NP-MRD: Showing NP-Card for (3r,4r,5r,6s)-2-{[(1s,2s,4s,5s,6r,10s)-2-(hydroxymethyl)-10-{[(3r,4s,5s,6r)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}-3,9-dioxatricyclo[4.4.0.0²,⁴]dec-7-en-5-yl]oxy}-6-methyloxane-3,4,5-triol (NP0234148)

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Record Information

Version

2.0

Created at

2022-09-06 16:01:14 UTC

Updated at

2022-09-06 16:01:14 UTC

NP-MRD ID

NP0234148

Secondary Accession Numbers

None

Natural Product Identification

Common Name

(3r,4r,5r,6s)-2-{[(1s,2s,4s,5s,6r,10s)-2-(hydroxymethyl)-10-{[(3r,4s,5s,6r)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}-3,9-dioxatricyclo[4.4.0.0²,⁴]dec-7-en-5-yl]oxy}-6-methyloxane-3,4,5-triol

Description

(3R,4R,5R,6S)-2-{[(1S,2S,4S,5S,6R,10S)-2-(hydroxymethyl)-10-{[(3R,4S,5S,6R)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}-3,9-dioxatricyclo[4.4.0.0²,⁴]Dec-7-en-5-yl]oxy}-6-methyloxane-3,4,5-triol 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. (3r,4r,5r,6s)-2-{[(1s,2s,4s,5s,6r,10s)-2-(hydroxymethyl)-10-{[(3r,4s,5s,6r)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}-3,9-dioxatricyclo[4.4.0.0²,⁴]dec-7-en-5-yl]oxy}-6-methyloxane-3,4,5-triol is found in Verbascum dentifolium. Based on a literature review very few articles have been published on (3R,4R,5R,6S)-2-{[(1S,2S,4S,5S,6R,10S)-2-(hydroxymethyl)-10-{[(3R,4S,5S,6R)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}-3,9-dioxatricyclo[4.4.0.0²,⁴]Dec-7-en-5-yl]oxy}-6-methyloxane-3,4,5-triol.

Structure

MOL 3D MOL SDF PDB SMILES InChI


  Mrv1652309062218012D          

 35 39  0  0  1  0            999 V2000
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M  END

     RDKit          3D

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M  END


  Mrv1652309062218012D          

 35 39  0  0  1  0            999 V2000
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 14 15  1  0  0  0  0
 15 16  1  0  0  0  0
 16 17  1  0  0  0  0
 17 18  1  6  0  0  0
 18 19  1  0  0  0  0
 17 20  1  0  0  0  0
 20 21  1  1  0  0  0
 20 22  1  0  0  0  0
 22 23  1  6  0  0  0
 22 24  1  0  0  0  0
 15 24  1  0  0  0  0
 24 25  1  1  0  0  0
 13 26  1  0  0  0  0
 26 27  1  0  0  0  0
 27 28  2  0  0  0  0
 29 28  1  1  0  0  0
  6 29  1  0  0  0  0
 12 29  1  0  0  0  0
  4 30  1  0  0  0  0
 30 31  1  1  0  0  0
 30 32  1  0  0  0  0
 32 33  1  1  0  0  0
 32 34  1  0  0  0  0
  2 34  1  0  0  0  0
 34 35  1  6  0  0  0
M  END
> <DATABASE_ID>
NP0234148

> <DATABASE_NAME>
NP-MRD

> <SMILES>
C[C@@H]1OC(O[C@@H]2[C@@H]3O[C@]3(CO)[C@@H]3[C@H]2C=CO[C@H]3OC2O[C@H](CO)[C@@H](O)[C@H](O)[C@H]2O)[C@H](O)[C@H](O)[C@H]1O

> <INCHI_IDENTIFIER>
InChI=1S/C21H32O14/c1-6-10(24)12(26)14(28)19(31-6)33-16-7-2-3-30-18(9(7)21(5-23)17(16)35-21)34-20-15(29)13(27)11(25)8(4-22)32-20/h2-3,6-20,22-29H,4-5H2,1H3/t6-,7+,8+,9+,10-,11+,12+,13-,14+,15+,16-,17-,18-,19?,20?,21+/m0/s1

> <INCHI_KEY>
GRLJTTHDCMSLHP-VBUSABLASA-N

> <FORMULA>
C21H32O14

> <MOLECULAR_WEIGHT>
508.473

> <EXACT_MASS>
508.17920571

> <JCHEM_ACCEPTOR_COUNT>
14

> <JCHEM_ATOM_COUNT>
67

> <JCHEM_AVERAGE_POLARIZABILITY>
48.807361398011274

> <JCHEM_BIOAVAILABILITY>
0

> <JCHEM_DONOR_COUNT>
8

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(3R,4R,5R,6S)-2-{[(1S,2S,4S,5S,6R,10S)-2-(hydroxymethyl)-10-{[(3R,4S,5S,6R)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}-3,9-dioxatricyclo[4.4.0.0^{2,4}]dec-7-en-5-yl]oxy}-6-methyloxane-3,4,5-triol

> <JCHEM_LOGP>
-4.155729288666667

> <JCHEM_MDDR_LIKE_RULE>
1

> <JCHEM_NUMBER_OF_RINGS>
5

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
12.43588197736555

> <JCHEM_PKA_STRONGEST_ACIDIC>
11.912558093090343

> <JCHEM_PKA_STRONGEST_BASIC>
-2.9810847601929344

> <JCHEM_POLAR_SURFACE_AREA>
220.51999999999995

> <JCHEM_REFRACTIVITY>
108.06110000000002

> <JCHEM_ROTATABLE_BOND_COUNT>
6

> <JCHEM_RULE_OF_FIVE>
0

> <JCHEM_TRADITIONAL_IUPAC>
(3R,4R,5R,6S)-2-{[(1S,2S,4S,5S,6R,10S)-2-(hydroxymethyl)-10-{[(3R,4S,5S,6R)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}-3,9-dioxatricyclo[4.4.0.0^{2,4}]dec-7-en-5-yl]oxy}-6-methyloxane-3,4,5-triol

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 06-SEP-22   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   06-SEP-22         0                                  
HETATM    1  C   UNK     0      -1.451   4.576   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0      -0.064   5.245   0.000  0.00  0.00           C+0
HETATM    3  O   UNK     0       1.209   4.379   0.000  0.00  0.00           O+0
HETATM    4  C   UNK     0       2.596   5.048   0.000  0.00  0.00           C+0
HETATM    5  O   UNK     0       3.869   4.182   0.000  0.00  0.00           O+0
HETATM    6  C   UNK     0       3.755   2.646   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       4.931   1.651   0.000  0.00  0.00           C+0
HETATM    8  O   UNK     0       5.874   0.433   0.000  0.00  0.00           O+0
HETATM    9  C   UNK     0       4.348   0.226   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0       4.395  -1.314   0.000  0.00  0.00           C+0
HETATM   11  O   UNK     0       5.752  -2.042   0.000  0.00  0.00           O+0
HETATM   12  C   UNK     0       2.812   0.339   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0       1.700  -0.726   0.000  0.00  0.00           C+0
HETATM   14  O   UNK     0       2.066  -2.222   0.000  0.00  0.00           O+0
HETATM   15  C   UNK     0       0.954  -3.287   0.000  0.00  0.00           C+0
HETATM   16  O   UNK     0       1.320  -4.783   0.000  0.00  0.00           O+0
HETATM   17  C   UNK     0       0.208  -5.848   0.000  0.00  0.00           C+0
HETATM   18  C   UNK     0       0.575  -7.343   0.000  0.00  0.00           C+0
HETATM   19  O   UNK     0      -0.538  -8.409   0.000  0.00  0.00           O+0
HETATM   20  C   UNK     0      -1.270  -5.417   0.000  0.00  0.00           C+0
HETATM   21  O   UNK     0      -2.383  -6.482   0.000  0.00  0.00           O+0
HETATM   22  C   UNK     0      -1.637  -3.921   0.000  0.00  0.00           C+0
HETATM   23  O   UNK     0      -3.115  -3.491   0.000  0.00  0.00           O+0
HETATM   24  C   UNK     0      -0.524  -2.856   0.000  0.00  0.00           C+0
HETATM   25  O   UNK     0      -0.891  -1.360   0.000  0.00  0.00           O+0
HETATM   26  O   UNK     0       0.221  -0.295   0.000  0.00  0.00           O+0
HETATM   27  C   UNK     0      -0.145   1.201   0.000  0.00  0.00           C+0
HETATM   28  C   UNK     0       0.967   2.266   0.000  0.00  0.00           C+0
HETATM   29  C   UNK     0       2.446   1.835   0.000  0.00  0.00           C+0
HETATM   30  C   UNK     0       2.710   6.584   0.000  0.00  0.00           C+0
HETATM   31  O   UNK     0       4.097   7.253   0.000  0.00  0.00           O+0
HETATM   32  C   UNK     0       1.437   7.450   0.000  0.00  0.00           C+0
HETATM   33  O   UNK     0       1.551   8.986   0.000  0.00  0.00           O+0
HETATM   34  C   UNK     0       0.050   6.781   0.000  0.00  0.00           C+0
HETATM   35  O   UNK     0      -1.223   7.647   0.000  0.00  0.00           O+0
CONECT    1    2                                                            
CONECT    2    1    3   34                                                  
CONECT    3    2    4                                                       
CONECT    4    3    5   30                                                  
CONECT    5    4    6                                                       
CONECT    6    5    7   29                                                  
CONECT    7    6    8    9                                                  
CONECT    8    7    9                                                       
CONECT    9    8    7   10   12                                             
CONECT   10    9   11                                                       
CONECT   11   10                                                            
CONECT   12    9   13   29                                                  
CONECT   13   12   14   26                                                  
CONECT   14   13   15                                                       
CONECT   15   14   16   24                                                  
CONECT   16   15   17                                                       
CONECT   17   16   18   20                                                  
CONECT   18   17   19                                                       
CONECT   19   18                                                            
CONECT   20   17   21   22                                                  
CONECT   21   20                                                            
CONECT   22   20   23   24                                                  
CONECT   23   22                                                            
CONECT   24   22   15   25                                                  
CONECT   25   24                                                            
CONECT   26   13   27                                                       
CONECT   27   26   28                                                       
CONECT   28   27   29                                                       
CONECT   29   28    6   12                                                  
CONECT   30    4   31   32                                                  
CONECT   31   30                                                            
CONECT   32   30   33   34                                                  
CONECT   33   32                                                            
CONECT   34   32    2   35                                                  
CONECT   35   34                                                            
MASTER        0    0    0    0    0    0    0    0   35    0   78    0
END

View in JSmol

Synonyms

Not Available

Chemical Formula

C₂₁H₃₂O₁₄

Average Mass

508.4730 Da

Monoisotopic Mass

508.17921 Da

IUPAC Name

Not Available

Traditional Name

Not Available

CAS Registry Number

Not Available

SMILES

C[C@@H]1OC(O[C@@H]2[C@@H]3O[C@]3(CO)[C@@H]3[C@H]2C=CO[C@H]3OC2O[C@H](CO)[C@@H](O)[C@H](O)[C@H]2O)[C@H](O)[C@H](O)[C@H]1O

InChI Identifier

InChI=1S/C21H32O14/c1-6-10(24)12(26)14(28)19(31-6)33-16-7-2-3-30-18(9(7)21(5-23)17(16)35-21)34-20-15(29)13(27)11(25)8(4-22)32-20/h2-3,6-20,22-29H,4-5H2,1H3/t6-,7+,8+,9+,10-,11+,12+,13-,14+,15+,16-,17-,18-,19?,20?,21+/m0/s1

InChI Key

GRLJTTHDCMSLHP-VBUSABLASA-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
Verbascum dentifolium	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
Oxane
Monosaccharide
Secondary alcohol
Oxacycle
Organoheterocyclic compound
Polyol
Ether
Oxirane
Dialkyl ether
Acetal
Hydrocarbon derivative
Primary alcohol
Alcohol
Aliphatic heteropolycyclic compound

Molecular Framework

Aliphatic heteropolycyclic 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

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

163029879

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

LOTUS database [Link]

Showing NP-Card for (3r,4r,5r,6s)-2-{[(1s,2s,4s,5s,6r,10s)-2-(hydroxymethyl)-10-{[(3r,4s,5s,6r)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}-3,9-dioxatricyclo[4.4.0.0²,⁴]dec-7-en-5-yl]oxy}-6-methyloxane-3,4,5-triol (NP0234148)

MOL for NP0234148 ((3r,4r,5r,6s)-2-{[(1s,2s,4s,5s,6r,10s)-2-(hydroxymethyl)-10-{[(3r,4s,5s,6r)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}-3,9-dioxatricyclo[4.4.0.0²,⁴]dec-7-en-5-yl]oxy}-6-methyloxane-3,4,5-triol)

3D MOL for NP0234148 ((3r,4r,5r,6s)-2-{[(1s,2s,4s,5s,6r,10s)-2-(hydroxymethyl)-10-{[(3r,4s,5s,6r)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}-3,9-dioxatricyclo[4.4.0.0²,⁴]dec-7-en-5-yl]oxy}-6-methyloxane-3,4,5-triol)

3D SDF for NP0234148 ((3r,4r,5r,6s)-2-{[(1s,2s,4s,5s,6r,10s)-2-(hydroxymethyl)-10-{[(3r,4s,5s,6r)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}-3,9-dioxatricyclo[4.4.0.0²,⁴]dec-7-en-5-yl]oxy}-6-methyloxane-3,4,5-triol)

3D-SDF for NP0234148 ((3r,4r,5r,6s)-2-{[(1s,2s,4s,5s,6r,10s)-2-(hydroxymethyl)-10-{[(3r,4s,5s,6r)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}-3,9-dioxatricyclo[4.4.0.0²,⁴]dec-7-en-5-yl]oxy}-6-methyloxane-3,4,5-triol)

PDB for NP0234148 ((3r,4r,5r,6s)-2-{[(1s,2s,4s,5s,6r,10s)-2-(hydroxymethyl)-10-{[(3r,4s,5s,6r)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}-3,9-dioxatricyclo[4.4.0.0²,⁴]dec-7-en-5-yl]oxy}-6-methyloxane-3,4,5-triol)

3D PDB for NP0234148 ((3r,4r,5r,6s)-2-{[(1s,2s,4s,5s,6r,10s)-2-(hydroxymethyl)-10-{[(3r,4s,5s,6r)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}-3,9-dioxatricyclo[4.4.0.0²,⁴]dec-7-en-5-yl]oxy}-6-methyloxane-3,4,5-triol)

SMILES for NP0234148 ((3r,4r,5r,6s)-2-{[(1s,2s,4s,5s,6r,10s)-2-(hydroxymethyl)-10-{[(3r,4s,5s,6r)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}-3,9-dioxatricyclo[4.4.0.0²,⁴]dec-7-en-5-yl]oxy}-6-methyloxane-3,4,5-triol)

INCHI for NP0234148 ((3r,4r,5r,6s)-2-{[(1s,2s,4s,5s,6r,10s)-2-(hydroxymethyl)-10-{[(3r,4s,5s,6r)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}-3,9-dioxatricyclo[4.4.0.0²,⁴]dec-7-en-5-yl]oxy}-6-methyloxane-3,4,5-triol)

Structure for NP0234148 ((3r,4r,5r,6s)-2-{[(1s,2s,4s,5s,6r,10s)-2-(hydroxymethyl)-10-{[(3r,4s,5s,6r)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}-3,9-dioxatricyclo[4.4.0.0²,⁴]dec-7-en-5-yl]oxy}-6-methyloxane-3,4,5-triol)

3D Structure for NP0234148 ((3r,4r,5r,6s)-2-{[(1s,2s,4s,5s,6r,10s)-2-(hydroxymethyl)-10-{[(3r,4s,5s,6r)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}-3,9-dioxatricyclo[4.4.0.0²,⁴]dec-7-en-5-yl]oxy}-6-methyloxane-3,4,5-triol)