NP-MRD: Showing NP-Card for 3,8-dihydroxy-5-methoxy-1-{[(2s,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}xanthen-9-one (NP0251744)

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Record Information

Version

2.0

Created at

2022-09-07 15:01:52 UTC

Updated at

2022-09-07 15:01:52 UTC

NP-MRD ID

NP0251744

Secondary Accession Numbers

None

Natural Product Identification

Common Name

3,8-dihydroxy-5-methoxy-1-{[(2s,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}xanthen-9-one

Description

1-O-Primeverosyl-3,8-dihydroxy-5-methoxyxanthone belongs to the class of organic compounds known as xanthones. These are polycyclic aromatic compounds containing a xanthene moiety conjugated to a ketone group at carbon 9. Xanthene is a tricyclic compound made up of two benzene rings linearly fused to each other through a pyran ring. 3,8-dihydroxy-5-methoxy-1-{[(2s,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}xanthen-9-one was first documented in 2002 (PMID: 12377236). Based on a literature review very few articles have been published on 1-O-Primeverosyl-3,8-dihydroxy-5-methoxyxanthone.

Structure

MOL 3D MOL SDF PDB SMILES InChI


  Mrv1652309072217012D          

 40 44  0  0  1  0            999 V2000
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M  END

     RDKit          3D

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M  END


  Mrv1652309072217012D          

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  1  2  1  0  0  0  0
  2  3  1  0  0  0  0
  3  4  1  0  0  0  0
  4  5  2  0  0  0  0
  5  6  1  0  0  0  0
  6  7  1  0  0  0  0
  6  8  2  0  0  0  0
  8  9  1  0  0  0  0
  9 10  2  0  0  0  0
  9 11  1  0  0  0  0
 11 12  2  0  0  0  0
 12 13  1  0  0  0  0
 14 13  1  6  0  0  0
 14 15  1  0  0  0  0
 15 16  1  0  0  0  0
 16 17  1  6  0  0  0
 17 18  1  0  0  0  0
 19 18  1  6  0  0  0
 19 20  1  0  0  0  0
 20 21  1  0  0  0  0
 21 22  1  0  0  0  0
 22 23  1  1  0  0  0
 22 24  1  0  0  0  0
 24 25  1  6  0  0  0
 24 26  1  0  0  0  0
 19 26  1  0  0  0  0
 26 27  1  1  0  0  0
 16 28  1  0  0  0  0
 28 29  1  1  0  0  0
 28 30  1  0  0  0  0
 30 31  1  6  0  0  0
 30 32  1  0  0  0  0
 14 32  1  0  0  0  0
 32 33  1  1  0  0  0
 12 34  1  0  0  0  0
 34 35  2  0  0  0  0
 35 36  1  0  0  0  0
 35 37  1  0  0  0  0
 37 38  2  0  0  0  0
 11 38  1  0  0  0  0
 38 39  1  0  0  0  0
 39 40  1  0  0  0  0
  3 40  2  0  0  0  0
  8 40  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0251744

> <DATABASE_NAME>
NP-MRD

> <SMILES>
COC1=C2OC3=CC(O)=CC(O[C@@H]4O[C@H](CO[C@@H]5OC[C@@H](O)[C@H](O)[C@H]5O)[C@@H](O)[C@H](O)[C@H]4O)=C3C(=O)C2=C(O)C=C1

> <INCHI_IDENTIFIER>
InChI=1S/C25H28O15/c1-35-11-3-2-9(27)15-19(31)16-12(38-23(11)15)4-8(26)5-13(16)39-25-22(34)20(32)18(30)14(40-25)7-37-24-21(33)17(29)10(28)6-36-24/h2-5,10,14,17-18,20-22,24-30,32-34H,6-7H2,1H3/t10-,14-,17+,18-,20+,21-,22-,24+,25-/m1/s1

> <INCHI_KEY>
USBLWLBBDROWFR-CENUTXNQSA-N

> <FORMULA>
C25H28O15

> <MOLECULAR_WEIGHT>
568.484

> <EXACT_MASS>
568.142820202

> <JCHEM_ACCEPTOR_COUNT>
14

> <JCHEM_ATOM_COUNT>
68

> <JCHEM_AVERAGE_POLARIZABILITY>
53.87958012031163

> <JCHEM_BIOAVAILABILITY>
0

> <JCHEM_DONOR_COUNT>
8

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
3,8-dihydroxy-5-methoxy-1-{[(2S,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}-9H-xanthen-9-one

> <JCHEM_LOGP>
-0.8672958073333334

> <JCHEM_MDDR_LIKE_RULE>
1

> <JCHEM_NUMBER_OF_RINGS>
5

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
8.884666775978172

> <JCHEM_PKA_STRONGEST_ACIDIC>
7.437027262460782

> <JCHEM_PKA_STRONGEST_BASIC>
-3.526580404084756

> <JCHEM_POLAR_SURFACE_AREA>
234.28999999999996

> <JCHEM_REFRACTIVITY>
127.81740000000005

> <JCHEM_ROTATABLE_BOND_COUNT>
6

> <JCHEM_RULE_OF_FIVE>
0

> <JCHEM_TRADITIONAL_IUPAC>
3,8-dihydroxy-5-methoxy-1-{[(2S,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}xanthen-9-one

> <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       2.667  -7.700   0.000  0.00  0.00           C+0
HETATM    2  O   UNK     0       4.001  -6.930   0.000  0.00  0.00           O+0
HETATM    3  C   UNK     0       4.001  -5.390   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       2.667  -4.620   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       2.667  -3.080   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       4.001  -2.310   0.000  0.00  0.00           C+0
HETATM    7  O   UNK     0       4.001  -0.770   0.000  0.00  0.00           O+0
HETATM    8  C   UNK     0       5.335  -3.080   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0       6.668  -2.310   0.000  0.00  0.00           C+0
HETATM   10  O   UNK     0       6.668  -0.770   0.000  0.00  0.00           O+0
HETATM   11  C   UNK     0       8.002  -3.080   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0       9.336  -2.310   0.000  0.00  0.00           C+0
HETATM   13  O   UNK     0       9.336  -0.770   0.000  0.00  0.00           O+0
HETATM   14  C   UNK     0      10.669   0.000   0.000  0.00  0.00           C+0
HETATM   15  O   UNK     0      10.669   1.540   0.000  0.00  0.00           O+0
HETATM   16  C   UNK     0      12.003   2.310   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0      12.003   3.850   0.000  0.00  0.00           C+0
HETATM   18  O   UNK     0      10.669   4.620   0.000  0.00  0.00           O+0
HETATM   19  C   UNK     0      10.669   6.160   0.000  0.00  0.00           C+0
HETATM   20  O   UNK     0       9.336   6.930   0.000  0.00  0.00           O+0
HETATM   21  C   UNK     0       9.336   8.470   0.000  0.00  0.00           C+0
HETATM   22  C   UNK     0      10.669   9.240   0.000  0.00  0.00           C+0
HETATM   23  O   UNK     0      10.669  10.780   0.000  0.00  0.00           O+0
HETATM   24  C   UNK     0      12.003   8.470   0.000  0.00  0.00           C+0
HETATM   25  O   UNK     0      13.337   9.240   0.000  0.00  0.00           O+0
HETATM   26  C   UNK     0      12.003   6.930   0.000  0.00  0.00           C+0
HETATM   27  O   UNK     0      13.337   6.160   0.000  0.00  0.00           O+0
HETATM   28  C   UNK     0      13.337   1.540   0.000  0.00  0.00           C+0
HETATM   29  O   UNK     0      14.670   2.310   0.000  0.00  0.00           O+0
HETATM   30  C   UNK     0      13.337  -0.000   0.000  0.00  0.00           C+0
HETATM   31  O   UNK     0      14.670  -0.770   0.000  0.00  0.00           O+0
HETATM   32  C   UNK     0      12.003  -0.770   0.000  0.00  0.00           C+0
HETATM   33  O   UNK     0      12.003  -2.310   0.000  0.00  0.00           O+0
HETATM   34  C   UNK     0      10.669  -3.080   0.000  0.00  0.00           C+0
HETATM   35  C   UNK     0      10.669  -4.620   0.000  0.00  0.00           C+0
HETATM   36  O   UNK     0      12.003  -5.390   0.000  0.00  0.00           O+0
HETATM   37  C   UNK     0       9.336  -5.390   0.000  0.00  0.00           C+0
HETATM   38  C   UNK     0       8.002  -4.620   0.000  0.00  0.00           C+0
HETATM   39  O   UNK     0       6.668  -5.390   0.000  0.00  0.00           O+0
HETATM   40  C   UNK     0       5.335  -4.620   0.000  0.00  0.00           C+0
CONECT    1    2                                                            
CONECT    2    1    3                                                       
CONECT    3    2    4   40                                                  
CONECT    4    3    5                                                       
CONECT    5    4    6                                                       
CONECT    6    5    7    8                                                  
CONECT    7    6                                                            
CONECT    8    6    9   40                                                  
CONECT    9    8   10   11                                                  
CONECT   10    9                                                            
CONECT   11    9   12   38                                                  
CONECT   12   11   13   34                                                  
CONECT   13   12   14                                                       
CONECT   14   13   15   32                                                  
CONECT   15   14   16                                                       
CONECT   16   15   17   28                                                  
CONECT   17   16   18                                                       
CONECT   18   17   19                                                       
CONECT   19   18   20   26                                                  
CONECT   20   19   21                                                       
CONECT   21   20   22                                                       
CONECT   22   21   23   24                                                  
CONECT   23   22                                                            
CONECT   24   22   25   26                                                  
CONECT   25   24                                                            
CONECT   26   24   19   27                                                  
CONECT   27   26                                                            
CONECT   28   16   29   30                                                  
CONECT   29   28                                                            
CONECT   30   28   31   32                                                  
CONECT   31   30                                                            
CONECT   32   30   14   33                                                  
CONECT   33   32                                                            
CONECT   34   12   35                                                       
CONECT   35   34   36   37                                                  
CONECT   36   35                                                            
CONECT   37   35   38                                                       
CONECT   38   37   11   39                                                  
CONECT   39   38   40                                                       
CONECT   40   39    3    8                                                  
MASTER        0    0    0    0    0    0    0    0   40    0   88    0
END

View in JSmol

Synonyms

Not Available

Chemical Formula

C₂₅H₂₈O₁₅

Average Mass

568.4840 Da

Monoisotopic Mass

568.14282 Da

IUPAC Name

3,8-dihydroxy-5-methoxy-1-{[(2S,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}-9H-xanthen-9-one

Traditional Name

3,8-dihydroxy-5-methoxy-1-{[(2S,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}xanthen-9-one

CAS Registry Number

Not Available

SMILES

COC1=C2OC3=CC(O)=CC(O[C@@H]4O[C@H](CO[C@@H]5OC[C@@H](O)[C@H](O)[C@H]5O)[C@@H](O)[C@H](O)[C@H]4O)=C3C(=O)C2=C(O)C=C1

InChI Identifier

InChI=1S/C25H28O15/c1-35-11-3-2-9(27)15-19(31)16-12(38-23(11)15)4-8(26)5-13(16)39-25-22(34)20(32)18(30)14(40-25)7-37-24-21(33)17(29)10(28)6-36-24/h2-5,10,14,17-18,20-22,24-30,32-34H,6-7H2,1H3/t10-,14-,17+,18-,20+,21-,22-,24+,25-/m1/s1

InChI Key

USBLWLBBDROWFR-CENUTXNQSA-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

Not Available

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as xanthones. These are polycyclic aromatic compounds containing a xanthene moiety conjugated to a ketone group at carbon 9. Xanthene is a tricyclic compound made up of two benzene rings linearly fused to each other through a pyran ring.

Kingdom

Organic compounds

Super Class

Organoheterocyclic compounds

Class

Benzopyrans

Sub Class

1-benzopyrans

Direct Parent

Xanthones

Alternative Parents

Substituents

Phenolic glycoside
Xanthone
Chromone
Disaccharide
Glycosyl compound
O-glycosyl compound
Anisole
Alkyl aryl ether
1-hydroxy-2-unsubstituted benzenoid
Pyranone
Pyran
Oxane
Benzenoid
Vinylogous ester
Heteroaromatic compound
Vinylogous acid
Secondary alcohol
Oxacycle
Acetal
Polyol
Ether
Organooxygen compound
Organic oxygen compound
Alcohol
Organic oxide
Hydrocarbon derivative
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	-0.87	ChemAxon
pKa (Strongest Acidic)	7.44	ChemAxon
pKa (Strongest Basic)	-3.5	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	14	ChemAxon
Hydrogen Donor Count	8	ChemAxon
Polar Surface Area	234.29 Å²	ChemAxon
Rotatable Bond Count	6	ChemAxon
Refractivity	127.82 m³·mol⁻¹	ChemAxon
Polarizability	53.88 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

11968853

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

Menkovic N, Savikin-Fodulovic K, Bulatovic V, Aljancic I, Juranic N, Macura S, Vajs V, Milosavljevic S: Xanthones from Swertia punctata. Phytochemistry. 2002 Oct;61(4):415-20. doi: 10.1016/s0031-9422(02)00231-5. [PubMed:12377236 ]
LOTUS database [Link]

Showing NP-Card for 3,8-dihydroxy-5-methoxy-1-{[(2s,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}xanthen-9-one (NP0251744)

MOL for NP0251744 (3,8-dihydroxy-5-methoxy-1-{[(2s,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}xanthen-9-one)

3D MOL for NP0251744 (3,8-dihydroxy-5-methoxy-1-{[(2s,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}xanthen-9-one)

3D SDF for NP0251744 (3,8-dihydroxy-5-methoxy-1-{[(2s,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}xanthen-9-one)

3D-SDF for NP0251744 (3,8-dihydroxy-5-methoxy-1-{[(2s,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}xanthen-9-one)

PDB for NP0251744 (3,8-dihydroxy-5-methoxy-1-{[(2s,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}xanthen-9-one)

3D PDB for NP0251744 (3,8-dihydroxy-5-methoxy-1-{[(2s,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}xanthen-9-one)

SMILES for NP0251744 (3,8-dihydroxy-5-methoxy-1-{[(2s,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}xanthen-9-one)

INCHI for NP0251744 (3,8-dihydroxy-5-methoxy-1-{[(2s,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}xanthen-9-one)

Structure for NP0251744 (3,8-dihydroxy-5-methoxy-1-{[(2s,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}xanthen-9-one)

3D Structure for NP0251744 (3,8-dihydroxy-5-methoxy-1-{[(2s,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}xanthen-9-one)