NP-MRD: Showing NP-Card for (-)-Virescenoside S (NP0079353)

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Record Information

Version

2.0

Created at

2022-04-29 00:23:02 UTC

Updated at

2022-04-29 00:23:02 UTC

NP-MRD ID

NP0079353

Secondary Accession Numbers

None

Natural Product Identification

Common Name

(-)-Virescenoside S

Description

(1S,4aR,4bR,7R,9R,10aR)-7-ethenyl-9-hydroxy-1,4a,7,10a-tetramethyl-1-({[(2R,3S,4R,5R,6R)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}methyl)-1,2,3,4,4a,4b,5,6,7,9,10,10a-dodecahydrophenanthren-2-one belongs to the class of organic compounds known as steroidal glycosides. These are sterol lipids containing a carbohydrate moiety glycosidically linked to the steroid skeleton. (-)-Virescenoside S is found in Sagenomella striatispora. Based on a literature review very few articles have been published on (1S,4aR,4bR,7R,9R,10aR)-7-ethenyl-9-hydroxy-1,4a,7,10a-tetramethyl-1-({[(2R,3S,4R,5R,6R)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}methyl)-1,2,3,4,4a,4b,5,6,7,9,10,10a-dodecahydrophenanthren-2-one.

Structure

MOL 3D MOL SDF PDB SMILES InChI


  Mrv1652304292202232D          

 35 38  0  0  1  0            999 V2000
    2.7770    1.1270    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
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M  END

     RDKit          3D

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M  END


  Mrv1652304292202232D          

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  5  6  2  0  0  0  0
  5  7  1  0  0  0  0
  1  7  1  0  0  0  0
  4  8  1  1  0  0  0
  4  9  1  6  0  0  0
  9 10  1  0  0  0  0
 11 10  1  6  0  0  0
 11 12  1  0  0  0  0
 12 13  1  0  0  0  0
 13 14  1  0  0  0  0
 14 15  1  0  0  0  0
 15 16  1  0  0  0  0
 11 16  1  0  0  0  0
 16 17  1  6  0  0  0
 15 18  1  1  0  0  0
 14 19  1  6  0  0  0
 13 20  1  6  0  0  0
 20 21  1  0  0  0  0
  3 22  1  0  0  0  0
 22 23  1  0  0  0  0
 23 24  1  0  0  0  0
 24 25  2  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
 29 28  1  6  0  0  0
  2 29  1  0  0  0  0
 24 29  1  0  0  0  0
 26 30  1  1  0  0  0
 30 31  2  0  0  0  0
 26 32  1  6  0  0  0
 23 33  1  1  0  0  0
  3 34  1  1  0  0  0
  2 35  1  6  0  0  0
M  END
> <DATABASE_ID>
NP0079353

> <DATABASE_NAME>
NP-MRD

> <SMILES>
C[C@@]1(CC[C@H]2C(=C1)[C@H](O)C[C@@]1(C)[C@@](C)(CO[C@@H]3O[C@H](CO)[C@H](O)[C@@H](O)[C@@H]3O)C(=O)CC[C@]21C)C=C

> <INCHI_IDENTIFIER>
InChI=1S/C27H42O8/c1-6-24(2)9-7-16-15(11-24)17(29)12-27(5)25(16,3)10-8-19(30)26(27,4)14-34-23-22(33)21(32)20(31)18(13-28)35-23/h6,11,16-18,20-23,28-29,31-33H,1,7-10,12-14H2,2-5H3/t16-,17+,18+,20-,21+,22-,23+,24-,25+,26-,27+/m0/s1

> <INCHI_KEY>
KZXYHMBFZGKDMN-ZBAFKBEGSA-N

> <FORMULA>
C27H42O8

> <MOLECULAR_WEIGHT>
494.625

> <EXACT_MASS>
494.287968312

> <JCHEM_ACCEPTOR_COUNT>
8

> <JCHEM_ATOM_COUNT>
77

> <JCHEM_AVERAGE_POLARIZABILITY>
53.76342918413526

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
5

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(1S,4aR,4bR,7R,9R,10aR)-7-ethenyl-9-hydroxy-1,4a,7,10a-tetramethyl-1-({[(2R,3S,4R,5R,6R)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}methyl)-1,2,3,4,4a,4b,5,6,7,9,10,10a-dodecahydrophenanthren-2-one

> <ALOGPS_LOGP>
1.15

> <JCHEM_LOGP>
1.2258378693333327

> <ALOGPS_LOGS>
-3.13

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
4

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
13.200239054496262

> <JCHEM_PKA_STRONGEST_ACIDIC>
12.210942430548943

> <JCHEM_PKA_STRONGEST_BASIC>
-0.8910903885183757

> <JCHEM_POLAR_SURFACE_AREA>
136.68

> <JCHEM_REFRACTIVITY>
129.4894

> <JCHEM_ROTATABLE_BOND_COUNT>
5

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
3.66e-01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
(1S,4aR,4bR,7R,9R,10aR)-7-ethenyl-9-hydroxy-1,4a,7,10a-tetramethyl-1-({[(2R,3S,4R,5R,6R)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}methyl)-4,4b,5,6,9,10-hexahydro-3H-phenanthren-2-one

> <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       5.184   2.104   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       4.414   0.770   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       5.184  -0.564   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       6.724  -0.564   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       7.494   0.770   0.000  0.00  0.00           C+0
HETATM    6  O   UNK     0       9.034   0.770   0.000  0.00  0.00           O+0
HETATM    7  C   UNK     0       6.724   2.104   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0       6.777  -2.103   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0       8.030  -1.380   0.000  0.00  0.00           C+0
HETATM   10  O   UNK     0       7.976  -2.919   0.000  0.00  0.00           O+0
HETATM   11  C   UNK     0       9.282  -3.735   0.000  0.00  0.00           C+0
HETATM   12  O   UNK     0      10.642  -3.012   0.000  0.00  0.00           O+0
HETATM   13  C   UNK     0      11.948  -3.828   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0      11.894  -5.367   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0      10.534  -6.090   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0       9.228  -5.274   0.000  0.00  0.00           C+0
HETATM   17  O   UNK     0       7.868  -5.997   0.000  0.00  0.00           O+0
HETATM   18  O   UNK     0      10.480  -7.629   0.000  0.00  0.00           O+0
HETATM   19  O   UNK     0      13.200  -6.183   0.000  0.00  0.00           O+0
HETATM   20  C   UNK     0      13.307  -3.105   0.000  0.00  0.00           C+0
HETATM   21  O   UNK     0      14.613  -3.921   0.000  0.00  0.00           O+0
HETATM   22  C   UNK     0       4.414  -1.897   0.000  0.00  0.00           C+0
HETATM   23  C   UNK     0       2.874  -1.897   0.000  0.00  0.00           C+0
HETATM   24  C   UNK     0       2.104  -0.564   0.000  0.00  0.00           C+0
HETATM   25  C   UNK     0       0.564  -0.564   0.000  0.00  0.00           C+0
HETATM   26  C   UNK     0      -0.206   0.770   0.000  0.00  0.00           C+0
HETATM   27  C   UNK     0       0.564   2.104   0.000  0.00  0.00           C+0
HETATM   28  C   UNK     0       2.104   2.104   0.000  0.00  0.00           C+0
HETATM   29  C   UNK     0       2.874   0.770   0.000  0.00  0.00           C+0
HETATM   30  C   UNK     0      -1.566   0.047   0.000  0.00  0.00           C+0
HETATM   31  C   UNK     0      -1.620  -1.492   0.000  0.00  0.00           C+0
HETATM   32  C   UNK     0      -1.566   1.493   0.000  0.00  0.00           C+0
HETATM   33  O   UNK     0       2.104  -3.231   0.000  0.00  0.00           O+0
HETATM   34  C   UNK     0       5.954  -1.897   0.000  0.00  0.00           C+0
HETATM   35  C   UNK     0       3.644   2.104   0.000  0.00  0.00           C+0
CONECT    1    2    7                                                       
CONECT    2    1    3   29   35                                             
CONECT    3    2    4   22   34                                             
CONECT    4    3    5    8    9                                             
CONECT    5    4    6    7                                                  
CONECT    6    5                                                            
CONECT    7    5    1                                                       
CONECT    8    4                                                            
CONECT    9    4   10                                                       
CONECT   10    9   11                                                       
CONECT   11   10   12   16                                                  
CONECT   12   11   13                                                       
CONECT   13   12   14   20                                                  
CONECT   14   13   15   19                                                  
CONECT   15   14   16   18                                                  
CONECT   16   15   11   17                                                  
CONECT   17   16                                                            
CONECT   18   15                                                            
CONECT   19   14                                                            
CONECT   20   13   21                                                       
CONECT   21   20                                                            
CONECT   22    3   23                                                       
CONECT   23   22   24   33                                                  
CONECT   24   23   25   29                                                  
CONECT   25   24   26                                                       
CONECT   26   25   27   30   32                                             
CONECT   27   26   28                                                       
CONECT   28   27   29                                                       
CONECT   29   28    2   24                                                  
CONECT   30   26   31                                                       
CONECT   31   30                                                            
CONECT   32   26                                                            
CONECT   33   23                                                            
CONECT   34    3                                                            
CONECT   35    2                                                            
MASTER        0    0    0    0    0    0    0    0   35    0   76    0
END

View in JSmol

Synonyms

Not Available

Chemical Formula

C₂₇H₄₂O₈

Average Mass

494.6250 Da

Monoisotopic Mass

494.28797 Da

IUPAC Name

Traditional Name

(1S,4aR,4bR,7R,9R,10aR)-7-ethenyl-9-hydroxy-1,4a,7,10a-tetramethyl-1-({[(2R,3S,4R,5R,6R)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}methyl)-4,4b,5,6,9,10-hexahydro-3H-phenanthren-2-one

CAS Registry Number

Not Available

SMILES

C[C@@]1(CC[C@H]2C(=C1)[C@H](O)C[C@@]1(C)[C@@](C)(CO[C@@H]3O[C@H](CO)[C@H](O)[C@@H](O)[C@@H]3O)C(=O)CC[C@]21C)C=C

InChI Identifier

InChI=1S/C27H42O8/c1-6-24(2)9-7-16-15(11-24)17(29)12-27(5)25(16,3)10-8-19(30)26(27,4)14-34-23-22(33)21(32)20(31)18(13-28)35-23/h6,11,16-18,20-23,28-29,31-33H,1,7-10,12-14H2,2-5H3/t16-,17+,18+,20-,21+,22-,23+,24-,25+,26-,27+/m0/s1

InChI Key

KZXYHMBFZGKDMN-ZBAFKBEGSA-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
Sagenomella striatispora	LOTUS Database	35616633

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as steroidal glycosides. These are sterol lipids containing a carbohydrate moiety glycosidically linked to the steroid skeleton.

Kingdom

Organic compounds

Super Class

Lipids and lipid-like molecules

Class

Steroids and steroid derivatives

Sub Class

Steroidal glycosides

Direct Parent

Steroidal glycosides

Alternative Parents

Substituents

Diterpene glycoside
Steroidal glycoside
20-norclerodane diterpenoid
Pimarane diterpenoid
Diterpenoid
Hydroxysteroid
6-hydroxysteroid
Terpene glycoside
Phenanthrene
Hydrophenanthrene
Hexose monosaccharide
O-glycosyl compound
Glycosyl compound
Oxane
Monosaccharide
Cyclic alcohol
Cyclic ketone
Secondary alcohol
Ketone
Oxacycle
Organoheterocyclic compound
Polyol
Acetal
Organic oxygen compound
Organic oxide
Hydrocarbon derivative
Primary alcohol
Organooxygen compound
Carbonyl group
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
logP	1.15	ALOGPS
logP	1.23	ChemAxon
logS	-3.1	ALOGPS
pKa (Strongest Acidic)	12.21	ChemAxon
pKa (Strongest Basic)	-0.89	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	8	ChemAxon
Hydrogen Donor Count	5	ChemAxon
Polar Surface Area	136.68 Å²	ChemAxon
Rotatable Bond Count	5	ChemAxon
Refractivity	129.49 m³·mol⁻¹	ChemAxon
Polarizability	53.76 Å³	ChemAxon
Number of Rings	4	ChemAxon
Bioavailability	Yes	ChemAxon
Rule of Five	Yes	ChemAxon
Ghose Filter	No	ChemAxon
Veber's Rule	No	ChemAxon
MDDR-like Rule	No	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

163104821

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

Not Available

Showing NP-Card for (-)-Virescenoside S (NP0079353)

MOL for NP0079353 ((-)-Virescenoside S)

3D MOL for NP0079353 ((-)-Virescenoside S)

3D SDF for NP0079353 ((-)-Virescenoside S)

3D-SDF for NP0079353 ((-)-Virescenoside S)

PDB for NP0079353 ((-)-Virescenoside S)

3D PDB for NP0079353 ((-)-Virescenoside S)

SMILES for NP0079353 ((-)-Virescenoside S)

INCHI for NP0079353 ((-)-Virescenoside S)

Structure for NP0079353 ((-)-Virescenoside S)

3D Structure for NP0079353 ((-)-Virescenoside S)