NP-MRD: Showing NP-Card for Digiferruginol omega-primeveroside (NP0085442)

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Record Information

Version

2.0

Created at

2022-04-29 05:58:06 UTC

Updated at

2022-04-29 05:58:06 UTC

NP-MRD ID

NP0085442

Secondary Accession Numbers

None

Natural Product Identification

Common Name

Digiferruginol omega-primeveroside

Description

1-Hydroxy-2-[(6-O-beta-D-xylopyranosyl-beta-D-glucopyranosyloxy)methyl]-9,10-anthraquinone 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. Digiferruginol omega-primeveroside is found in Morinda citrifolia . Based on a literature review very few articles have been published on 1-Hydroxy-2-[(6-O-beta-D-xylopyranosyl-beta-D-glucopyranosyloxy)methyl]-9,10-anthraquinone.

Structure

MOL 3D MOL SDF PDB SMILES InChI


  Mrv1652304292207582D          

 39 43  0  0  1  0            999 V2000
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M  END

     RDKit          3D

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M  END


  Mrv1652304292207582D          

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 10 28  1  0  0  0  0
 28 29  1  1  0  0  0
  7 30  2  0  0  0  0
  3 30  1  0  0  0  0
 30 31  1  0  0  0  0
  4 32  1  0  0  0  0
 32 33  1  0  0  0  0
 33 34  2  0  0  0  0
 34 35  1  0  0  0  0
 35 36  2  0  0  0  0
 36 37  1  0  0  0  0
 37 38  2  0  0  0  0
 33 38  1  0  0  0  0
  2 38  1  0  0  0  0
 32 39  2  0  0  0  0
M  END
> <DATABASE_ID>
NP0085442

> <DATABASE_NAME>
NP-MRD

> <SMILES>
O[C@@H]1CO[C@@H](OC[C@H]2O[C@@H](OCC3=C(O)C4=C(C=C3)C(=O)C3=CC=CC=C3C4=O)[C@H](O)[C@@H](O)[C@@H]2O)[C@H](O)[C@H]1O

> <INCHI_IDENTIFIER>
InChI=1S/C26H28O13/c27-14-8-37-25(23(34)20(14)31)38-9-15-21(32)22(33)24(35)26(39-15)36-7-10-5-6-13-16(17(10)28)19(30)12-4-2-1-3-11(12)18(13)29/h1-6,14-15,20-28,31-35H,7-9H2/t14-,15-,20+,21-,22+,23-,24-,25+,26-/m1/s1

> <INCHI_KEY>
BMOUMJCDDOLCGR-XZCSSYBOSA-N

> <FORMULA>
C26H28O13

> <MOLECULAR_WEIGHT>
548.497

> <EXACT_MASS>
548.152990962

> <JCHEM_ACCEPTOR_COUNT>
13

> <JCHEM_ATOM_COUNT>
67

> <JCHEM_AVERAGE_POLARIZABILITY>
54.20080178253846

> <JCHEM_BIOAVAILABILITY>
0

> <JCHEM_DONOR_COUNT>
7

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

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

> <ALOGPS_LOGP>
-0.22

> <JCHEM_LOGP>
-0.4135453636666663

> <ALOGPS_LOGS>
-2.28

> <JCHEM_MDDR_LIKE_RULE>
1

> <JCHEM_NUMBER_OF_RINGS>
5

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
11.928075909453588

> <JCHEM_PKA_STRONGEST_ACIDIC>
7.831963923663224

> <JCHEM_PKA_STRONGEST_BASIC>
-3.526580404084756

> <JCHEM_POLAR_SURFACE_AREA>
212.67

> <JCHEM_REFRACTIVITY>
128.81190000000004

> <JCHEM_ROTATABLE_BOND_COUNT>
6

> <JCHEM_RULE_OF_FIVE>
0

> <ALOGPS_SOLUBILITY>
2.87e+00 g/l

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

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 29-APR-22   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   29-APR-22         0                                  
HETATM    1  O   UNK     0       4.001   3.850   0.000  0.00  0.00           O+0
HETATM    2  C   UNK     0       4.001   2.310   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       5.335   1.540   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       6.668  -0.770   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       8.002  -0.000   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       8.002   1.540   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0       9.336   2.310   0.000  0.00  0.00           C+0
HETATM    9  O   UNK     0       9.336   3.850   0.000  0.00  0.00           O+0
HETATM   10  C   UNK     0      10.669   4.620   0.000  0.00  0.00           C+0
HETATM   11  O   UNK     0      10.669   6.160   0.000  0.00  0.00           O+0
HETATM   12  C   UNK     0      12.003   6.930   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0      12.003   8.470   0.000  0.00  0.00           C+0
HETATM   14  O   UNK     0      13.337   9.240   0.000  0.00  0.00           O+0
HETATM   15  C   UNK     0      13.337  10.780   0.000  0.00  0.00           C+0
HETATM   16  O   UNK     0      12.003  11.550   0.000  0.00  0.00           O+0
HETATM   17  C   UNK     0      12.003  13.090   0.000  0.00  0.00           C+0
HETATM   18  C   UNK     0      13.337  13.860   0.000  0.00  0.00           C+0
HETATM   19  O   UNK     0      13.337  15.400   0.000  0.00  0.00           O+0
HETATM   20  C   UNK     0      14.670  13.090   0.000  0.00  0.00           C+0
HETATM   21  O   UNK     0      16.004  13.860   0.000  0.00  0.00           O+0
HETATM   22  C   UNK     0      14.670  11.550   0.000  0.00  0.00           C+0
HETATM   23  O   UNK     0      16.004  10.780   0.000  0.00  0.00           O+0
HETATM   24  C   UNK     0      13.337   6.160   0.000  0.00  0.00           C+0
HETATM   25  O   UNK     0      14.670   6.930   0.000  0.00  0.00           O+0
HETATM   26  C   UNK     0      13.337   4.620   0.000  0.00  0.00           C+0
HETATM   27  O   UNK     0      14.670   3.850   0.000  0.00  0.00           O+0
HETATM   28  C   UNK     0      12.003   3.850   0.000  0.00  0.00           C+0
HETATM   29  O   UNK     0      12.003   2.310   0.000  0.00  0.00           O+0
HETATM   30  C   UNK     0       6.668   2.310   0.000  0.00  0.00           C+0
HETATM   31  O   UNK     0       6.668   3.850   0.000  0.00  0.00           O+0
HETATM   32  C   UNK     0       4.001  -0.770   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       1.334  -0.770   0.000  0.00  0.00           C+0
HETATM   35  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM   36  C   UNK     0       0.000   1.540   0.000  0.00  0.00           C+0
HETATM   37  C   UNK     0       1.334   2.310   0.000  0.00  0.00           C+0
HETATM   38  C   UNK     0       2.667   1.540   0.000  0.00  0.00           C+0
HETATM   39  O   UNK     0       4.001  -2.310   0.000  0.00  0.00           O+0
CONECT    1    2                                                            
CONECT    2    1    3   38                                                  
CONECT    3    2    4   30                                                  
CONECT    4    3    5   32                                                  
CONECT    5    4    6                                                       
CONECT    6    5    7                                                       
CONECT    7    6    8   30                                                  
CONECT    8    7    9                                                       
CONECT    9    8   10                                                       
CONECT   10    9   11   28                                                  
CONECT   11   10   12                                                       
CONECT   12   11   13   24                                                  
CONECT   13   12   14                                                       
CONECT   14   13   15                                                       
CONECT   15   14   16   22                                                  
CONECT   16   15   17                                                       
CONECT   17   16   18                                                       
CONECT   18   17   19   20                                                  
CONECT   19   18                                                            
CONECT   20   18   21   22                                                  
CONECT   21   20                                                            
CONECT   22   20   15   23                                                  
CONECT   23   22                                                            
CONECT   24   12   25   26                                                  
CONECT   25   24                                                            
CONECT   26   24   27   28                                                  
CONECT   27   26                                                            
CONECT   28   26   10   29                                                  
CONECT   29   28                                                            
CONECT   30    7    3   31                                                  
CONECT   31   30                                                            
CONECT   32    4   33   39                                                  
CONECT   33   32   34   38                                                  
CONECT   34   33   35                                                       
CONECT   35   34   36                                                       
CONECT   36   35   37                                                       
CONECT   37   36   38                                                       
CONECT   38   37   33    2                                                  
CONECT   39   32                                                            
MASTER        0    0    0    0    0    0    0    0   39    0   86    0
END

View in JSmol

Synonyms

Value	Source
1-Hydroxy-2-[(6-O-b-D-xylopyranosyl-b-D-glucopyranosyloxy)methyl]-9,10-anthraquinone	Generator
1-Hydroxy-2-[(6-O-β-D-xylopyranosyl-β-D-glucopyranosyloxy)methyl]-9,10-anthraquinone	Generator

Chemical Formula

C₂₆H₂₈O₁₃

Average Mass

548.4970 Da

Monoisotopic Mass

548.15299 Da

IUPAC Name

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

Traditional Name

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

CAS Registry Number

Not Available

SMILES

O[C@@H]1CO[C@@H](OC[C@H]2O[C@@H](OCC3=C(O)C4=C(C=C3)C(=O)C3=CC=CC=C3C4=O)[C@H](O)[C@@H](O)[C@@H]2O)[C@H](O)[C@H]1O

InChI Identifier

InChI=1S/C26H28O13/c27-14-8-37-25(23(34)20(14)31)38-9-15-21(32)22(33)24(35)26(39-15)36-7-10-5-6-13-16(17(10)28)19(30)12-4-2-1-3-11(12)18(13)29/h1-6,14-15,20-28,31-35H,7-9H2/t14-,15-,20+,21-,22+,23-,24-,25+,26-/m1/s1

InChI Key

BMOUMJCDDOLCGR-XZCSSYBOSA-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
Morinda citrifolia	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

9,10-anthraquinone
Anthraquinone
Disaccharide
Glycosyl compound
O-glycosyl compound
Aryl ketone
1-hydroxy-4-unsubstituted benzenoid
Oxane
Vinylogous acid
Secondary alcohol
Ketone
Polyol
Acetal
Organoheterocyclic compound
Oxacycle
Organooxygen compound
Hydrocarbon derivative
Organic oxide
Organic oxygen 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	-0.22	ALOGPS
logP	-0.41	ChemAxon
logS	-2.3	ALOGPS
pKa (Strongest Acidic)	7.83	ChemAxon
pKa (Strongest Basic)	-3.5	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	13	ChemAxon
Hydrogen Donor Count	7	ChemAxon
Polar Surface Area	212.67 Å²	ChemAxon
Rotatable Bond Count	6	ChemAxon
Refractivity	128.81 m³·mol⁻¹	ChemAxon
Polarizability	54.2 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

C00055309

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

102477526

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

Not Available

Showing NP-Card for Digiferruginol omega-primeveroside (NP0085442)

MOL for NP0085442 (Digiferruginol omega-primeveroside)

3D MOL for NP0085442 (Digiferruginol omega-primeveroside)

3D SDF for NP0085442 (Digiferruginol omega-primeveroside)

3D-SDF for NP0085442 (Digiferruginol omega-primeveroside)

PDB for NP0085442 (Digiferruginol omega-primeveroside)

3D PDB for NP0085442 (Digiferruginol omega-primeveroside)

SMILES for NP0085442 (Digiferruginol omega-primeveroside)

INCHI for NP0085442 (Digiferruginol omega-primeveroside)

Structure for NP0085442 (Digiferruginol omega-primeveroside)

3D Structure for NP0085442 (Digiferruginol omega-primeveroside)