NP-MRD: Showing NP-Card for (2r,3s,4s,5r,6r)-2-({[(2r,3r,4s,5s,6r)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}methyl)-6-[(2,6,6-trimethylcyclohex-1-en-1-yl)methoxy]oxane-3,4,5-triol (NP0247540)

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Record Information

Version

2.0

Created at

2022-09-07 09:25:44 UTC

Updated at

2022-09-07 09:25:45 UTC

NP-MRD ID

NP0247540

Secondary Accession Numbers

None

Natural Product Identification

Common Name

(2r,3s,4s,5r,6r)-2-({[(2r,3r,4s,5s,6r)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}methyl)-6-[(2,6,6-trimethylcyclohex-1-en-1-yl)methoxy]oxane-3,4,5-triol

Description

Nuciferoside belongs to the class of organic compounds known as o-glycosyl compounds. These are glycoside in which a sugar group is bonded through one carbon to another group via a O-glycosidic bond. (2r,3s,4s,5r,6r)-2-({[(2r,3r,4s,5s,6r)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}methyl)-6-[(2,6,6-trimethylcyclohex-1-en-1-yl)methoxy]oxane-3,4,5-triol is found in Nelumbo nucifera. (2r,3s,4s,5r,6r)-2-({[(2r,3r,4s,5s,6r)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}methyl)-6-[(2,6,6-trimethylcyclohex-1-en-1-yl)methoxy]oxane-3,4,5-triol was first documented in 2010 (PMID: 20118551). Based on a literature review very few articles have been published on Nuciferoside.

Structure

MOL 3D MOL SDF PDB SMILES InChI


  Mrv1652309072211252D          

 33 35  0  0  1  0            999 V2000
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M  END

     RDKit          3D

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M  END


  Mrv1652309072211252D          

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  2 33  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0247540

> <DATABASE_NAME>
NP-MRD

> <SMILES>
CC1=C(CO[C@@H]2O[C@H](CO[C@@H]3O[C@H](CO)[C@@H](O)[C@H](O)[C@H]3O)[C@@H](O)[C@H](O)[C@H]2O)C(C)(C)CCC1

> <INCHI_IDENTIFIER>
InChI=1S/C22H38O11/c1-10-5-4-6-22(2,3)11(10)8-30-20-19(29)17(27)15(25)13(33-20)9-31-21-18(28)16(26)14(24)12(7-23)32-21/h12-21,23-29H,4-9H2,1-3H3/t12-,13-,14-,15-,16+,17+,18-,19-,20-,21-/m1/s1

> <INCHI_KEY>
WFJDTYSQBHCNGC-LWZURRPWSA-N

> <FORMULA>
C22H38O11

> <MOLECULAR_WEIGHT>
478.535

> <EXACT_MASS>
478.241412044

> <JCHEM_ACCEPTOR_COUNT>
11

> <JCHEM_ATOM_COUNT>
71

> <JCHEM_AVERAGE_POLARIZABILITY>
49.75217775505997

> <JCHEM_BIOAVAILABILITY>
0

> <JCHEM_DONOR_COUNT>
7

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(2R,3S,4S,5R,6R)-2-({[(2R,3R,4S,5S,6R)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}methyl)-6-[(2,6,6-trimethylcyclohex-1-en-1-yl)methoxy]oxane-3,4,5-triol

> <JCHEM_LOGP>
-1.443163355000001

> <JCHEM_MDDR_LIKE_RULE>
1

> <JCHEM_NUMBER_OF_RINGS>
3

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
12.432768802375158

> <JCHEM_PKA_STRONGEST_ACIDIC>
11.910526586105258

> <JCHEM_PKA_STRONGEST_BASIC>
-2.981083422322401

> <JCHEM_POLAR_SURFACE_AREA>
178.53

> <JCHEM_REFRACTIVITY>
112.91160000000002

> <JCHEM_ROTATABLE_BOND_COUNT>
7

> <JCHEM_RULE_OF_FIVE>
0

> <JCHEM_TRADITIONAL_IUPAC>
(2R,3S,4S,5R,6R)-2-({[(2R,3R,4S,5S,6R)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}methyl)-6-[(2,6,6-trimethylcyclohex-1-en-1-yl)methoxy]oxane-3,4,5-triol

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 07-SEP-22   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   07-SEP-22         0                                  
HETATM    1  C   UNK     0       5.335 -12.320   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       6.668 -11.550   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       6.668 -10.010   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       5.335  -9.240   0.000  0.00  0.00           C+0
HETATM    5  O   UNK     0       5.335  -7.700   0.000  0.00  0.00           O+0
HETATM    6  C   UNK     0       4.001  -6.930   0.000  0.00  0.00           C+0
HETATM    7  O   UNK     0       4.001  -5.390   0.000  0.00  0.00           O+0
HETATM    8  C   UNK     0       2.667  -4.620   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0       2.667  -3.080   0.000  0.00  0.00           C+0
HETATM   10  O   UNK     0       1.334  -2.310   0.000  0.00  0.00           O+0
HETATM   11  C   UNK     0       1.334  -0.770   0.000  0.00  0.00           C+0
HETATM   12  O   UNK     0       0.000   0.000   0.000  0.00  0.00           O+0
HETATM   13  C   UNK     0       0.000   1.540   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0      -1.334   2.310   0.000  0.00  0.00           C+0
HETATM   15  O   UNK     0      -1.334   3.850   0.000  0.00  0.00           O+0
HETATM   16  C   UNK     0       1.334   2.310   0.000  0.00  0.00           C+0
HETATM   17  O   UNK     0       1.334   3.850   0.000  0.00  0.00           O+0
HETATM   18  C   UNK     0       2.667   1.540   0.000  0.00  0.00           C+0
HETATM   19  O   UNK     0       4.001   2.310   0.000  0.00  0.00           O+0
HETATM   20  C   UNK     0       2.667   0.000   0.000  0.00  0.00           C+0
HETATM   21  O   UNK     0       4.001  -0.770   0.000  0.00  0.00           O+0
HETATM   22  C   UNK     0       1.334  -5.390   0.000  0.00  0.00           C+0
HETATM   23  O   UNK     0       0.000  -4.620   0.000  0.00  0.00           O+0
HETATM   24  C   UNK     0       1.334  -6.930   0.000  0.00  0.00           C+0
HETATM   25  O   UNK     0       0.000  -7.700   0.000  0.00  0.00           O+0
HETATM   26  C   UNK     0       2.667  -7.700   0.000  0.00  0.00           C+0
HETATM   27  O   UNK     0       2.667  -9.240   0.000  0.00  0.00           O+0
HETATM   28  C   UNK     0       8.002  -9.240   0.000  0.00  0.00           C+0
HETATM   29  C   UNK     0       7.012  -8.060   0.000  0.00  0.00           C+0
HETATM   30  C   UNK     0       8.992  -8.060   0.000  0.00  0.00           C+0
HETATM   31  C   UNK     0       9.336 -10.010   0.000  0.00  0.00           C+0
HETATM   32  C   UNK     0       9.336 -11.550   0.000  0.00  0.00           C+0
HETATM   33  C   UNK     0       8.002 -12.320   0.000  0.00  0.00           C+0
CONECT    1    2                                                            
CONECT    2    1    3   33                                                  
CONECT    3    2    4   28                                                  
CONECT    4    3    5                                                       
CONECT    5    4    6                                                       
CONECT    6    5    7   26                                                  
CONECT    7    6    8                                                       
CONECT    8    7    9   22                                                  
CONECT    9    8   10                                                       
CONECT   10    9   11                                                       
CONECT   11   10   12   20                                                  
CONECT   12   11   13                                                       
CONECT   13   12   14   16                                                  
CONECT   14   13   15                                                       
CONECT   15   14                                                            
CONECT   16   13   17   18                                                  
CONECT   17   16                                                            
CONECT   18   16   19   20                                                  
CONECT   19   18                                                            
CONECT   20   18   11   21                                                  
CONECT   21   20                                                            
CONECT   22    8   23   24                                                  
CONECT   23   22                                                            
CONECT   24   22   25   26                                                  
CONECT   25   24                                                            
CONECT   26   24    6   27                                                  
CONECT   27   26                                                            
CONECT   28    3   29   30   31                                             
CONECT   29   28                                                            
CONECT   30   28                                                            
CONECT   31   28   32                                                       
CONECT   32   31   33                                                       
CONECT   33   32    2                                                       
MASTER        0    0    0    0    0    0    0    0   33    0   70    0
END

View in JSmol

Synonyms

Not Available

Chemical Formula

C₂₂H₃₈O₁₁

Average Mass

478.5350 Da

Monoisotopic Mass

478.24141 Da

IUPAC Name

(2R,3S,4S,5R,6R)-2-({[(2R,3R,4S,5S,6R)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}methyl)-6-[(2,6,6-trimethylcyclohex-1-en-1-yl)methoxy]oxane-3,4,5-triol

Traditional Name

(2R,3S,4S,5R,6R)-2-({[(2R,3R,4S,5S,6R)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}methyl)-6-[(2,6,6-trimethylcyclohex-1-en-1-yl)methoxy]oxane-3,4,5-triol

CAS Registry Number

Not Available

SMILES

CC1=C(CO[C@@H]2O[C@H](CO[C@@H]3O[C@H](CO)[C@@H](O)[C@H](O)[C@H]3O)[C@@H](O)[C@H](O)[C@H]2O)C(C)(C)CCC1

InChI Identifier

InChI=1S/C22H38O11/c1-10-5-4-6-22(2,3)11(10)8-30-20-19(29)17(27)15(25)13(33-20)9-31-21-18(28)16(26)14(24)12(7-23)32-21/h12-21,23-29H,4-9H2,1-3H3/t12-,13-,14-,15-,16+,17+,18-,19-,20-,21-/m1/s1

InChI Key

WFJDTYSQBHCNGC-LWZURRPWSA-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
Nelumbo nucifera	LOTUS Database	35616633

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as o-glycosyl compounds. These are glycoside in which a sugar group is bonded through one carbon to another group via a O-glycosidic bond.

Kingdom

Organic compounds

Super Class

Organic oxygen compounds

Class

Organooxygen compounds

Sub Class

Carbohydrates and carbohydrate conjugates

Direct Parent

O-glycosyl compounds

Alternative Parents

Substituents

O-glycosyl compound
Disaccharide
Oxane
Secondary alcohol
Oxacycle
Organoheterocyclic compound
Polyol
Acetal
Hydrocarbon derivative
Primary alcohol
Alcohol
Aliphatic heteromonocyclic compound

Molecular Framework

Aliphatic 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	-1.4	ChemAxon
pKa (Strongest Acidic)	11.91	ChemAxon
pKa (Strongest Basic)	-3	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	11	ChemAxon
Hydrogen Donor Count	7	ChemAxon
Polar Surface Area	178.53 Å²	ChemAxon
Rotatable Bond Count	7	ChemAxon
Refractivity	112.91 m³·mol⁻¹	ChemAxon
Polarizability	49.75 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

102169927

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

Jung HA, Jung YJ, Hyun SK, Min BS, Kim DW, Jung JH, Choi JS: Selective cholinesterase inhibitory activities of a new monoterpene diglycoside and other constituents from Nelumbo nucifera stamens. Biol Pharm Bull. 2010;33(2):267-72. doi: 10.1248/bpb.33.267. [PubMed:20118551 ]
LOTUS database [Link]

Showing NP-Card for (2r,3s,4s,5r,6r)-2-({[(2r,3r,4s,5s,6r)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}methyl)-6-[(2,6,6-trimethylcyclohex-1-en-1-yl)methoxy]oxane-3,4,5-triol (NP0247540)

MOL for NP0247540 ((2r,3s,4s,5r,6r)-2-({[(2r,3r,4s,5s,6r)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}methyl)-6-[(2,6,6-trimethylcyclohex-1-en-1-yl)methoxy]oxane-3,4,5-triol)

3D MOL for NP0247540 ((2r,3s,4s,5r,6r)-2-({[(2r,3r,4s,5s,6r)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}methyl)-6-[(2,6,6-trimethylcyclohex-1-en-1-yl)methoxy]oxane-3,4,5-triol)

3D SDF for NP0247540 ((2r,3s,4s,5r,6r)-2-({[(2r,3r,4s,5s,6r)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}methyl)-6-[(2,6,6-trimethylcyclohex-1-en-1-yl)methoxy]oxane-3,4,5-triol)

3D-SDF for NP0247540 ((2r,3s,4s,5r,6r)-2-({[(2r,3r,4s,5s,6r)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}methyl)-6-[(2,6,6-trimethylcyclohex-1-en-1-yl)methoxy]oxane-3,4,5-triol)

PDB for NP0247540 ((2r,3s,4s,5r,6r)-2-({[(2r,3r,4s,5s,6r)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}methyl)-6-[(2,6,6-trimethylcyclohex-1-en-1-yl)methoxy]oxane-3,4,5-triol)

3D PDB for NP0247540 ((2r,3s,4s,5r,6r)-2-({[(2r,3r,4s,5s,6r)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}methyl)-6-[(2,6,6-trimethylcyclohex-1-en-1-yl)methoxy]oxane-3,4,5-triol)

SMILES for NP0247540 ((2r,3s,4s,5r,6r)-2-({[(2r,3r,4s,5s,6r)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}methyl)-6-[(2,6,6-trimethylcyclohex-1-en-1-yl)methoxy]oxane-3,4,5-triol)

INCHI for NP0247540 ((2r,3s,4s,5r,6r)-2-({[(2r,3r,4s,5s,6r)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}methyl)-6-[(2,6,6-trimethylcyclohex-1-en-1-yl)methoxy]oxane-3,4,5-triol)

Structure for NP0247540 ((2r,3s,4s,5r,6r)-2-({[(2r,3r,4s,5s,6r)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}methyl)-6-[(2,6,6-trimethylcyclohex-1-en-1-yl)methoxy]oxane-3,4,5-triol)

3D Structure for NP0247540 ((2r,3s,4s,5r,6r)-2-({[(2r,3r,4s,5s,6r)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}methyl)-6-[(2,6,6-trimethylcyclohex-1-en-1-yl)methoxy]oxane-3,4,5-triol)