NP-MRD: Showing NP-Card for 2-(2-{[1,3-dihydroxy-1-(4-hydroxy-3-methoxyphenyl)propan-2-yl]oxy}-5-(3-hydroxypropyl)phenoxy)-6-(hydroxymethyl)oxane-3,4,5-triol (NP0322248)

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Record Information

Version

2.0

Created at

2022-09-12 00:55:05 UTC

Updated at

2022-09-12 00:55:05 UTC

NP-MRD ID

NP0322248

Secondary Accession Numbers

None

Natural Product Identification

Common Name

2-(2-{[1,3-dihydroxy-1-(4-hydroxy-3-methoxyphenyl)propan-2-yl]oxy}-5-(3-hydroxypropyl)phenoxy)-6-(hydroxymethyl)oxane-3,4,5-triol

Description

2-(2-{[1,3-Dihydroxy-1-(4-hydroxy-3-methoxyphenyl)propan-2-yl]oxy}-5-(3-hydroxypropyl)phenoxy)-6-(hydroxymethyl)oxane-3,4,5-triol 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. 2-(2-{[1,3-dihydroxy-1-(4-hydroxy-3-methoxyphenyl)propan-2-yl]oxy}-5-(3-hydroxypropyl)phenoxy)-6-(hydroxymethyl)oxane-3,4,5-triol is found in Iodes cirrhosa and Lonicera gracilipes. 2-(2-{[1,3-Dihydroxy-1-(4-hydroxy-3-methoxyphenyl)propan-2-yl]oxy}-5-(3-hydroxypropyl)phenoxy)-6-(hydroxymethyl)oxane-3,4,5-triol is an extremely weak basic (essentially neutral) compound (based on its pKa).

Structure

MOL 3D MOL SDF PDB SMILES InChI


  Mrv1533004251513452D          

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M  END

     RDKit          3D

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M  END


  Mrv1533004251513452D          

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 10 12  1  0  0  0  0
 12 13  1  0  0  0  0
 13 14  1  0  0  0  0
 12 15  1  0  0  0  0
 15 16  1  0  0  0  0
 16 17  2  0  0  0  0
 17 18  1  0  0  0  0
 18 19  2  0  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  0  0  0  0
 19 24  1  0  0  0  0
 24 25  2  0  0  0  0
 16 25  1  0  0  0  0
 25 26  1  0  0  0  0
 26 27  1  0  0  0  0
 27 28  1  0  0  0  0
 28 29  1  0  0  0  0
 29 30  1  0  0  0  0
 30 31  1  0  0  0  0
 29 32  1  0  0  0  0
 32 33  1  0  0  0  0
 32 34  1  0  0  0  0
 34 35  1  0  0  0  0
 34 36  1  0  0  0  0
 27 36  1  0  0  0  0
 36 37  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0322248

> <DATABASE_NAME>
NP-MRD

> <SMILES>
COC1=CC(=CC=C1O)C(O)C(CO)OC1=CC=C(CCCO)C=C1OC1OC(CO)C(O)C(O)C1O

> <INCHI_IDENTIFIER>
InChI=1S/C25H34O12/c1-34-17-10-14(5-6-15(17)29)21(30)19(11-27)35-16-7-4-13(3-2-8-26)9-18(16)36-25-24(33)23(32)22(31)20(12-28)37-25/h4-7,9-10,19-33H,2-3,8,11-12H2,1H3

> <INCHI_KEY>
XFMPEFQVKDOPPT-UHFFFAOYSA-N

> <FORMULA>
C25H34O12

> <MOLECULAR_WEIGHT>
526.535

> <EXACT_MASS>
526.205026535

> <JCHEM_ACCEPTOR_COUNT>
12

> <JCHEM_ATOM_COUNT>
71

> <JCHEM_AVERAGE_POLARIZABILITY>
53.338949477804825

> <JCHEM_BIOAVAILABILITY>
0

> <JCHEM_DONOR_COUNT>
8

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
2-(2-{[1,3-dihydroxy-1-(4-hydroxy-3-methoxyphenyl)propan-2-yl]oxy}-5-(3-hydroxypropyl)phenoxy)-6-(hydroxymethyl)oxane-3,4,5-triol

> <ALOGPS_LOGP>
-0.20

> <JCHEM_LOGP>
-0.7876121159999996

> <ALOGPS_LOGS>
-2.87

> <JCHEM_MDDR_LIKE_RULE>
1

> <JCHEM_NUMBER_OF_RINGS>
3

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
12.177772766248783

> <JCHEM_PKA_STRONGEST_ACIDIC>
9.906490419960985

> <JCHEM_PKA_STRONGEST_BASIC>
-2.3774159967632285

> <JCHEM_POLAR_SURFACE_AREA>
198.76

> <JCHEM_REFRACTIVITY>
127.8001

> <JCHEM_ROTATABLE_BOND_COUNT>
12

> <JCHEM_RULE_OF_FIVE>
0

> <ALOGPS_SOLUBILITY>
7.14e-01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
2-(2-{[1,3-dihydroxy-1-(4-hydroxy-3-methoxyphenyl)propan-2-yl]oxy}-5-(3-hydroxypropyl)phenoxy)-6-(hydroxymethyl)oxane-3,4,5-triol

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 25-APR-15   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   25-APR-15         0                                  
HETATM    1  C   UNK     0      -5.335  -0.000   0.000  0.00  0.00           C+0
HETATM    2  O   UNK     0      -4.001  -0.770   0.000  0.00  0.00           O+0
HETATM    3  C   UNK     0      -4.001  -2.310   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0      -2.667  -3.080   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0      -2.667  -4.620   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0      -4.001  -5.390   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0      -5.335  -4.620   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0      -5.335  -3.080   0.000  0.00  0.00           C+0
HETATM    9  O   UNK     0      -6.668  -2.310   0.000  0.00  0.00           O+0
HETATM   10  C   UNK     0      -1.334  -5.390   0.000  0.00  0.00           C+0
HETATM   11  O   UNK     0      -1.334  -6.930   0.000  0.00  0.00           O+0
HETATM   12  C   UNK     0       0.000  -4.620   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0       0.000  -3.080   0.000  0.00  0.00           C+0
HETATM   14  O   UNK     0      -1.334  -2.310   0.000  0.00  0.00           O+0
HETATM   15  O   UNK     0       1.334  -5.390   0.000  0.00  0.00           O+0
HETATM   16  C   UNK     0       2.667  -4.620   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0       4.001  -5.390   0.000  0.00  0.00           C+0
HETATM   18  C   UNK     0       5.335  -4.620   0.000  0.00  0.00           C+0
HETATM   19  C   UNK     0       5.335  -3.080   0.000  0.00  0.00           C+0
HETATM   20  C   UNK     0       6.668  -2.310   0.000  0.00  0.00           C+0
HETATM   21  C   UNK     0       8.002  -3.080   0.000  0.00  0.00           C+0
HETATM   22  C   UNK     0       9.336  -2.310   0.000  0.00  0.00           C+0
HETATM   23  O   UNK     0      10.669  -3.080   0.000  0.00  0.00           O+0
HETATM   24  C   UNK     0       4.001  -2.310   0.000  0.00  0.00           C+0
HETATM   25  C   UNK     0       2.667  -3.080   0.000  0.00  0.00           C+0
HETATM   26  O   UNK     0       1.334  -2.310   0.000  0.00  0.00           O+0
HETATM   27  C   UNK     0       1.334  -0.770   0.000  0.00  0.00           C+0
HETATM   28  O   UNK     0       0.000  -0.000   0.000  0.00  0.00           O+0
HETATM   29  C   UNK     0       0.000   1.540   0.000  0.00  0.00           C+0
HETATM   30  C   UNK     0      -1.334   2.310   0.000  0.00  0.00           C+0
HETATM   31  O   UNK     0      -1.334   3.850   0.000  0.00  0.00           O+0
HETATM   32  C   UNK     0       1.334   2.310   0.000  0.00  0.00           C+0
HETATM   33  O   UNK     0       1.334   3.850   0.000  0.00  0.00           O+0
HETATM   34  C   UNK     0       2.667   1.540   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       2.667  -0.000   0.000  0.00  0.00           C+0
HETATM   37  O   UNK     0       4.001  -0.770   0.000  0.00  0.00           O+0
CONECT    1    2                                                            
CONECT    2    1    3                                                       
CONECT    3    2    4    8                                                  
CONECT    4    3    5                                                       
CONECT    5    4    6   10                                                  
CONECT    6    5    7                                                       
CONECT    7    6    8                                                       
CONECT    8    7    3    9                                                  
CONECT    9    8                                                            
CONECT   10    5   11   12                                                  
CONECT   11   10                                                            
CONECT   12   10   13   15                                                  
CONECT   13   12   14                                                       
CONECT   14   13                                                            
CONECT   15   12   16                                                       
CONECT   16   15   17   25                                                  
CONECT   17   16   18                                                       
CONECT   18   17   19                                                       
CONECT   19   18   20   24                                                  
CONECT   20   19   21                                                       
CONECT   21   20   22                                                       
CONECT   22   21   23                                                       
CONECT   23   22                                                            
CONECT   24   19   25                                                       
CONECT   25   24   16   26                                                  
CONECT   26   25   27                                                       
CONECT   27   26   28   36                                                  
CONECT   28   27   29                                                       
CONECT   29   28   30   32                                                  
CONECT   30   29   31                                                       
CONECT   31   30                                                            
CONECT   32   29   33   34                                                  
CONECT   33   32                                                            
CONECT   34   32   35   36                                                  
CONECT   35   34                                                            
CONECT   36   34   27   37                                                  
CONECT   37   36                                                            
MASTER        0    0    0    0    0    0    0    0   37    0   78    0
END

View in JSmol

Synonyms

Not Available

Chemical Formula

C₂₅H₃₄O₁₂

Average Mass

526.5350 Da

Monoisotopic Mass

526.20503 Da

IUPAC Name

2-(2-{[1,3-dihydroxy-1-(4-hydroxy-3-methoxyphenyl)propan-2-yl]oxy}-5-(3-hydroxypropyl)phenoxy)-6-(hydroxymethyl)oxane-3,4,5-triol

Traditional Name

2-(2-{[1,3-dihydroxy-1-(4-hydroxy-3-methoxyphenyl)propan-2-yl]oxy}-5-(3-hydroxypropyl)phenoxy)-6-(hydroxymethyl)oxane-3,4,5-triol

CAS Registry Number

Not Available

SMILES

COC1=CC(=CC=C1O)C(O)C(CO)OC1=CC=C(CCCO)C=C1OC1OC(CO)C(O)C(O)C1O

InChI Identifier

InChI=1S/C25H34O12/c1-34-17-10-14(5-6-15(17)29)21(30)19(11-27)35-16-7-4-13(3-2-8-26)9-18(16)36-25-24(33)23(32)22(31)20(12-28)37-25/h4-7,9-10,19-33H,2-3,8,11-12H2,1H3

InChI Key

XFMPEFQVKDOPPT-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
Iodes cirrhosa	LOTUS Database	35616633
Lonicera gracilipes	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
Phenolic glycoside
Hexose monosaccharide
Glycosyl compound
O-glycosyl compound
Methoxyphenol
Anisole
Phenoxy compound
Phenol ether
Methoxybenzene
1-hydroxy-2-unsubstituted benzenoid
Alkyl aryl ether
Phenol
Benzenoid
Monocyclic benzene moiety
Monosaccharide
Oxane
Secondary alcohol
Oxacycle
Acetal
Ether
Organoheterocyclic compound
Polyol
Hydrocarbon derivative
Organic oxygen compound
Alcohol
Organooxygen compound
Aromatic alcohol
Primary alcohol
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	-0.2	ALOGPS
logP	-0.79	ChemAxon
logS	-2.9	ALOGPS
pKa (Strongest Acidic)	9.91	ChemAxon
pKa (Strongest Basic)	-2.4	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	12	ChemAxon
Refractivity	127.8 m³·mol⁻¹	ChemAxon
Polarizability	53.34 Å³	ChemAxon
Number of Rings	3	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

76448220

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

LOTUS database [Link]

Showing NP-Card for 2-(2-{[1,3-dihydroxy-1-(4-hydroxy-3-methoxyphenyl)propan-2-yl]oxy}-5-(3-hydroxypropyl)phenoxy)-6-(hydroxymethyl)oxane-3,4,5-triol (NP0322248)

MOL for NP0322248 (2-(2-{[1,3-dihydroxy-1-(4-hydroxy-3-methoxyphenyl)propan-2-yl]oxy}-5-(3-hydroxypropyl)phenoxy)-6-(hydroxymethyl)oxane-3,4,5-triol)

3D MOL for NP0322248 (2-(2-{[1,3-dihydroxy-1-(4-hydroxy-3-methoxyphenyl)propan-2-yl]oxy}-5-(3-hydroxypropyl)phenoxy)-6-(hydroxymethyl)oxane-3,4,5-triol)

3D SDF for NP0322248 (2-(2-{[1,3-dihydroxy-1-(4-hydroxy-3-methoxyphenyl)propan-2-yl]oxy}-5-(3-hydroxypropyl)phenoxy)-6-(hydroxymethyl)oxane-3,4,5-triol)

3D-SDF for NP0322248 (2-(2-{[1,3-dihydroxy-1-(4-hydroxy-3-methoxyphenyl)propan-2-yl]oxy}-5-(3-hydroxypropyl)phenoxy)-6-(hydroxymethyl)oxane-3,4,5-triol)

PDB for NP0322248 (2-(2-{[1,3-dihydroxy-1-(4-hydroxy-3-methoxyphenyl)propan-2-yl]oxy}-5-(3-hydroxypropyl)phenoxy)-6-(hydroxymethyl)oxane-3,4,5-triol)

3D PDB for NP0322248 (2-(2-{[1,3-dihydroxy-1-(4-hydroxy-3-methoxyphenyl)propan-2-yl]oxy}-5-(3-hydroxypropyl)phenoxy)-6-(hydroxymethyl)oxane-3,4,5-triol)

SMILES for NP0322248 (2-(2-{[1,3-dihydroxy-1-(4-hydroxy-3-methoxyphenyl)propan-2-yl]oxy}-5-(3-hydroxypropyl)phenoxy)-6-(hydroxymethyl)oxane-3,4,5-triol)

INCHI for NP0322248 (2-(2-{[1,3-dihydroxy-1-(4-hydroxy-3-methoxyphenyl)propan-2-yl]oxy}-5-(3-hydroxypropyl)phenoxy)-6-(hydroxymethyl)oxane-3,4,5-triol)

Structure for NP0322248 (2-(2-{[1,3-dihydroxy-1-(4-hydroxy-3-methoxyphenyl)propan-2-yl]oxy}-5-(3-hydroxypropyl)phenoxy)-6-(hydroxymethyl)oxane-3,4,5-triol)

3D Structure for NP0322248 (2-(2-{[1,3-dihydroxy-1-(4-hydroxy-3-methoxyphenyl)propan-2-yl]oxy}-5-(3-hydroxypropyl)phenoxy)-6-(hydroxymethyl)oxane-3,4,5-triol)