NP-MRD: Showing NP-Card for (+)-Sonchuside D (NP0073743)

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Record Information

Version

2.0

Created at

2022-04-28 18:58:04 UTC

Updated at

2022-04-28 18:58:05 UTC

NP-MRD ID

NP0073743

Secondary Accession Numbers

None

Natural Product Identification

Common Name

(+)-Sonchuside D

Description

(3AR,5R,9S,11aS)-6,10-dimethyl-3-methylidene-2-oxo-9-{[(2R,3R,4S,5R,6R)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}-2H,3H,3aH,4H,5H,8H,9H,11aH-cyclodeca[b]furan-5-yl 2-(4-methoxyphenyl)acetate belongs to the class of organic compounds known as germacranolides and derivatives. These are sesquiterpene lactones with a structure based on the germacranolide skeleton, characterized by a gamma lactone fused to a 1,7-dimethylcyclodec-1-ene moiety. (+)-Sonchuside D is found in Sonchus asper (L.) Hill and Sonchus oleraceus L. . Based on a literature review very few articles have been published on (3aR,5R,9S,11aS)-6,10-dimethyl-3-methylidene-2-oxo-9-{[(2R,3R,4S,5R,6R)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}-2H,3H,3aH,4H,5H,8H,9H,11aH-cyclodeca[b]furan-5-yl 2-(4-methoxyphenyl)acetate.

Structure

MOL 3D MOL SDF PDB SMILES InChI


  Mrv1652304282220582D          

 41 44  0  0  1  0            999 V2000
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  3 41  1  0  0  0  0
M  END

     RDKit          3D

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M  END


  Mrv1652304282220582D          

 41 44  0  0  1  0            999 V2000
    2.8579    0.8250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
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   -2.0945    0.4125    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7846   -0.2549    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0396   -1.0396    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289   -0.8250    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145   -1.2375    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0000   -0.8250    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145   -2.0625    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0000   -2.4750    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0000   -3.3000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7145   -3.7125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4289   -3.3000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4289   -2.4750    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7145   -2.0625    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1434   -3.7125    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1434   -4.5375    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.1434   -1.2375    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  2  3  2  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
  6  7  1  0  0  0  0
  7  8  1  0  0  0  0
  8  9  2  0  0  0  0
  9 10  1  0  0  0  0
  1 10  1  0  0  0  0
 10 11  1  1  0  0  0
 12 11  1  1  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
 16 17  1  0  0  0  0
 12 17  1  0  0  0  0
 16 18  1  1  0  0  0
 18 19  1  0  0  0  0
 15 20  1  1  0  0  0
 14 21  1  1  0  0  0
 13 22  1  6  0  0  0
  9 23  1  0  0  0  0
  7 24  1  1  0  0  0
 24 25  1  0  0  0  0
 25 26  2  0  0  0  0
 25 27  1  0  0  0  0
  6 27  1  6  0  0  0
 27 28  2  0  0  0  0
  4 29  1  1  0  0  0
 29 30  1  0  0  0  0
 30 31  2  0  0  0  0
 30 32  1  0  0  0  0
 32 33  1  0  0  0  0
 33 34  2  0  0  0  0
 34 35  1  0  0  0  0
 35 36  2  0  0  0  0
 36 37  1  0  0  0  0
 37 38  2  0  0  0  0
 33 38  1  0  0  0  0
 36 39  1  0  0  0  0
 39 40  1  0  0  0  0
  3 41  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0073743

> <DATABASE_NAME>
NP-MRD

> <SMILES>
COC1=CC=C(CC(=O)O[C@@H]2C[C@H]3[C@@H](OC(=O)C3=C)\C=C(C)\[C@H](C\C=C2\C)O[C@@H]2O[C@H](CO)[C@H](O)[C@H](O)[C@H]2O)C=C1

> <INCHI_IDENTIFIER>
InChI=1S/C30H38O11/c1-15-5-10-21(40-30-28(35)27(34)26(33)24(14-31)41-30)16(2)11-23-20(17(3)29(36)39-23)13-22(15)38-25(32)12-18-6-8-19(37-4)9-7-18/h5-9,11,20-24,26-28,30-31,33-35H,3,10,12-14H2,1-2,4H3/b15-5-,16-11+/t20-,21+,22-,23+,24-,26+,27+,28-,30-/m1/s1

> <INCHI_KEY>
NOBPRNPEBCFZMU-RGOLDHRRSA-N

> <FORMULA>
C30H38O11

> <MOLECULAR_WEIGHT>
574.623

> <EXACT_MASS>
574.241412044

> <JCHEM_ACCEPTOR_COUNT>
9

> <JCHEM_ATOM_COUNT>
79

> <JCHEM_AVERAGE_POLARIZABILITY>
59.815612266556435

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
4

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(3aR,5R,9S,11aS)-6,10-dimethyl-3-methylidene-2-oxo-9-{[(2R,3R,4S,5R,6R)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}-2H,3H,3aH,4H,5H,8H,9H,11aH-cyclodeca[b]furan-5-yl 2-(4-methoxyphenyl)acetate

> <ALOGPS_LOGP>
1.25

> <JCHEM_LOGP>
1.701502831333333

> <ALOGPS_LOGS>
-3.51

> <JCHEM_MDDR_LIKE_RULE>
1

> <JCHEM_NUMBER_OF_RINGS>
4

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
13.199902786024598

> <JCHEM_PKA_STRONGEST_ACIDIC>
12.210081692726696

> <JCHEM_PKA_STRONGEST_BASIC>
-2.9810836857239913

> <JCHEM_POLAR_SURFACE_AREA>
161.20999999999998

> <JCHEM_REFRACTIVITY>
145.72729999999996

> <JCHEM_ROTATABLE_BOND_COUNT>
8

> <JCHEM_RULE_OF_FIVE>
0

> <ALOGPS_SOLUBILITY>
1.76e-01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
(3aR,5R,9S,11aS)-6,10-dimethyl-3-methylidene-2-oxo-9-{[(2R,3R,4S,5R,6R)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}-3aH,4H,5H,8H,9H,11aH-cyclodeca[b]furan-5-yl (4-methoxyphenyl)acetate

> <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       5.335   1.540   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       5.335  -0.000   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       4.001  -0.770   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       2.667  -0.000   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       1.334  -0.770   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0      -0.000  -0.000   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0      -0.000   1.540   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0       1.334   2.310   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0       2.667   1.540   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0       4.001   2.310   0.000  0.00  0.00           C+0
HETATM   11  O   UNK     0       4.001   3.850   0.000  0.00  0.00           O+0
HETATM   12  C   UNK     0       5.335   4.620   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0       5.335   6.160   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0       6.668   6.930   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0       8.002   6.160   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0       8.002   4.620   0.000  0.00  0.00           C+0
HETATM   17  O   UNK     0       6.668   3.850   0.000  0.00  0.00           O+0
HETATM   18  C   UNK     0       9.336   3.850   0.000  0.00  0.00           C+0
HETATM   19  O   UNK     0      10.669   4.620   0.000  0.00  0.00           O+0
HETATM   20  O   UNK     0       9.336   6.930   0.000  0.00  0.00           O+0
HETATM   21  O   UNK     0       6.668   8.470   0.000  0.00  0.00           O+0
HETATM   22  O   UNK     0       4.001   6.930   0.000  0.00  0.00           O+0
HETATM   23  C   UNK     0       3.573   0.294   0.000  0.00  0.00           C+0
HETATM   24  O   UNK     0      -1.465   2.016   0.000  0.00  0.00           O+0
HETATM   25  C   UNK     0      -2.370   0.770   0.000  0.00  0.00           C+0
HETATM   26  O   UNK     0      -3.910   0.770   0.000  0.00  0.00           O+0
HETATM   27  C   UNK     0      -1.465  -0.476   0.000  0.00  0.00           C+0
HETATM   28  C   UNK     0      -1.941  -1.941   0.000  0.00  0.00           C+0
HETATM   29  O   UNK     0       2.667  -1.540   0.000  0.00  0.00           O+0
HETATM   30  C   UNK     0       1.334  -2.310   0.000  0.00  0.00           C+0
HETATM   31  O   UNK     0      -0.000  -1.540   0.000  0.00  0.00           O+0
HETATM   32  C   UNK     0       1.334  -3.850   0.000  0.00  0.00           C+0
HETATM   33  C   UNK     0      -0.000  -4.620   0.000  0.00  0.00           C+0
HETATM   34  C   UNK     0      -0.000  -6.160   0.000  0.00  0.00           C+0
HETATM   35  C   UNK     0      -1.334  -6.930   0.000  0.00  0.00           C+0
HETATM   36  C   UNK     0      -2.667  -6.160   0.000  0.00  0.00           C+0
HETATM   37  C   UNK     0      -2.667  -4.620   0.000  0.00  0.00           C+0
HETATM   38  C   UNK     0      -1.334  -3.850   0.000  0.00  0.00           C+0
HETATM   39  O   UNK     0      -4.001  -6.930   0.000  0.00  0.00           O+0
HETATM   40  C   UNK     0      -4.001  -8.470   0.000  0.00  0.00           C+0
HETATM   41  C   UNK     0       4.001  -2.310   0.000  0.00  0.00           C+0
CONECT    1    2   10                                                       
CONECT    2    1    3                                                       
CONECT    3    2    4   41                                                  
CONECT    4    3    5   29                                                  
CONECT    5    4    6                                                       
CONECT    6    5    7   27                                                  
CONECT    7    6    8   24                                                  
CONECT    8    7    9                                                       
CONECT    9    8   10   23                                                  
CONECT   10    9    1   11                                                  
CONECT   11   10   12                                                       
CONECT   12   11   13   17                                                  
CONECT   13   12   14   22                                                  
CONECT   14   13   15   21                                                  
CONECT   15   14   16   20                                                  
CONECT   16   15   17   18                                                  
CONECT   17   16   12                                                       
CONECT   18   16   19                                                       
CONECT   19   18                                                            
CONECT   20   15                                                            
CONECT   21   14                                                            
CONECT   22   13                                                            
CONECT   23    9                                                            
CONECT   24    7   25                                                       
CONECT   25   24   26   27                                                  
CONECT   26   25                                                            
CONECT   27   25    6   28                                                  
CONECT   28   27                                                            
CONECT   29    4   30                                                       
CONECT   30   29   31   32                                                  
CONECT   31   30                                                            
CONECT   32   30   33                                                       
CONECT   33   32   34   38                                                  
CONECT   34   33   35                                                       
CONECT   35   34   36                                                       
CONECT   36   35   37   39                                                  
CONECT   37   36   38                                                       
CONECT   38   37   33                                                       
CONECT   39   36   40                                                       
CONECT   40   39                                                            
CONECT   41    3                                                            
MASTER        0    0    0    0    0    0    0    0   41    0   88    0
END

View in JSmol

Synonyms

Value	Source
(3AR,5R,9S,11as)-6,10-dimethyl-3-methylidene-2-oxo-9-{[(2R,3R,4S,5R,6R)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}-2H,3H,3ah,4H,5H,8H,9H,11ah-cyclodeca[b]furan-5-yl 2-(4-methoxyphenyl)acetic acid	Generator

Chemical Formula

C₃₀H₃₈O₁₁

Average Mass

574.6230 Da

Monoisotopic Mass

574.24141 Da

IUPAC Name

(3aR,5R,9S,11aS)-6,10-dimethyl-3-methylidene-2-oxo-9-{[(2R,3R,4S,5R,6R)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}-2H,3H,3aH,4H,5H,8H,9H,11aH-cyclodeca[b]furan-5-yl 2-(4-methoxyphenyl)acetate

Traditional Name

(3aR,5R,9S,11aS)-6,10-dimethyl-3-methylidene-2-oxo-9-{[(2R,3R,4S,5R,6R)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}-3aH,4H,5H,8H,9H,11aH-cyclodeca[b]furan-5-yl (4-methoxyphenyl)acetate

CAS Registry Number

Not Available

SMILES

COC1=CC=C(CC(=O)O[C@@H]2C[C@H]3[C@@H](OC(=O)C3=C)\C=C(C)\[C@H](C\C=C2\C)O[C@@H]2O[C@H](CO)[C@H](O)[C@H](O)[C@H]2O)C=C1

InChI Identifier

InChI=1S/C30H38O11/c1-15-5-10-21(40-30-28(35)27(34)26(33)24(14-31)41-30)16(2)11-23-20(17(3)29(36)39-23)13-22(15)38-25(32)12-18-6-8-19(37-4)9-7-18/h5-9,11,20-24,26-28,30-31,33-35H,3,10,12-14H2,1-2,4H3/b15-5-,16-11+/t20-,21+,22-,23+,24-,26+,27+,28-,30-/m1/s1

InChI Key

NOBPRNPEBCFZMU-RGOLDHRRSA-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
Sonchus asper	Plant	KNApSAcK
Sonchus oleraceus L.	Plant	KNApSAcK

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as germacranolides and derivatives. These are sesquiterpene lactones with a structure based on the germacranolide skeleton, characterized by a gamma lactone fused to a 1,7-dimethylcyclodec-1-ene moiety.

Kingdom

Organic compounds

Super Class

Lipids and lipid-like molecules

Class

Prenol lipids

Sub Class

Terpene lactones

Direct Parent

Germacranolides and derivatives

Alternative Parents

Substituents

Terpene glycoside
Germacranolide
Sesquiterpenoid
Germacrane sesquiterpenoid
Hexose monosaccharide
O-glycosyl compound
Glycosyl compound
Phenoxy compound
Methoxybenzene
Phenol ether
Anisole
Alkyl aryl ether
Benzenoid
Oxane
Monosaccharide
Gamma butyrolactone
Dicarboxylic acid or derivatives
Monocyclic benzene moiety
Alpha,beta-unsaturated carboxylic ester
Enoate ester
Tetrahydrofuran
Secondary alcohol
Lactone
Carboxylic acid ester
Oxacycle
Organoheterocyclic compound
Polyol
Ether
Carboxylic acid derivative
Acetal
Organic oxygen compound
Organic oxide
Hydrocarbon derivative
Primary alcohol
Organooxygen compound
Carbonyl group
Alcohol
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	1.25	ALOGPS
logP	1.7	ChemAxon
logS	-3.5	ALOGPS
pKa (Strongest Acidic)	12.21	ChemAxon
pKa (Strongest Basic)	-3	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	9	ChemAxon
Hydrogen Donor Count	4	ChemAxon
Polar Surface Area	161.21 Å²	ChemAxon
Rotatable Bond Count	8	ChemAxon
Refractivity	145.73 m³·mol⁻¹	ChemAxon
Polarizability	59.82 Å³	ChemAxon
Number of Rings	4	ChemAxon
Bioavailability	Yes	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

163088778

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

Not Available

Showing NP-Card for (+)-Sonchuside D (NP0073743)

MOL for NP0073743 ((+)-Sonchuside D)

3D MOL for NP0073743 ((+)-Sonchuside D)

3D SDF for NP0073743 ((+)-Sonchuside D)

3D-SDF for NP0073743 ((+)-Sonchuside D)

PDB for NP0073743 ((+)-Sonchuside D)

3D PDB for NP0073743 ((+)-Sonchuside D)

SMILES for NP0073743 ((+)-Sonchuside D)

INCHI for NP0073743 ((+)-Sonchuside D)

Structure for NP0073743 ((+)-Sonchuside D)

3D Structure for NP0073743 ((+)-Sonchuside D)