                            
CONECT   27   11                                                            
CONECT   28   10                                                            
CONECT   29    9                                                            
CONECT   30    5   31   32                                                  
CONECT   31   30                                                            
CONECT   32   30   33   39                                                  
CONECT   33   32   34   36                                                  
CONECT   34   33    4   35                                                  
CONECT   35   34                                                            
CONECT   36   33   37                                                       
CONECT   37   36   38   41                                                  
CONECT   38   37   39                                                       
CONECT   39   38   32   40                                                  
CONECT   40   39                                                            
CONECT   41   37                                                            
CONECT   42    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

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,3S,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

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

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(C=C(C)C=C3O)C(=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-WDNHTQQASA-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
Cassia torosa	Plant	KNApSAcK
Rhamnus virgata	Plant	KNApSAcK
Rheum palmatum	Plant	KNApSAcK

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

Anthraquinone
9,10-anthraquinone
Phenolic glycoside
O-glycosyl compound
Glycosyl compound
Disaccharide
Aryl ketone
Anisole
1-hydroxy-4-unsubstituted benzenoid
1-hydroxy-2-unsubstituted benzenoid
Alkyl aryl ether
Oxane
Vinylogous acid
Secondary alcohol
Ketone
Oxacycle
Organoheterocyclic compound
Polyol
Ether
Acetal
Organic oxygen compound
Organic oxide
Hydrocarbon derivative
Primary alcohol
Organooxygen compound
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	-0.3	ALOGPS
logP	-0.72	ChemAxon
logS	-2.2	ALOGPS
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

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

161959697

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

Not Available

Showing NP-Card for Physcion 8-gentiobioside (NP0051630)

MOL for NP0051630 (Physcion 8-gentiobioside)

3D MOL for NP0051630 (Physcion 8-gentiobioside)

3D SDF for NP0051630 (Physcion 8-gentiobioside)

3D-SDF for NP0051630 (Physcion 8-gentiobioside)

PDB for NP0051630 (Physcion 8-gentiobioside)

3D PDB for NP0051630 (Physcion 8-gentiobioside)

SMILES for NP0051630 (Physcion 8-gentiobioside)

INCHI for NP0051630 (Physcion 8-gentiobioside)

Structure for NP0051630 (Physcion 8-gentiobioside)

3D Structure for NP0051630 (Physcion 8-gentiobioside)