NP-MRD: Showing NP-Card for 2-({6,13-dihydroxy-14-methoxy-3,10-dioxo-2,9-dioxatetracyclo[6.6.2.0⁴,¹⁶.0¹¹,¹⁵]hexadeca-1(15),4,6,8(16),11,13-hexaen-7-yl}oxy)-4,5-dihydroxy-6-methyloxan-3-yl acetate (NP0266646)

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Record Information

Version

2.0

Created at

2022-09-08 11:03:11 UTC

Updated at

2022-09-08 11:03:12 UTC

NP-MRD ID

NP0266646

Secondary Accession Numbers

None

Natural Product Identification

Common Name

2-({6,13-dihydroxy-14-methoxy-3,10-dioxo-2,9-dioxatetracyclo[6.6.2.0⁴,¹⁶.0¹¹,¹⁵]hexadeca-1(15),4,6,8(16),11,13-hexaen-7-yl}oxy)-4,5-dihydroxy-6-methyloxan-3-yl acetate

Description

(8S,8'S)-Secoisolariciresinol 9-xyloside belongs to the class of organic compounds known as lignan glycosides. These are aromatic polycyclic compounds containing a carbohydrate component glycosidically linked to a lignan moiety. They include 1-aryltetralin lactones (8S,8'S)-Secoisolariciresinol 9-xyloside is an extremely weak basic (essentially neutral) compound (based on its pKa). Outside of the human body, (8S,8'S)-Secoisolariciresinol 9-xyloside has been detected, but not quantified in, herbs and spices and tea. 2-({6,13-dihydroxy-14-methoxy-3,10-dioxo-2,9-dioxatetracyclo[6.6.2.0⁴,¹⁶.0¹¹,¹⁵]hexadeca-1(15),4,6,8(16),11,13-hexaen-7-yl}oxy)-4,5-dihydroxy-6-methyloxan-3-yl acetate is found in Eucalyptus globulus. This could make (8S,8's)-secoisolariciresinol 9-xyloside a potential biomarker for the consumption of these foods.

Structure

MOL 3D MOL SDF PDB SMILES InChI


  Mrv0541 05061309332D          

 36 40  0  0  0  0            999 V2000
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    2.8875   -1.5395    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
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   -2.8875   -1.5395    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0625   -4.3974    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.0625   -1.5395    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
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    3.3000   -0.8250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
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M  END

     RDKit          3D

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M  END


  Mrv0541 05061309332D          

 36 40  0  0  0  0            999 V2000
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M  END
> <DATABASE_ID>
NP0266646

> <DATABASE_NAME>
NP-MRD

> <SMILES>
COC1=C(O)C=C2C(=O)OC3=C4C(=CC(O)=C3OC3OC(C)C(O)C(O)C3OC(C)=O)C(=O)OC1=C24

> <INCHI_IDENTIFIER>
InChI=1S/C23H20O13/c1-6-14(27)15(28)20(33-7(2)24)23(32-6)36-17-11(26)5-9-13-12-8(22(30)35-19(13)17)4-10(25)16(31-3)18(12)34-21(9)29/h4-6,14-15,20,23,25-28H,1-3H3

> <INCHI_KEY>
XOBMJVRDRZBSBR-UHFFFAOYSA-N

> <FORMULA>
C23H20O13

> <MOLECULAR_WEIGHT>
504.3971

> <EXACT_MASS>
504.090390726

> <JCHEM_ACCEPTOR_COUNT>
10

> <JCHEM_AVERAGE_POLARIZABILITY>
47.198504207456466

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
4

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
2-({6,13-dihydroxy-14-methoxy-3,10-dioxo-2,9-dioxatetracyclo[6.6.2.0⁴,¹⁶.0¹¹,¹⁵]hexadeca-1(15),4,6,8(16),11,13-hexaen-7-yl}oxy)-4,5-dihydroxy-6-methyloxan-3-yl acetate

> <ALOGPS_LOGP>
1.56

> <JCHEM_LOGP>
0.3817837576666659

> <ALOGPS_LOGS>
-2.59

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
5

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-2

> <JCHEM_PKA>
6.4983040816862925

> <JCHEM_PKA_STRONGEST_ACIDIC>
5.802129143977902

> <JCHEM_PKA_STRONGEST_BASIC>
-3.612922563839045

> <JCHEM_POLAR_SURFACE_AREA>
187.50999999999993

> <JCHEM_REFRACTIVITY>
114.84209999999996

> <JCHEM_ROTATABLE_BOND_COUNT>
5

> <JCHEM_RULE_OF_FIVE>
0

> <ALOGPS_SOLUBILITY>
1.29e+00 g/l

> <JCHEM_TRADITIONAL_IUPAC>
2-({6,13-dihydroxy-14-methoxy-3,10-dioxo-2,9-dioxatetracyclo[6.6.2.0⁴,¹⁶.0¹¹,¹⁵]hexadeca-1(15),4,6,8(16),11,13-hexaen-7-yl}oxy)-4,5-dihydroxy-6-methyloxan-3-yl acetate

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 06-MAY-13   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   06-MAY-13         0                                  
HETATM    1  C   UNK     0      -6.160  -1.540   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0      -3.080  -9.542   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       5.390   2.461   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       5.390  -2.874   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0      -0.770  -0.206   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0      -5.390  -2.874   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0      -3.850  -8.208   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0       3.850  -2.874   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0       0.770  -0.206   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0       6.160  -1.540   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0      -1.540  -1.540   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0       3.080  -1.540   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0       1.540  -1.540   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0      -6.160  -4.207   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0      -5.390  -5.541   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0       5.390  -0.206   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0      -0.770  -2.874   0.000  0.00  0.00           C+0
HETATM   18  C   UNK     0       3.850  -0.206   0.000  0.00  0.00           C+0
HETATM   19  C   UNK     0       0.770  -2.874   0.000  0.00  0.00           C+0
HETATM   20  C   UNK     0      -3.850  -5.541   0.000  0.00  0.00           C+0
HETATM   21  C   UNK     0       1.540   1.127   0.000  0.00  0.00           C+0
HETATM   22  C   UNK     0       3.080  -4.207   0.000  0.00  0.00           C+0
HETATM   23  C   UNK     0      -3.080  -4.207   0.000  0.00  0.00           C+0
HETATM   24  O   UNK     0      -5.390  -8.208   0.000  0.00  0.00           O+0
HETATM   25  O   UNK     0       7.700  -1.540   0.000  0.00  0.00           O+0
HETATM   26  O   UNK     0      -3.080  -1.540   0.000  0.00  0.00           O+0
HETATM   27  O   UNK     0      -7.700  -4.207   0.000  0.00  0.00           O+0
HETATM   28  O   UNK     0      -6.160  -6.875   0.000  0.00  0.00           O+0
HETATM   29  O   UNK     0       0.770   2.461   0.000  0.00  0.00           O+0
HETATM   30  O   UNK     0       3.850  -5.541   0.000  0.00  0.00           O+0
HETATM   31  O   UNK     0       6.160   1.127   0.000  0.00  0.00           O+0
HETATM   32  O   UNK     0      -3.850  -2.874   0.000  0.00  0.00           O+0
HETATM   33  O   UNK     0      -3.080  -6.875   0.000  0.00  0.00           O+0
HETATM   34  O   UNK     0       3.080   1.127   0.000  0.00  0.00           O+0
HETATM   35  O   UNK     0       1.540  -4.207   0.000  0.00  0.00           O+0
HETATM   36  O   UNK     0      -1.540  -4.207   0.000  0.00  0.00           O+0
CONECT    1    6                                                            
CONECT    2    7                                                            
CONECT    3   31                                                            
CONECT    4    8   10                                                       
CONECT    5    9   11                                                       
CONECT    6    1   14   32                                                  
CONECT    7    2   24   33                                                  
CONECT    8    4   12   22                                                  
CONECT    9    5   13   21                                                  
CONECT   10    4   16   25                                                  
CONECT   11    5   17   26                                                  
CONECT   12    8   13   18                                                  
CONECT   13    9   12   19                                                  
CONECT   14    6   15   27                                                  
CONECT   15   14   20   28                                                  
CONECT   16   10   18   31                                                  
CONECT   17   11   19   36                                                  
CONECT   18   12   16   34                                                  
CONECT   19   13   17   35                                                  
CONECT   20   15   23   33                                                  
CONECT   21    9   29   34                                                  
CONECT   22    8   30   35                                                  
CONECT   23   20   32   36                                                  
CONECT   24    7                                                            
CONECT   25   10                                                            
CONECT   26   11                                                            
CONECT   27   14                                                            
CONECT   28   15                                                            
CONECT   29   21                                                            
CONECT   30   22                                                            
CONECT   31    3   16                                                       
CONECT   32    6   23                                                       
CONECT   33    7   20                                                       
CONECT   34   18   21                                                       
CONECT   35   19   22                                                       
CONECT   36   17   23                                                       
MASTER        0    0    0    0    0    0    0    0   36    0   80    0
END

View in JSmol

Synonyms

Value	Source
2-({6,13-dihydroxy-14-methoxy-3,10-dioxo-2,9-dioxatetracyclo[6.6.2.0⁴,¹⁶.0¹¹,¹⁵]hexadeca-1(15),4,6,8(16),11,13-hexaen-7-yl}oxy)-4,5-dihydroxy-6-methyloxan-3-yl acetic acid	Generator
3-Methylellagate 8-(2-acetylrhamnoside)	Generator

Chemical Formula

C₂₃H₂₀O₁₃

Average Mass

504.3971 Da

Monoisotopic Mass

504.09039 Da

IUPAC Name

2-({6,13-dihydroxy-14-methoxy-3,10-dioxo-2,9-dioxatetracyclo[6.6.2.0⁴,¹⁶.0¹¹,¹⁵]hexadeca-1(15),4,6,8(16),11,13-hexaen-7-yl}oxy)-4,5-dihydroxy-6-methyloxan-3-yl acetate

Traditional Name

2-({6,13-dihydroxy-14-methoxy-3,10-dioxo-2,9-dioxatetracyclo[6.6.2.0⁴,¹⁶.0¹¹,¹⁵]hexadeca-1(15),4,6,8(16),11,13-hexaen-7-yl}oxy)-4,5-dihydroxy-6-methyloxan-3-yl acetate

CAS Registry Number

Not Available

SMILES

COC1=C(O)C=C2C(=O)OC3=C4C(=CC(O)=C3OC3OC(C)C(O)C(O)C3OC(C)=O)C(=O)OC1=C24

InChI Identifier

InChI=1S/C23H20O13/c1-6-14(27)15(28)20(33-7(2)24)23(32-6)36-17-11(26)5-9-13-12-8(22(30)35-19(13)17)4-10(25)16(31-3)18(12)34-21(9)29/h4-6,14-15,20,23,25-28H,1-3H3

InChI Key

XOBMJVRDRZBSBR-UHFFFAOYSA-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
Eucalyptus globulus	LOTUS Database	35616633

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as lignan glycosides. These are aromatic polycyclic compounds containing a carbohydrate component glycosidically linked to a lignan moiety. They include 1-aryltetralin lactones.

Kingdom

Organic compounds

Super Class

Lignans, neolignans and related compounds

Class

Lignan glycosides

Sub Class

Not Available

Direct Parent

Lignan glycosides

Alternative Parents

Substituents

Lignan glycoside
Dibenzylbutane lignan skeleton
Glycosyl compound
O-glycosyl compound
Methoxyphenol
Pentose monosaccharide
Phenoxy compound
Anisole
Methoxybenzene
Phenol ether
1-hydroxy-2-unsubstituted benzenoid
Alkyl aryl ether
Phenol
Monocyclic benzene moiety
Benzenoid
Monosaccharide
Oxane
Secondary alcohol
Organoheterocyclic compound
Ether
Oxacycle
Acetal
Polyol
Organic oxygen compound
Alcohol
Primary alcohol
Organooxygen compound
Hydrocarbon derivative
Aromatic heteromonocyclic compound

Molecular Framework

Aromatic heteromonocyclic 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	1.56	ALOGPS
logP	0.38	ChemAxon
logS	-2.6	ALOGPS
pKa (Strongest Acidic)	5.8	ChemAxon
pKa (Strongest Basic)	-3.6	ChemAxon
Physiological Charge	-2	ChemAxon
Hydrogen Acceptor Count	10	ChemAxon
Hydrogen Donor Count	4	ChemAxon
Polar Surface Area	187.51 Å²	ChemAxon
Rotatable Bond Count	5	ChemAxon
Refractivity	114.84 m³·mol⁻¹	ChemAxon
Polarizability	47.2 Å³	ChemAxon
Number of Rings	5	ChemAxon
Bioavailability	Yes	ChemAxon
Rule of Five	No	ChemAxon
Ghose Filter	No	ChemAxon
Veber's Rule	No	ChemAxon
MDDR-like Rule	No	ChemAxon

External Links

HMDB ID

HMDB0037084

DrugBank ID

Not Available

Phenol Explorer Compound ID

Not Available

FoodDB ID

FDB016072

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

131752144

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

LOTUS database [Link]

Showing NP-Card for 2-({6,13-dihydroxy-14-methoxy-3,10-dioxo-2,9-dioxatetracyclo[6.6.2.0⁴,¹⁶.0¹¹,¹⁵]hexadeca-1(15),4,6,8(16),11,13-hexaen-7-yl}oxy)-4,5-dihydroxy-6-methyloxan-3-yl acetate (NP0266646)

MOL for NP0266646 (2-({6,13-dihydroxy-14-methoxy-3,10-dioxo-2,9-dioxatetracyclo[6.6.2.0⁴,¹⁶.0¹¹,¹⁵]hexadeca-1(15),4,6,8(16),11,13-hexaen-7-yl}oxy)-4,5-dihydroxy-6-methyloxan-3-yl acetate)

3D MOL for NP0266646 (2-({6,13-dihydroxy-14-methoxy-3,10-dioxo-2,9-dioxatetracyclo[6.6.2.0⁴,¹⁶.0¹¹,¹⁵]hexadeca-1(15),4,6,8(16),11,13-hexaen-7-yl}oxy)-4,5-dihydroxy-6-methyloxan-3-yl acetate)

3D SDF for NP0266646 (2-({6,13-dihydroxy-14-methoxy-3,10-dioxo-2,9-dioxatetracyclo[6.6.2.0⁴,¹⁶.0¹¹,¹⁵]hexadeca-1(15),4,6,8(16),11,13-hexaen-7-yl}oxy)-4,5-dihydroxy-6-methyloxan-3-yl acetate)

3D-SDF for NP0266646 (2-({6,13-dihydroxy-14-methoxy-3,10-dioxo-2,9-dioxatetracyclo[6.6.2.0⁴,¹⁶.0¹¹,¹⁵]hexadeca-1(15),4,6,8(16),11,13-hexaen-7-yl}oxy)-4,5-dihydroxy-6-methyloxan-3-yl acetate)

PDB for NP0266646 (2-({6,13-dihydroxy-14-methoxy-3,10-dioxo-2,9-dioxatetracyclo[6.6.2.0⁴,¹⁶.0¹¹,¹⁵]hexadeca-1(15),4,6,8(16),11,13-hexaen-7-yl}oxy)-4,5-dihydroxy-6-methyloxan-3-yl acetate)

3D PDB for NP0266646 (2-({6,13-dihydroxy-14-methoxy-3,10-dioxo-2,9-dioxatetracyclo[6.6.2.0⁴,¹⁶.0¹¹,¹⁵]hexadeca-1(15),4,6,8(16),11,13-hexaen-7-yl}oxy)-4,5-dihydroxy-6-methyloxan-3-yl acetate)

SMILES for NP0266646 (2-({6,13-dihydroxy-14-methoxy-3,10-dioxo-2,9-dioxatetracyclo[6.6.2.0⁴,¹⁶.0¹¹,¹⁵]hexadeca-1(15),4,6,8(16),11,13-hexaen-7-yl}oxy)-4,5-dihydroxy-6-methyloxan-3-yl acetate)

INCHI for NP0266646 (2-({6,13-dihydroxy-14-methoxy-3,10-dioxo-2,9-dioxatetracyclo[6.6.2.0⁴,¹⁶.0¹¹,¹⁵]hexadeca-1(15),4,6,8(16),11,13-hexaen-7-yl}oxy)-4,5-dihydroxy-6-methyloxan-3-yl acetate)

Structure for NP0266646 (2-({6,13-dihydroxy-14-methoxy-3,10-dioxo-2,9-dioxatetracyclo[6.6.2.0⁴,¹⁶.0¹¹,¹⁵]hexadeca-1(15),4,6,8(16),11,13-hexaen-7-yl}oxy)-4,5-dihydroxy-6-methyloxan-3-yl acetate)

3D Structure for NP0266646 (2-({6,13-dihydroxy-14-methoxy-3,10-dioxo-2,9-dioxatetracyclo[6.6.2.0⁴,¹⁶.0¹¹,¹⁵]hexadeca-1(15),4,6,8(16),11,13-hexaen-7-yl}oxy)-4,5-dihydroxy-6-methyloxan-3-yl acetate)