NP-MRD: Showing NP-Card for Diospyrosonaphthoside (NP0074409)

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Record Information

Version

2.0

Created at

2022-04-28 19:35:15 UTC

Updated at

2022-04-28 19:35:15 UTC

NP-MRD ID

NP0074409

Secondary Accession Numbers

None

Natural Product Identification

Common Name

Diospyrosonaphthoside

Description

(2S,3R,4R,5R,6S)-2-{[(2S,3R,4S,5R,6R)-4,5-dihydroxy-2-{[8-hydroxy-3-(hydroxymethyl)naphthalen-1-yl]oxy}-6-(hydroxymethyl)oxan-3-yl]oxy}-6-methyloxane-3,4,5-triol belongs to the class of organic compounds known as phenolic glycosides. These are organic compounds containing a phenolic structure attached to a glycosyl moiety. Some examples of phenolic structures include lignans, and flavonoids. Among the sugar units found in natural glycosides are D-glucose, L-Fructose, and L rhamnose. Diospyrosonaphthoside is found in Diospyros angustifolia and Diospyros virginiana. Based on a literature review very few articles have been published on (2S,3R,4R,5R,6S)-2-{[(2S,3R,4S,5R,6R)-4,5-dihydroxy-2-{[8-hydroxy-3-(hydroxymethyl)naphthalen-1-yl]oxy}-6-(hydroxymethyl)oxan-3-yl]oxy}-6-methyloxane-3,4,5-triol.

Structure

MOL 3D MOL SDF PDB SMILES InChI


  Mrv1652304282221352D          

 35 38  0  0  1  0            999 V2000
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   -0.7145   -1.2375    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
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    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 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7145    1.2375    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    1.2375    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
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M  END

     RDKit          3D

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M  END


  Mrv1652304282221352D          

 35 38  0  0  1  0            999 V2000
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M  END
> <DATABASE_ID>
NP0074409

> <DATABASE_NAME>
NP-MRD

> <SMILES>
C[C@@H]1O[C@@H](O[C@@H]2[C@@H](O)[C@@H](O)[C@@H](CO)O[C@H]2OC2=C3C(O)=CC=CC3=CC(CO)=C2)[C@H](O)[C@H](O)[C@H]1O

> <INCHI_IDENTIFIER>
InChI=1S/C23H30O12/c1-9-16(27)18(29)20(31)22(32-9)35-21-19(30)17(28)14(8-25)34-23(21)33-13-6-10(7-24)5-11-3-2-4-12(26)15(11)13/h2-6,9,14,16-31H,7-8H2,1H3/t9-,14+,16-,17-,18+,19-,20+,21+,22-,23+/m0/s1

> <INCHI_KEY>
DBGMSTRIFFXJCC-RQZGXQPASA-N

> <FORMULA>
C23H30O12

> <MOLECULAR_WEIGHT>
498.481

> <EXACT_MASS>
498.173726406

> <JCHEM_ACCEPTOR_COUNT>
12

> <JCHEM_ATOM_COUNT>
65

> <JCHEM_AVERAGE_POLARIZABILITY>
49.093319046977776

> <JCHEM_BIOAVAILABILITY>
0

> <JCHEM_DONOR_COUNT>
8

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(2S,3R,4R,5R,6S)-2-{[(2S,3R,4S,5R,6R)-4,5-dihydroxy-2-{[8-hydroxy-3-(hydroxymethyl)naphthalen-1-yl]oxy}-6-(hydroxymethyl)oxan-3-yl]oxy}-6-methyloxane-3,4,5-triol

> <ALOGPS_LOGP>
-1.02

> <JCHEM_LOGP>
-1.4037516103333334

> <ALOGPS_LOGS>
-1.81

> <JCHEM_MDDR_LIKE_RULE>
1

> <JCHEM_NUMBER_OF_RINGS>
4

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
12.099807461865343

> <JCHEM_PKA_STRONGEST_ACIDIC>
9.166885606736146

> <JCHEM_PKA_STRONGEST_BASIC>
-2.8620327506540804

> <JCHEM_POLAR_SURFACE_AREA>
198.76

> <JCHEM_REFRACTIVITY>
116.2999

> <JCHEM_ROTATABLE_BOND_COUNT>
6

> <JCHEM_RULE_OF_FIVE>
0

> <ALOGPS_SOLUBILITY>
7.77e+00 g/l

> <JCHEM_TRADITIONAL_IUPAC>
(2S,3R,4R,5R,6S)-2-{[(2S,3R,4S,5R,6R)-4,5-dihydroxy-2-{[8-hydroxy-3-(hydroxymethyl)naphthalen-1-yl]oxy}-6-(hydroxymethyl)oxan-3-yl]oxy}-6-methyloxane-3,4,5-triol

> <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      -1.334  -0.770   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0      -1.334  -2.310   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       0.000  -3.080   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       1.334  -2.310   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       1.334  -0.770   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       0.000  -0.000   0.000  0.00  0.00           C+0
HETATM    7  O   UNK     0       0.000   1.540   0.000  0.00  0.00           O+0
HETATM    8  C   UNK     0      -1.334   2.310   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   2.310   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0      -4.001   3.850   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0      -2.667   4.620   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0      -1.334   3.850   0.000  0.00  0.00           C+0
HETATM   14  O   UNK     0       0.000   4.620   0.000  0.00  0.00           O+0
HETATM   15  C   UNK     0       0.000   6.160   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0       1.334   6.930   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0       1.334   8.470   0.000  0.00  0.00           C+0
HETATM   18  C   UNK     0       0.000   9.240   0.000  0.00  0.00           C+0
HETATM   19  C   UNK     0      -1.334   8.470   0.000  0.00  0.00           C+0
HETATM   20  O   UNK     0      -1.334   6.930   0.000  0.00  0.00           O+0
HETATM   21  C   UNK     0      -2.667   9.240   0.000  0.00  0.00           C+0
HETATM   22  O   UNK     0       0.000  10.780   0.000  0.00  0.00           O+0
HETATM   23  O   UNK     0       2.667   9.240   0.000  0.00  0.00           O+0
HETATM   24  O   UNK     0       2.667   6.160   0.000  0.00  0.00           O+0
HETATM   25  O   UNK     0      -2.667   6.160   0.000  0.00  0.00           O+0
HETATM   26  O   UNK     0      -5.335   4.620   0.000  0.00  0.00           O+0
HETATM   27  C   UNK     0      -5.335   1.540   0.000  0.00  0.00           C+0
HETATM   28  O   UNK     0      -5.335   0.000   0.000  0.00  0.00           O+0
HETATM   29  C   UNK     0       2.667  -0.000   0.000  0.00  0.00           C+0
HETATM   30  C   UNK     0       4.001  -0.770   0.000  0.00  0.00           C+0
HETATM   31  C   UNK     0       4.001  -2.310   0.000  0.00  0.00           C+0
HETATM   32  C   UNK     0       2.667  -3.080   0.000  0.00  0.00           C+0
HETATM   33  O   UNK     0       2.667   1.540   0.000  0.00  0.00           O+0
HETATM   34  C   UNK     0      -2.667  -3.080   0.000  0.00  0.00           C+0
HETATM   35  O   UNK     0      -2.667  -4.620   0.000  0.00  0.00           O+0
CONECT    1    2    6                                                       
CONECT    2    1    3   34                                                  
CONECT    3    2    4                                                       
CONECT    4    3    5   32                                                  
CONECT    5    4    6   29                                                  
CONECT    6    5    1    7                                                  
CONECT    7    6    8                                                       
CONECT    8    7    9   13                                                  
CONECT    9    8   10                                                       
CONECT   10    9   11   27                                                  
CONECT   11   10   12   26                                                  
CONECT   12   11   13   25                                                  
CONECT   13   12    8   14                                                  
CONECT   14   13   15                                                       
CONECT   15   14   16   20                                                  
CONECT   16   15   17   24                                                  
CONECT   17   16   18   23                                                  
CONECT   18   17   19   22                                                  
CONECT   19   18   20   21                                                  
CONECT   20   19   15                                                       
CONECT   21   19                                                            
CONECT   22   18                                                            
CONECT   23   17                                                            
CONECT   24   16                                                            
CONECT   25   12                                                            
CONECT   26   11                                                            
CONECT   27   10   28                                                       
CONECT   28   27                                                            
CONECT   29    5   30   33                                                  
CONECT   30   29   31                                                       
CONECT   31   30   32                                                       
CONECT   32   31    4                                                       
CONECT   33   29                                                            
CONECT   34    2   35                                                       
CONECT   35   34                                                            
MASTER        0    0    0    0    0    0    0    0   35    0   76    0
END

View in JSmol

Synonyms

Not Available

Chemical Formula

C₂₃H₃₀O₁₂

Average Mass

498.4810 Da

Monoisotopic Mass

498.17373 Da

IUPAC Name

(2S,3R,4R,5R,6S)-2-{[(2S,3R,4S,5R,6R)-4,5-dihydroxy-2-{[8-hydroxy-3-(hydroxymethyl)naphthalen-1-yl]oxy}-6-(hydroxymethyl)oxan-3-yl]oxy}-6-methyloxane-3,4,5-triol

Traditional Name

(2S,3R,4R,5R,6S)-2-{[(2S,3R,4S,5R,6R)-4,5-dihydroxy-2-{[8-hydroxy-3-(hydroxymethyl)naphthalen-1-yl]oxy}-6-(hydroxymethyl)oxan-3-yl]oxy}-6-methyloxane-3,4,5-triol

CAS Registry Number

Not Available

SMILES

C[C@@H]1O[C@@H](O[C@@H]2[C@@H](O)[C@@H](O)[C@@H](CO)O[C@H]2OC2=C3C(O)=CC=CC3=CC(CO)=C2)[C@H](O)[C@H](O)[C@H]1O

InChI Identifier

InChI=1S/C23H30O12/c1-9-16(27)18(29)20(31)22(32-9)35-21-19(30)17(28)14(8-25)34-23(21)33-13-6-10(7-24)5-11-3-2-4-12(26)15(11)13/h2-6,9,14,16-31H,7-8H2,1H3/t9-,14+,16-,17-,18+,19-,20+,21+,22-,23+/m0/s1

InChI Key

DBGMSTRIFFXJCC-RQZGXQPASA-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
Diospyros angustifolia	Plant	KNApSAcK
Diospyros virginiana	LOTUS Database	35616633

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as phenolic glycosides. These are organic compounds containing a phenolic structure attached to a glycosyl moiety. Some examples of phenolic structures include lignans, and flavonoids. Among the sugar units found in natural glycosides are D-glucose, L-Fructose, and L rhamnose.

Kingdom

Organic compounds

Super Class

Organic oxygen compounds

Class

Organooxygen compounds

Sub Class

Carbohydrates and carbohydrate conjugates

Direct Parent

Phenolic glycosides

Alternative Parents

Substituents

Phenolic glycoside
O-glycosyl compound
1-naphthol
Disaccharide
Naphthalene
1-hydroxy-4-unsubstituted benzenoid
1-hydroxy-2-unsubstituted benzenoid
Benzenoid
Oxane
Secondary alcohol
Oxacycle
Organoheterocyclic compound
Polyol
Acetal
Hydrocarbon derivative
Aromatic alcohol
Primary alcohol
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	-1	ALOGPS
logP	-1.4	ChemAxon
logS	-1.8	ALOGPS
pKa (Strongest Acidic)	9.17	ChemAxon
pKa (Strongest Basic)	-2.9	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	12	ChemAxon
Hydrogen Donor Count	8	ChemAxon
Polar Surface Area	198.76 Å²	ChemAxon
Rotatable Bond Count	6	ChemAxon
Refractivity	116.3 m³·mol⁻¹	ChemAxon
Polarizability	49.09 Å³	ChemAxon
Number of Rings	4	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

163101384

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

Not Available

Showing NP-Card for Diospyrosonaphthoside (NP0074409)

MOL for NP0074409 (Diospyrosonaphthoside)

3D MOL for NP0074409 (Diospyrosonaphthoside)

3D SDF for NP0074409 (Diospyrosonaphthoside)

3D-SDF for NP0074409 (Diospyrosonaphthoside)

PDB for NP0074409 (Diospyrosonaphthoside)

3D PDB for NP0074409 (Diospyrosonaphthoside)

SMILES for NP0074409 (Diospyrosonaphthoside)

INCHI for NP0074409 (Diospyrosonaphthoside)

Structure for NP0074409 (Diospyrosonaphthoside)

3D Structure for NP0074409 (Diospyrosonaphthoside)