NP-MRD: Showing NP-Card for (-)-6-Desacetylscilliroside (NP0072675)

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Record Information

Version

2.0

Created at

2022-04-28 17:59:23 UTC

Updated at

2022-04-28 17:59:23 UTC

NP-MRD ID

NP0072675

Secondary Accession Numbers

None

Natural Product Identification

Common Name

(-)-6-Desacetylscilliroside

Description

Deacetylscilliroside belongs to the class of organic compounds known as bufanolides and derivatives. These are steroid lactones containing a pyran-2-one moiety linked to the C17 atom of a cyclopenta[a]phenanthrene derivative. (-)-6-Desacetylscilliroside is found in Urginea maritima . Based on a literature review very few articles have been published on Deacetylscilliroside.

Structure

MOL 3D MOL SDF PDB SMILES InChI


  Mrv1652304282219592D          

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M  END

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M  END


  Mrv1652304282219592D          

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   -0.5528    3.4925    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.9451    0.5269    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.2487    0.4185    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.6232    2.4441    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.3399    1.2325    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.8717    1.8632    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    5.5914    2.6391    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    6.1232    3.2699    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    6.9354    3.1246    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    7.2157    2.3487    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    6.6838    1.7180    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    8.0278    2.2035    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    8.5596    2.8342    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    7.4672    3.7553    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.8429    4.0458    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.7793    2.7844    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  2  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
  5  7  1  0  0  0  0
  7  8  1  0  0  0  0
  8  9  1  0  0  0  0
  9 10  1  0  0  0  0
  4 10  1  0  0  0  0
 10 11  1  6  0  0  0
  8 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
  7 15  1  6  0  0  0
 13 16  1  6  0  0  0
 13 17  1  0  0  0  0
 17 18  1  0  0  0  0
 18 19  1  0  0  0  0
 12 19  1  0  0  0  0
 17 20  1  6  0  0  0
 20 21  1  0  0  0  0
 21 22  2  0  0  0  0
 22 23  1  0  0  0  0
 23 24  2  0  0  0  0
 23 25  1  0  0  0  0
 25 26  1  0  0  0  0
 20 26  2  0  0  0  0
 12 27  1  6  0  0  0
  8 28  1  6  0  0  0
  5 29  1  6  0  0  0
  2 30  1  6  0  0  0
 31 30  1  1  0  0  0
 31 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
 35 36  1  0  0  0  0
 31 36  1  0  0  0  0
 35 37  1  1  0  0  0
 37 38  1  0  0  0  0
 34 39  1  6  0  0  0
 33 40  1  1  0  0  0
 32 41  1  6  0  0  0
M  END
> <DATABASE_ID>
NP0072675

> <DATABASE_NAME>
NP-MRD

> <SMILES>
C[C@]12CC[C@@H]3[C@@]4(C)CC[C@H](O[C@@H]5O[C@H](CO)[C@@H](O)[C@H](O)[C@H]5O)C=C4[C@H](O)C[C@@]3(O)[C@@]1(O)CC[C@@H]2C1=COC(=O)C=C1

> <INCHI_IDENTIFIER>
InChI=1S/C30H42O11/c1-27-8-5-16(40-26-25(36)24(35)23(34)20(13-31)41-26)11-18(27)19(32)12-29(37)21(27)7-9-28(2)17(6-10-30(28,29)38)15-3-4-22(33)39-14-15/h3-4,11,14,16-17,19-21,23-26,31-32,34-38H,5-10,12-13H2,1-2H3/t16-,17+,19+,20+,21+,23+,24-,25+,26+,27-,28+,29-,30+/m0/s1

> <INCHI_KEY>
XLCCXBCMWUOBIG-GBLFHTIZSA-N

> <FORMULA>
C30H42O11

> <MOLECULAR_WEIGHT>
578.655

> <EXACT_MASS>
578.272712172

> <JCHEM_ACCEPTOR_COUNT>
10

> <JCHEM_ATOM_COUNT>
83

> <JCHEM_AVERAGE_POLARIZABILITY>
60.38398253399028

> <JCHEM_BIOAVAILABILITY>
0

> <JCHEM_DONOR_COUNT>
7

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
5-[(1R,2R,5S,8R,10S,11R,14S,15R)-8,10,11-trihydroxy-2,15-dimethyl-5-{[(2R,3R,4S,5S,6R)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}tetracyclo[8.7.0.0^{2,7}.0^{11,15}]heptadec-6-en-14-yl]-2H-pyran-2-one

> <ALOGPS_LOGP>
-0.47

> <JCHEM_LOGP>
-1.0507435413333353

> <ALOGPS_LOGS>
-2.97

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
6

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
12.867447856945027

> <JCHEM_PKA_STRONGEST_ACIDIC>
12.149816766394904

> <JCHEM_PKA_STRONGEST_BASIC>
-2.981083683207145

> <JCHEM_POLAR_SURFACE_AREA>
186.37

> <JCHEM_REFRACTIVITY>
144.444

> <JCHEM_ROTATABLE_BOND_COUNT>
4

> <JCHEM_RULE_OF_FIVE>
0

> <ALOGPS_SOLUBILITY>
6.21e-01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
5-[(1R,2R,5S,8R,10S,11R,14S,15R)-8,10,11-trihydroxy-2,15-dimethyl-5-{[(2R,3R,4S,5S,6R)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}tetracyclo[8.7.0.0^{2,7}.0^{11,15}]heptadec-6-en-14-yl]pyran-2-one

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 28-APR-22   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   28-APR-22         0                                  
HETATM    1  C   UNK     0       7.929   4.020   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       8.452   2.572   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       7.459   1.394   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       5.943   1.666   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       5.420   3.114   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       6.413   4.291   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       3.904   3.385   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0       2.911   2.208   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0       3.434   0.759   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0       4.950   0.488   0.000  0.00  0.00           C+0
HETATM   11  O   UNK     0       5.474  -0.960   0.000  0.00  0.00           O+0
HETATM   12  C   UNK     0       1.395   2.479   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0       0.872   3.927   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0       1.865   5.104   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0       3.381   4.833   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0       0.200   5.313   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0      -0.667   3.877   0.000  0.00  0.00           C+0
HETATM   18  C   UNK     0      -1.095   2.398   0.000  0.00  0.00           C+0
HETATM   19  C   UNK     0       0.179   1.534   0.000  0.00  0.00           C+0
HETATM   20  C   UNK     0      -1.612   5.093   0.000  0.00  0.00           C+0
HETATM   21  C   UNK     0      -3.138   4.882   0.000  0.00  0.00           C+0
HETATM   22  C   UNK     0      -4.083   6.098   0.000  0.00  0.00           C+0
HETATM   23  C   UNK     0      -3.503   7.525   0.000  0.00  0.00           C+0
HETATM   24  O   UNK     0      -4.448   8.740   0.000  0.00  0.00           O+0
HETATM   25  O   UNK     0      -1.977   7.735   0.000  0.00  0.00           O+0
HETATM   26  C   UNK     0      -1.032   6.519   0.000  0.00  0.00           C+0
HETATM   27  O   UNK     0       1.764   0.984   0.000  0.00  0.00           O+0
HETATM   28  O   UNK     0       2.331   0.781   0.000  0.00  0.00           O+0
HETATM   29  C   UNK     0       4.897   4.562   0.000  0.00  0.00           C+0
HETATM   30  O   UNK     0       9.968   2.301   0.000  0.00  0.00           O+0
HETATM   31  C   UNK     0      10.961   3.478   0.000  0.00  0.00           C+0
HETATM   32  C   UNK     0      10.437   4.926   0.000  0.00  0.00           C+0
HETATM   33  C   UNK     0      11.430   6.104   0.000  0.00  0.00           C+0
HETATM   34  C   UNK     0      12.946   5.833   0.000  0.00  0.00           C+0
HETATM   35  C   UNK     0      13.469   4.384   0.000  0.00  0.00           C+0
HETATM   36  O   UNK     0      12.477   3.207   0.000  0.00  0.00           O+0
HETATM   37  C   UNK     0      14.985   4.113   0.000  0.00  0.00           C+0
HETATM   38  O   UNK     0      15.978   5.291   0.000  0.00  0.00           O+0
HETATM   39  O   UNK     0      13.939   7.010   0.000  0.00  0.00           O+0
HETATM   40  O   UNK     0      10.907   7.552   0.000  0.00  0.00           O+0
HETATM   41  O   UNK     0       8.921   5.197   0.000  0.00  0.00           O+0
CONECT    1    2    6                                                       
CONECT    2    1    3   30                                                  
CONECT    3    2    4                                                       
CONECT    4    3    5   10                                                  
CONECT    5    4    6    7   29                                             
CONECT    6    5    1                                                       
CONECT    7    5    8   15                                                  
CONECT    8    7    9   12   28                                             
CONECT    9    8   10                                                       
CONECT   10    9    4   11                                                  
CONECT   11   10                                                            
CONECT   12    8   13   19   27                                             
CONECT   13   12   14   16   17                                             
CONECT   14   13   15                                                       
CONECT   15   14    7                                                       
CONECT   16   13                                                            
CONECT   17   13   18   20                                                  
CONECT   18   17   19                                                       
CONECT   19   18   12                                                       
CONECT   20   17   21   26                                                  
CONECT   21   20   22                                                       
CONECT   22   21   23                                                       
CONECT   23   22   24   25                                                  
CONECT   24   23                                                            
CONECT   25   23   26                                                       
CONECT   26   25   20                                                       
CONECT   27   12                                                            
CONECT   28    8                                                            
CONECT   29    5                                                            
CONECT   30    2   31                                                       
CONECT   31   30   32   36                                                  
CONECT   32   31   33   41                                                  
CONECT   33   32   34   40                                                  
CONECT   34   33   35   39                                                  
CONECT   35   34   36   37                                                  
CONECT   36   35   31                                                       
CONECT   37   35   38                                                       
CONECT   38   37                                                            
CONECT   39   34                                                            
CONECT   40   33                                                            
CONECT   41   32                                                            
MASTER        0    0    0    0    0    0    0    0   41    0   92    0
END

View in JSmol

Synonyms

Not Available

Chemical Formula

C₃₀H₄₂O₁₁

Average Mass

578.6550 Da

Monoisotopic Mass

578.27271 Da

IUPAC Name

5-[(1R,2R,5S,8R,10S,11R,14S,15R)-8,10,11-trihydroxy-2,15-dimethyl-5-{[(2R,3R,4S,5S,6R)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}tetracyclo[8.7.0.0^{2,7}.0^{11,15}]heptadec-6-en-14-yl]-2H-pyran-2-one

Traditional Name

CAS Registry Number

Not Available

SMILES

C[C@]12CC[C@@H]3[C@@]4(C)CC[C@H](O[C@@H]5O[C@H](CO)[C@@H](O)[C@H](O)[C@H]5O)C=C4[C@H](O)C[C@@]3(O)[C@@]1(O)CC[C@@H]2C1=COC(=O)C=C1

InChI Identifier

InChI=1S/C30H42O11/c1-27-8-5-16(40-26-25(36)24(35)23(34)20(13-31)41-26)11-18(27)19(32)12-29(37)21(27)7-9-28(2)17(6-10-30(28,29)38)15-3-4-22(33)39-14-15/h3-4,11,14,16-17,19-21,23-26,31-32,34-38H,5-10,12-13H2,1-2H3/t16-,17+,19+,20+,21+,23+,24-,25+,26+,27-,28+,29-,30+/m0/s1

InChI Key

XLCCXBCMWUOBIG-GBLFHTIZSA-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
Drimia maritima	Plant	KNApSAcK

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as bufanolides and derivatives. These are steroid lactones containing a pyran-2-one moiety linked to the C17 atom of a cyclopenta[a]phenanthrene derivative.

Kingdom

Organic compounds

Super Class

Lipids and lipid-like molecules

Class

Steroids and steroid derivatives

Sub Class

Steroid lactones

Direct Parent

Bufanolides and derivatives

Alternative Parents

Substituents

Bufanolide-skeleton
Steroidal glycoside
14-hydroxysteroid
6-hydroxysteroid
Hydroxysteroid
Delta-4-steroid
Hexose monosaccharide
Glycosyl compound
O-glycosyl compound
Pyranone
Pyran
Oxane
Monosaccharide
Tertiary alcohol
Cyclic alcohol
Heteroaromatic compound
Secondary alcohol
Lactone
Organoheterocyclic compound
Polyol
Acetal
Oxacycle
Alcohol
Organic oxide
Primary alcohol
Hydrocarbon derivative
Organooxygen compound
Organic oxygen compound
Aromatic heteropolycyclic compound

Molecular Framework

Aromatic 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	-0.47	ALOGPS
logP	-1.1	ChemAxon
logS	-3	ALOGPS
pKa (Strongest Acidic)	12.15	ChemAxon
pKa (Strongest Basic)	-3	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	10	ChemAxon
Hydrogen Donor Count	7	ChemAxon
Polar Surface Area	186.37 Å²	ChemAxon
Rotatable Bond Count	4	ChemAxon
Refractivity	144.44 m³·mol⁻¹	ChemAxon
Polarizability	60.38 Å³	ChemAxon
Number of Rings	6	ChemAxon
Bioavailability	No	ChemAxon
Rule of Five	No	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

138827

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

157769

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

Not Available

Showing NP-Card for (-)-6-Desacetylscilliroside (NP0072675)

MOL for NP0072675 ((-)-6-Desacetylscilliroside)

3D MOL for NP0072675 ((-)-6-Desacetylscilliroside)

3D SDF for NP0072675 ((-)-6-Desacetylscilliroside)

3D-SDF for NP0072675 ((-)-6-Desacetylscilliroside)

PDB for NP0072675 ((-)-6-Desacetylscilliroside)

3D PDB for NP0072675 ((-)-6-Desacetylscilliroside)

SMILES for NP0072675 ((-)-6-Desacetylscilliroside)

INCHI for NP0072675 ((-)-6-Desacetylscilliroside)

Structure for NP0072675 ((-)-6-Desacetylscilliroside)

3D Structure for NP0072675 ((-)-6-Desacetylscilliroside)