NP-MRD: Showing NP-Card for (-)-Nymphaeoside A (NP0080035)

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Record Information

Version

2.0

Created at

2022-04-29 01:04:54 UTC

Updated at

2022-04-29 01:04:54 UTC

NP-MRD ID

NP0080035

Secondary Accession Numbers

None

Natural Product Identification

Common Name

(-)-Nymphaeoside A

Description

(2S,3R,4R,5R,6S)-2-{4-[(1S,2R)-1,3-dihydroxy-2-[4-(3-hydroxypropyl)-2,6-dimethoxyphenoxy]propyl]-2-methoxyphenoxy}-6-methyloxane-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. (-)-Nymphaeoside A is found in Nymphaea odorata . Based on a literature review very few articles have been published on (2S,3R,4R,5R,6S)-2-{4-[(1S,2R)-1,3-dihydroxy-2-[4-(3-hydroxypropyl)-2,6-dimethoxyphenoxy]propyl]-2-methoxyphenoxy}-6-methyloxane-3,4,5-triol.

Structure

MOL 3D MOL SDF PDB SMILES InChI


  Mrv1652304292203042D          

 39 41  0  0  1  0            999 V2000
   -2.8579   -2.4750    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   -3.5724   -2.8875    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
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 17 36  1  1  0  0  0
  3 37  1  6  0  0  0
  2 38  1  6  0  0  0
  1 39  1  1  0  0  0
M  END

     RDKit          3D

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M  END


  Mrv1652304292203042D          

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    3.5724   -2.8875    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.2868   -2.4750    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.2868   -1.6500    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000   -7.4250    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -4.2868   -4.1250    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -4.2868   -2.4750    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8579   -1.6500    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  2  3  1  0  0  0  0
  3  4  1  0  0  0  0
  4  5  1  0  0  0  0
  5  6  1  0  0  0  0
  1  6  1  0  0  0  0
  6  7  1  6  0  0  0
  4  8  1  1  0  0  0
  8  9  1  0  0  0  0
  9 10  2  0  0  0  0
 10 11  1  0  0  0  0
 11 12  1  0  0  0  0
 10 13  1  0  0  0  0
 13 14  2  0  0  0  0
 14 15  1  0  0  0  0
 15 16  2  0  0  0  0
  9 16  1  0  0  0  0
 14 17  1  0  0  0  0
 17 18  1  0  0  0  0
 18 19  1  0  0  0  0
 19 20  1  0  0  0  0
 18 21  1  6  0  0  0
 21 22  1  0  0  0  0
 22 23  2  0  0  0  0
 23 24  1  0  0  0  0
 24 25  1  0  0  0  0
 23 26  1  0  0  0  0
 26 27  2  0  0  0  0
 27 28  1  0  0  0  0
 28 29  2  0  0  0  0
 22 29  1  0  0  0  0
 29 30  1  0  0  0  0
 30 31  1  0  0  0  0
 27 32  1  0  0  0  0
 32 33  1  0  0  0  0
 33 34  1  0  0  0  0
 34 35  1  0  0  0  0
 17 36  1  1  0  0  0
  3 37  1  6  0  0  0
  2 38  1  6  0  0  0
  1 39  1  1  0  0  0
M  END
> <DATABASE_ID>
NP0080035

> <DATABASE_NAME>
NP-MRD

> <SMILES>
COC1=CC(CCCO)=CC(OC)=C1O[C@H](CO)[C@@H](O)C1=CC(OC)=C(O[C@@H]2O[C@@H](C)[C@H](O)[C@@H](O)[C@H]2O)C=C1

> <INCHI_IDENTIFIER>
InChI=1S/C27H38O12/c1-14-22(30)24(32)25(33)27(37-14)39-17-8-7-16(12-18(17)34-2)23(31)21(13-29)38-26-19(35-3)10-15(6-5-9-28)11-20(26)36-4/h7-8,10-12,14,21-25,27-33H,5-6,9,13H2,1-4H3/t14-,21+,22-,23-,24+,25+,27-/m0/s1

> <INCHI_KEY>
ZKBLRWHYLYZGFT-VSXHCUMBSA-N

> <FORMULA>
C27H38O12

> <MOLECULAR_WEIGHT>
554.589

> <EXACT_MASS>
554.236326664

> <JCHEM_ACCEPTOR_COUNT>
12

> <JCHEM_ATOM_COUNT>
77

> <JCHEM_AVERAGE_POLARIZABILITY>
57.74638198872937

> <JCHEM_BIOAVAILABILITY>
0

> <JCHEM_DONOR_COUNT>
6

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(2S,3R,4R,5R,6S)-2-{4-[(1S,2R)-1,3-dihydroxy-2-[4-(3-hydroxypropyl)-2,6-dimethoxyphenoxy]propyl]-2-methoxyphenoxy}-6-methyloxane-3,4,5-triol

> <ALOGPS_LOGP>
0.97

> <JCHEM_LOGP>
0.24752064099999868

> <ALOGPS_LOGS>
-3.17

> <JCHEM_MDDR_LIKE_RULE>
1

> <JCHEM_NUMBER_OF_RINGS>
3

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
13.020904664943917

> <JCHEM_PKA_STRONGEST_ACIDIC>
12.18004999849244

> <JCHEM_PKA_STRONGEST_BASIC>
-2.3774168059536303

> <JCHEM_POLAR_SURFACE_AREA>
176.76

> <JCHEM_REFRACTIVITY>
137.20190000000002

> <JCHEM_ROTATABLE_BOND_COUNT>
13

> <JCHEM_RULE_OF_FIVE>
0

> <ALOGPS_SOLUBILITY>
3.75e-01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
(2S,3R,4R,5R,6S)-2-{4-[(1S,2R)-1,3-dihydroxy-2-[4-(3-hydroxypropyl)-2,6-dimethoxyphenoxy]propyl]-2-methoxyphenoxy}-6-methyloxane-3,4,5-triol

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 29-APR-22   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   29-APR-22         0                                  
HETATM    1  C   UNK     0      -5.335  -4.620   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0      -6.668  -5.390   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0      -6.668  -6.930   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0      -5.335  -7.700   0.000  0.00  0.00           C+0
HETATM    5  O   UNK     0      -4.001  -6.930   0.000  0.00  0.00           O+0
HETATM    6  C   UNK     0      -4.001  -5.390   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0      -2.667  -4.620   0.000  0.00  0.00           C+0
HETATM    8  O   UNK     0      -5.335  -9.240   0.000  0.00  0.00           O+0
HETATM    9  C   UNK     0      -4.001 -10.010   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0      -2.667  -9.240   0.000  0.00  0.00           C+0
HETATM   11  O   UNK     0      -2.667  -7.700   0.000  0.00  0.00           O+0
HETATM   12  C   UNK     0      -1.334  -6.930   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0      -1.334 -10.010   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0      -1.334 -11.550   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0      -2.667 -12.320   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0      -4.001 -11.550   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0       0.000 -12.320   0.000  0.00  0.00           C+0
HETATM   18  C   UNK     0       1.334 -11.550   0.000  0.00  0.00           C+0
HETATM   19  C   UNK     0       2.667 -12.320   0.000  0.00  0.00           C+0
HETATM   20  O   UNK     0       2.667 -13.860   0.000  0.00  0.00           O+0
HETATM   21  O   UNK     0       1.334 -10.010   0.000  0.00  0.00           O+0
HETATM   22  C   UNK     0       2.667  -9.240   0.000  0.00  0.00           C+0
HETATM   23  C   UNK     0       2.667  -7.700   0.000  0.00  0.00           C+0
HETATM   24  O   UNK     0       1.334  -6.930   0.000  0.00  0.00           O+0
HETATM   25  C   UNK     0       1.334  -5.390   0.000  0.00  0.00           C+0
HETATM   26  C   UNK     0       4.001  -6.930   0.000  0.00  0.00           C+0
HETATM   27  C   UNK     0       5.335  -7.700   0.000  0.00  0.00           C+0
HETATM   28  C   UNK     0       5.335  -9.240   0.000  0.00  0.00           C+0
HETATM   29  C   UNK     0       4.001 -10.010   0.000  0.00  0.00           C+0
HETATM   30  O   UNK     0       4.001 -11.550   0.000  0.00  0.00           O+0
HETATM   31  C   UNK     0       5.335 -12.320   0.000  0.00  0.00           C+0
HETATM   32  C   UNK     0       6.668  -6.930   0.000  0.00  0.00           C+0
HETATM   33  C   UNK     0       6.668  -5.390   0.000  0.00  0.00           C+0
HETATM   34  C   UNK     0       8.002  -4.620   0.000  0.00  0.00           C+0
HETATM   35  O   UNK     0       8.002  -3.080   0.000  0.00  0.00           O+0
HETATM   36  O   UNK     0       0.000 -13.860   0.000  0.00  0.00           O+0
HETATM   37  O   UNK     0      -8.002  -7.700   0.000  0.00  0.00           O+0
HETATM   38  O   UNK     0      -8.002  -4.620   0.000  0.00  0.00           O+0
HETATM   39  O   UNK     0      -5.335  -3.080   0.000  0.00  0.00           O+0
CONECT    1    2    6   39                                                  
CONECT    2    1    3   38                                                  
CONECT    3    2    4   37                                                  
CONECT    4    3    5    8                                                  
CONECT    5    4    6                                                       
CONECT    6    5    1    7                                                  
CONECT    7    6                                                            
CONECT    8    4    9                                                       
CONECT    9    8   10   16                                                  
CONECT   10    9   11   13                                                  
CONECT   11   10   12                                                       
CONECT   12   11                                                            
CONECT   13   10   14                                                       
CONECT   14   13   15   17                                                  
CONECT   15   14   16                                                       
CONECT   16   15    9                                                       
CONECT   17   14   18   36                                                  
CONECT   18   17   19   21                                                  
CONECT   19   18   20                                                       
CONECT   20   19                                                            
CONECT   21   18   22                                                       
CONECT   22   21   23   29                                                  
CONECT   23   22   24   26                                                  
CONECT   24   23   25                                                       
CONECT   25   24                                                            
CONECT   26   23   27                                                       
CONECT   27   26   28   32                                                  
CONECT   28   27   29                                                       
CONECT   29   28   22   30                                                  
CONECT   30   29   31                                                       
CONECT   31   30                                                            
CONECT   32   27   33                                                       
CONECT   33   32   34                                                       
CONECT   34   33   35                                                       
CONECT   35   34                                                            
CONECT   36   17                                                            
CONECT   37    3                                                            
CONECT   38    2                                                            
CONECT   39    1                                                            
MASTER        0    0    0    0    0    0    0    0   39    0   82    0
END

View in JSmol

Synonyms

Not Available

Chemical Formula

C₂₇H₃₈O₁₂

Average Mass

554.5890 Da

Monoisotopic Mass

554.23633 Da

IUPAC Name

(2S,3R,4R,5R,6S)-2-{4-[(1S,2R)-1,3-dihydroxy-2-[4-(3-hydroxypropyl)-2,6-dimethoxyphenoxy]propyl]-2-methoxyphenoxy}-6-methyloxane-3,4,5-triol

Traditional Name

(2S,3R,4R,5R,6S)-2-{4-[(1S,2R)-1,3-dihydroxy-2-[4-(3-hydroxypropyl)-2,6-dimethoxyphenoxy]propyl]-2-methoxyphenoxy}-6-methyloxane-3,4,5-triol

CAS Registry Number

Not Available

SMILES

COC1=CC(CCCO)=CC(OC)=C1O[C@H](CO)[C@@H](O)C1=CC(OC)=C(O[C@@H]2O[C@@H](C)[C@H](O)[C@@H](O)[C@H]2O)C=C1

InChI Identifier

InChI=1S/C27H38O12/c1-14-22(30)24(32)25(33)27(37-14)39-17-8-7-16(12-18(17)34-2)23(31)21(13-29)38-26-19(35-3)10-15(6-5-9-28)11-20(26)36-4/h7-8,10-12,14,21-25,27-33H,5-6,9,13H2,1-4H3/t14-,21+,22-,23-,24+,25+,27-/m0/s1

InChI Key

ZKBLRWHYLYZGFT-VSXHCUMBSA-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
Nymphaea odorata	Plant	KNApSAcK

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
O-glycosyl compound
Glycosyl compound
M-dimethoxybenzene
Dimethoxybenzene
Phenoxy compound
Methoxybenzene
Phenol ether
Anisole
Alkyl aryl ether
Benzenoid
Oxane
Monosaccharide
Monocyclic benzene moiety
Secondary alcohol
Oxacycle
Organoheterocyclic compound
Polyol
Ether
Acetal
Organic oxygen compound
Hydrocarbon derivative
Aromatic alcohol
Primary alcohol
Organooxygen compound
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	0.97	ALOGPS
logP	0.25	ChemAxon
logS	-3.2	ALOGPS
pKa (Strongest Acidic)	12.18	ChemAxon
pKa (Strongest Basic)	-2.4	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	12	ChemAxon
Hydrogen Donor Count	6	ChemAxon
Polar Surface Area	176.76 Å²	ChemAxon
Rotatable Bond Count	13	ChemAxon
Refractivity	137.2 m³·mol⁻¹	ChemAxon
Polarizability	57.75 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

163026275

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

Not Available

Showing NP-Card for (-)-Nymphaeoside A (NP0080035)

MOL for NP0080035 ((-)-Nymphaeoside A)

3D MOL for NP0080035 ((-)-Nymphaeoside A)

3D SDF for NP0080035 ((-)-Nymphaeoside A)

3D-SDF for NP0080035 ((-)-Nymphaeoside A)

PDB for NP0080035 ((-)-Nymphaeoside A)

3D PDB for NP0080035 ((-)-Nymphaeoside A)

SMILES for NP0080035 ((-)-Nymphaeoside A)

INCHI for NP0080035 ((-)-Nymphaeoside A)

Structure for NP0080035 ((-)-Nymphaeoside A)

3D Structure for NP0080035 ((-)-Nymphaeoside A)