NP-MRD: Showing NP-Card for (3s,4s)-3,4-bis[(4-hydroxy-3-methoxyphenyl)methyl]-3-{[(2s,3r,4s,5s,6r)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}oxolan-2-one (NP0298474)

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Record Information

Version

2.0

Created at

2022-09-10 09:44:48 UTC

Updated at

2022-09-10 09:44:48 UTC

NP-MRD ID

NP0298474

Secondary Accession Numbers

None

Natural Product Identification

Common Name

(3s,4s)-3,4-bis[(4-hydroxy-3-methoxyphenyl)methyl]-3-{[(2s,3r,4s,5s,6r)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}oxolan-2-one

Description

858127-38-5 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. (3s,4s)-3,4-bis[(4-hydroxy-3-methoxyphenyl)methyl]-3-{[(2s,3r,4s,5s,6r)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}oxolan-2-one is found in Trachelospermum jasminoides. Based on a literature review very few articles have been published on 858127-38-5.

Structure

MOL 3D MOL SDF PDB SMILES InChI


  Mrv1652309102211442D          

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M  END

     RDKit          3D

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  Mrv1652309102211442D          

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  8  9  1  0  0  0  0
  9 10  1  0  0  0  0
 10 11  2  0  0  0  0
 10 12  1  0  0  0  0
  7 12  1  0  0  0  0
 12 13  1  6  0  0  0
 13 14  1  0  0  0  0
 14 15  2  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
 17 19  1  0  0  0  0
 19 20  1  0  0  0  0
 20 21  1  0  0  0  0
 19 22  2  0  0  0  0
 14 22  1  0  0  0  0
 12 23  1  1  0  0  0
 24 23  1  6  0  0  0
 24 25  1  0  0  0  0
 25 26  1  0  0  0  0
 26 27  1  6  0  0  0
 27 28  1  0  0  0  0
 26 29  1  0  0  0  0
 29 30  1  1  0  0  0
 29 31  1  0  0  0  0
 31 32  1  6  0  0  0
 31 33  1  0  0  0  0
 24 33  1  0  0  0  0
 33 34  1  1  0  0  0
  5 35  2  0  0  0  0
 35 36  1  0  0  0  0
 36 37  2  0  0  0  0
  3 37  1  0  0  0  0
 37 38  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0298474

> <DATABASE_NAME>
NP-MRD

> <SMILES>
COC1=CC(C[C@H]2COC(=O)[C@@]2(CC2=CC=C(O)C(OC)=C2)O[C@@H]2O[C@H](CO)[C@@H](O)[C@H](O)[C@H]2O)=CC=C1O

> <INCHI_IDENTIFIER>
InChI=1S/C26H32O12/c1-34-18-8-13(3-5-16(18)28)7-15-12-36-25(33)26(15,10-14-4-6-17(29)19(9-14)35-2)38-24-23(32)22(31)21(30)20(11-27)37-24/h3-6,8-9,15,20-24,27-32H,7,10-12H2,1-2H3/t15-,20+,21+,22-,23+,24-,26-/m0/s1

> <INCHI_KEY>
YAVQULWQXQRTKS-KOFHWYBRSA-N

> <FORMULA>
C26H32O12

> <MOLECULAR_WEIGHT>
536.53

> <EXACT_MASS>
536.18937647

> <JCHEM_ACCEPTOR_COUNT>
11

> <JCHEM_ATOM_COUNT>
70

> <JCHEM_AVERAGE_POLARIZABILITY>
53.166059749134526

> <JCHEM_BIOAVAILABILITY>
0

> <JCHEM_DONOR_COUNT>
6

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(3S,4S)-3,4-bis[(4-hydroxy-3-methoxyphenyl)methyl]-3-{[(2S,3R,4S,5S,6R)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}oxolan-2-one

> <JCHEM_LOGP>
0.6591710093333341

> <JCHEM_MDDR_LIKE_RULE>
1

> <JCHEM_NUMBER_OF_RINGS>
4

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
10.24203358668323

> <JCHEM_PKA_STRONGEST_ACIDIC>
9.642309118088885

> <JCHEM_PKA_STRONGEST_BASIC>
-2.981083882469405

> <JCHEM_POLAR_SURFACE_AREA>
184.6

> <JCHEM_REFRACTIVITY>
129.50290000000004

> <JCHEM_ROTATABLE_BOND_COUNT>
9

> <JCHEM_RULE_OF_FIVE>
0

> <JCHEM_TRADITIONAL_IUPAC>
(3S,4S)-3,4-bis[(4-hydroxy-3-methoxyphenyl)methyl]-3-{[(2S,3R,4S,5S,6R)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}oxolan-2-one

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 10-SEP-22   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   10-SEP-22         0                                  
HETATM    1  C   UNK     0       8.406  -5.466   0.000  0.00  0.00           C+0
HETATM    2  O   UNK     0       7.262  -4.436   0.000  0.00  0.00           O+0
HETATM    3  C   UNK     0       5.797  -4.912   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       4.653  -3.881   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       3.188  -4.357   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       2.044  -3.327   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       0.579  -3.803   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0       0.103  -5.267   0.000  0.00  0.00           C+0
HETATM    9  O   UNK     0      -1.437  -5.267   0.000  0.00  0.00           O+0
HETATM   10  C   UNK     0      -1.913  -3.803   0.000  0.00  0.00           C+0
HETATM   11  O   UNK     0      -3.377  -3.327   0.000  0.00  0.00           O+0
HETATM   12  C   UNK     0      -0.667  -2.898   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0      -1.423  -1.556   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0      -2.963  -1.540   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0      -3.719  -0.198   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0      -5.259  -0.182   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0      -6.043  -1.508   0.000  0.00  0.00           C+0
HETATM   18  O   UNK     0      -7.582  -1.491   0.000  0.00  0.00           O+0
HETATM   19  C   UNK     0      -5.287  -2.849   0.000  0.00  0.00           C+0
HETATM   20  O   UNK     0      -6.071  -4.175   0.000  0.00  0.00           O+0
HETATM   21  C   UNK     0      -5.315  -5.516   0.000  0.00  0.00           C+0
HETATM   22  C   UNK     0      -3.747  -2.865   0.000  0.00  0.00           C+0
HETATM   23  O   UNK     0       0.089  -1.556   0.000  0.00  0.00           O+0
HETATM   24  C   UNK     0      -0.695  -0.230   0.000  0.00  0.00           C+0
HETATM   25  O   UNK     0      -2.235  -0.246   0.000  0.00  0.00           O+0
HETATM   26  C   UNK     0      -3.019   1.079   0.000  0.00  0.00           C+0
HETATM   27  C   UNK     0      -4.559   1.063   0.000  0.00  0.00           C+0
HETATM   28  O   UNK     0      -5.342   2.388   0.000  0.00  0.00           O+0
HETATM   29  C   UNK     0      -2.263   2.421   0.000  0.00  0.00           C+0
HETATM   30  O   UNK     0      -3.047   3.746   0.000  0.00  0.00           O+0
HETATM   31  C   UNK     0      -0.723   2.437   0.000  0.00  0.00           C+0
HETATM   32  O   UNK     0       0.033   3.779   0.000  0.00  0.00           O+0
HETATM   33  C   UNK     0       0.061   1.111   0.000  0.00  0.00           C+0
HETATM   34  O   UNK     0       1.601   1.127   0.000  0.00  0.00           O+0
HETATM   35  C   UNK     0       2.868  -5.864   0.000  0.00  0.00           C+0
HETATM   36  C   UNK     0       4.012  -6.894   0.000  0.00  0.00           C+0
HETATM   37  C   UNK     0       5.477  -6.418   0.000  0.00  0.00           C+0
HETATM   38  O   UNK     0       6.621  -7.449   0.000  0.00  0.00           O+0
CONECT    1    2                                                            
CONECT    2    1    3                                                       
CONECT    3    2    4   37                                                  
CONECT    4    3    5                                                       
CONECT    5    4    6   35                                                  
CONECT    6    5    7                                                       
CONECT    7    6    8   12                                                  
CONECT    8    7    9                                                       
CONECT    9    8   10                                                       
CONECT   10    9   11   12                                                  
CONECT   11   10                                                            
CONECT   12   10    7   13   23                                             
CONECT   13   12   14                                                       
CONECT   14   13   15   22                                                  
CONECT   15   14   16                                                       
CONECT   16   15   17                                                       
CONECT   17   16   18   19                                                  
CONECT   18   17                                                            
CONECT   19   17   20   22                                                  
CONECT   20   19   21                                                       
CONECT   21   20                                                            
CONECT   22   19   14                                                       
CONECT   23   12   24                                                       
CONECT   24   23   25   33                                                  
CONECT   25   24   26                                                       
CONECT   26   25   27   29                                                  
CONECT   27   26   28                                                       
CONECT   28   27                                                            
CONECT   29   26   30   31                                                  
CONECT   30   29                                                            
CONECT   31   29   32   33                                                  
CONECT   32   31                                                            
CONECT   33   31   24   34                                                  
CONECT   34   33                                                            
CONECT   35    5   36                                                       
CONECT   36   35   37                                                       
CONECT   37   36    3   38                                                  
CONECT   38   37                                                            
MASTER        0    0    0    0    0    0    0    0   38    0   82    0
END

View in JSmol

Synonyms

Not Available

Chemical Formula

C₂₆H₃₂O₁₂

Average Mass

536.5300 Da

Monoisotopic Mass

536.18938 Da

IUPAC Name

(3S,4S)-3,4-bis[(4-hydroxy-3-methoxyphenyl)methyl]-3-{[(2S,3R,4S,5S,6R)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}oxolan-2-one

Traditional Name

(3S,4S)-3,4-bis[(4-hydroxy-3-methoxyphenyl)methyl]-3-{[(2S,3R,4S,5S,6R)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}oxolan-2-one

CAS Registry Number

Not Available

SMILES

COC1=CC(C[C@H]2COC(=O)[C@@]2(CC2=CC=C(O)C(OC)=C2)O[C@@H]2O[C@H](CO)[C@@H](O)[C@H](O)[C@H]2O)=CC=C1O

InChI Identifier

InChI=1S/C26H32O12/c1-34-18-8-13(3-5-16(18)28)7-15-12-36-25(33)26(15,10-14-4-6-17(29)19(9-14)35-2)38-24-23(32)22(31)21(30)20(11-27)37-24/h3-6,8-9,15,20-24,27-32H,7,10-12H2,1-2H3/t15-,20+,21+,22-,23+,24-,26-/m0/s1

InChI Key

YAVQULWQXQRTKS-KOFHWYBRSA-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
Trachelospermum jasminoides	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
Dibenzylbutyrolactone
Lignan lactone
Tetrahydrofuran lignan
9,9p-epoxylignan
Furanoid lignan
Fatty acyl glycoside
Fatty acyl glycoside of mono- or disaccharide
Glycosyl compound
O-glycosyl compound
Methoxyphenol
Methoxybenzene
Anisole
Phenol ether
Phenoxy compound
Alkyl aryl ether
Phenol
1-hydroxy-2-unsubstituted benzenoid
Benzenoid
Fatty acyl
Monocyclic benzene moiety
Oxane
Monosaccharide
Gamma butyrolactone
Tetrahydrofuran
Secondary alcohol
Carboxylic acid ester
Lactone
Acetal
Monocarboxylic acid or derivatives
Ether
Oxacycle
Carboxylic acid derivative
Polyol
Organoheterocyclic compound
Organic oxygen compound
Alcohol
Organooxygen compound
Carbonyl group
Primary alcohol
Organic oxide
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	0.66	ChemAxon
pKa (Strongest Acidic)	9.64	ChemAxon
pKa (Strongest Basic)	-3	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	11	ChemAxon
Hydrogen Donor Count	6	ChemAxon
Polar Surface Area	184.6 Å²	ChemAxon
Rotatable Bond Count	9	ChemAxon
Refractivity	129.5 m³·mol⁻¹	ChemAxon
Polarizability	53.17 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

114951848

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

154702993

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

LOTUS database [Link]

Showing NP-Card for (3s,4s)-3,4-bis[(4-hydroxy-3-methoxyphenyl)methyl]-3-{[(2s,3r,4s,5s,6r)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}oxolan-2-one (NP0298474)

MOL for NP0298474 ((3s,4s)-3,4-bis[(4-hydroxy-3-methoxyphenyl)methyl]-3-{[(2s,3r,4s,5s,6r)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}oxolan-2-one)

3D MOL for NP0298474 ((3s,4s)-3,4-bis[(4-hydroxy-3-methoxyphenyl)methyl]-3-{[(2s,3r,4s,5s,6r)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}oxolan-2-one)

3D SDF for NP0298474 ((3s,4s)-3,4-bis[(4-hydroxy-3-methoxyphenyl)methyl]-3-{[(2s,3r,4s,5s,6r)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}oxolan-2-one)

3D-SDF for NP0298474 ((3s,4s)-3,4-bis[(4-hydroxy-3-methoxyphenyl)methyl]-3-{[(2s,3r,4s,5s,6r)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}oxolan-2-one)

PDB for NP0298474 ((3s,4s)-3,4-bis[(4-hydroxy-3-methoxyphenyl)methyl]-3-{[(2s,3r,4s,5s,6r)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}oxolan-2-one)

3D PDB for NP0298474 ((3s,4s)-3,4-bis[(4-hydroxy-3-methoxyphenyl)methyl]-3-{[(2s,3r,4s,5s,6r)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}oxolan-2-one)

SMILES for NP0298474 ((3s,4s)-3,4-bis[(4-hydroxy-3-methoxyphenyl)methyl]-3-{[(2s,3r,4s,5s,6r)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}oxolan-2-one)

INCHI for NP0298474 ((3s,4s)-3,4-bis[(4-hydroxy-3-methoxyphenyl)methyl]-3-{[(2s,3r,4s,5s,6r)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}oxolan-2-one)

Structure for NP0298474 ((3s,4s)-3,4-bis[(4-hydroxy-3-methoxyphenyl)methyl]-3-{[(2s,3r,4s,5s,6r)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}oxolan-2-one)

3D Structure for NP0298474 ((3s,4s)-3,4-bis[(4-hydroxy-3-methoxyphenyl)methyl]-3-{[(2s,3r,4s,5s,6r)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}oxolan-2-one)