NP-MRD: Showing NP-Card for Cucurbitacin S (NP0052182)

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Record Information

Version

2.0

Created at

2022-04-27 23:19:59 UTC

Updated at

2022-04-27 23:19:59 UTC

NP-MRD ID

NP0052182

Secondary Accession Numbers

None

Natural Product Identification

Common Name

Cucurbitacin S

Description

Cucurbitacin s belongs to the class of organic compounds known as 11-oxosteroids. These are steroid derivatives carrying a C=O group at the 11-position of the steroid skeleton. Thus, cucurbitacin S is considered to be a sterol. Cucurbitacin S is found in Bryonia dioica and Cucurbita foetidissima. Cucurbitacin S was first documented in 2008 (PMID: 19177898). Based on a literature review very few articles have been published on Cucurbitacin s.

Structure

MOL 3D MOL SDF PDB SMILES InChI


  Mrv1652304282201192D          

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M  END

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  8  9  1  0  0  0  0
  9 10  2  0  0  0  0
  9 11  1  0  0  0  0
 11 12  1  0  0  0  0
 12 13  1  0  0  0  0
  7 13  1  0  0  0  0
 13 14  1  0  0  0  0
 15 14  1  6  0  0  0
 16 15  1  1  0  0  0
 12 16  1  0  0  0  0
 16 17  1  0  0  0  0
 17 18  1  0  0  0  0
 18 19  2  0  0  0  0
 18 20  1  0  0  0  0
 20 21  1  0  0  0  0
 21 22  1  0  0  0  0
 15 22  1  0  0  0  0
 21 23  1  1  0  0  0
 23 24  1  0  0  0  0
 23 25  1  0  0  0  0
 23 26  1  0  0  0  0
 17 27  1  6  0  0  0
 13 28  1  6  0  0  0
 12 29  1  1  0  0  0
  8 30  1  1  0  0  0
  4 31  1  0  0  0  0
 31 32  1  0  0  0  0
  1 32  1  0  0  0  0
 32 33  2  0  0  0  0
 31 34  1  0  0  0  0
 31 35  1  0  0  0  0
  1 36  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0052182

> <DATABASE_NAME>
NP-MRD

> <SMILES>
C[C@H]1[C@H]2[C@@H](C[C@@]3(C)[C@@H]4CC=C5[C@@H](C=C(O)C(=O)C5(C)C)[C@]4(C)C(=O)C[C@]23C)O[C@@H](CC1=O)C(C)(C)O

> <INCHI_IDENTIFIER>
InChI=1S/C30H42O6/c1-15-18(31)12-23(27(4,5)35)36-20-13-28(6)21-10-9-16-17(11-19(32)25(34)26(16,2)3)30(21,8)22(33)14-29(28,7)24(15)20/h9,11,15,17,20-21,23-24,32,35H,10,12-14H2,1-8H3/t15-,17-,20-,21+,23+,24+,28+,29-,30+/m1/s1

> <INCHI_KEY>
MBYLRWSUZLFUTO-PQNVQGKDSA-N

> <FORMULA>
C30H42O6

> <MOLECULAR_WEIGHT>
498.66

> <EXACT_MASS>
498.298139072

> <JCHEM_ACCEPTOR_COUNT>
6

> <JCHEM_ATOM_COUNT>
78

> <JCHEM_AVERAGE_POLARIZABILITY>
56.09191738354506

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
2

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(1S,2S,4R,6S,9S,10R,11R,14R,15R)-17-hydroxy-6-(2-hydroxypropan-2-yl)-2,9,11,14,19,19-hexamethyl-5-oxapentacyclo[12.8.0.0^{2,11}.0^{4,10}.0^{15,20}]docosa-16,20-diene-8,13,18-trione

> <ALOGPS_LOGP>
3.61

> <JCHEM_LOGP>
4.070897379666667

> <ALOGPS_LOGS>
-5.19

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
5

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
14.299681519044668

> <JCHEM_PKA_STRONGEST_ACIDIC>
9.122368910181345

> <JCHEM_PKA_STRONGEST_BASIC>
-3.100825673050582

> <JCHEM_POLAR_SURFACE_AREA>
100.90000000000002

> <JCHEM_REFRACTIVITY>
138.6862

> <JCHEM_ROTATABLE_BOND_COUNT>
1

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
3.19e-03 g/l

> <JCHEM_TRADITIONAL_IUPAC>
(1S,2S,4R,6S,9S,10R,11R,14R,15R)-17-hydroxy-6-(2-hydroxypropan-2-yl)-2,9,11,14,19,19-hexamethyl-5-oxapentacyclo[12.8.0.0^{2,11}.0^{4,10}.0^{15,20}]docosa-16,20-diene-8,13,18-trione

> <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      11.878  -0.482   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0      10.345  -0.633   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       9.448   0.619   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0      10.084   2.022   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       9.187   3.274   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       7.655   3.123   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       7.019   1.720   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0       7.916   0.468   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0       7.280  -0.934   0.000  0.00  0.00           C+0
HETATM   10  O   UNK     0       8.177  -2.186   0.000  0.00  0.00           O+0
HETATM   11  C   UNK     0       5.748  -1.085   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0       4.851   0.167   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0       5.486   1.569   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0       4.349   2.607   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0       3.010   1.846   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0       3.320   0.338   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0       2.334  -0.845   0.000  0.00  0.00           C+0
HETATM   18  C   UNK     0       0.795  -0.812   0.000  0.00  0.00           C+0
HETATM   19  O   UNK     0       0.097  -2.185   0.000  0.00  0.00           O+0
HETATM   20  C   UNK     0      -0.139   0.413   0.000  0.00  0.00           C+0
HETATM   21  C   UNK     0       0.236   1.906   0.000  0.00  0.00           C+0
HETATM   22  O   UNK     0       1.637   2.544   0.000  0.00  0.00           O+0
HETATM   23  C   UNK     0      -0.947   2.892   0.000  0.00  0.00           C+0
HETATM   24  C   UNK     0      -2.130   3.878   0.000  0.00  0.00           C+0
HETATM   25  C   UNK     0      -1.933   1.709   0.000  0.00  0.00           C+0
HETATM   26  O   UNK     0       0.039   4.075   0.000  0.00  0.00           O+0
HETATM   27  C   UNK     0       2.972  -2.247   0.000  0.00  0.00           C+0
HETATM   28  C   UNK     0       5.972   3.031   0.000  0.00  0.00           C+0
HETATM   29  C   UNK     0       4.072  -1.162   0.000  0.00  0.00           C+0
HETATM   30  C   UNK     0       8.813  -0.783   0.000  0.00  0.00           C+0
HETATM   31  C   UNK     0      11.617   2.173   0.000  0.00  0.00           C+0
HETATM   32  C   UNK     0      12.514   0.921   0.000  0.00  0.00           C+0
HETATM   33  O   UNK     0      14.046   1.072   0.000  0.00  0.00           O+0
HETATM   34  C   UNK     0      11.519   3.710   0.000  0.00  0.00           C+0
HETATM   35  C   UNK     0      12.836   3.113   0.000  0.00  0.00           C+0
HETATM   36  O   UNK     0      12.775  -1.734   0.000  0.00  0.00           O+0
CONECT    1    2   32   36                                                  
CONECT    2    1    3                                                       
CONECT    3    2    4    8                                                  
CONECT    4    3    5   31                                                  
CONECT    5    4    6                                                       
CONECT    6    5    7                                                       
CONECT    7    6    8   13                                                  
CONECT    8    7    3    9   30                                             
CONECT    9    8   10   11                                                  
CONECT   10    9                                                            
CONECT   11    9   12                                                       
CONECT   12   11   13   16   29                                             
CONECT   13   12    7   14   28                                             
CONECT   14   13   15                                                       
CONECT   15   14   16   22                                                  
CONECT   16   15   12   17                                                  
CONECT   17   16   18   27                                                  
CONECT   18   17   19   20                                                  
CONECT   19   18                                                            
CONECT   20   18   21                                                       
CONECT   21   20   22   23                                                  
CONECT   22   21   15                                                       
CONECT   23   21   24   25   26                                             
CONECT   24   23                                                            
CONECT   25   23                                                            
CONECT   26   23                                                            
CONECT   27   17                                                            
CONECT   28   13                                                            
CONECT   29   12                                                            
CONECT   30    8                                                            
CONECT   31    4   32   34   35                                             
CONECT   32   31    1   33                                                  
CONECT   33   32                                                            
CONECT   34   31                                                            
CONECT   35   31                                                            
CONECT   36    1                                                            
MASTER        0    0    0    0    0    0    0    0   36    0   80    0
END

View in JSmol

Synonyms

Value	Source
Cucurbitacin	MeSH
Cucurbitacins	MeSH

Chemical Formula

C₃₀H₄₂O₆

Average Mass

498.6600 Da

Monoisotopic Mass

498.29814 Da

IUPAC Name

(1S,2S,4R,6S,9S,10R,11R,14R,15R)-17-hydroxy-6-(2-hydroxypropan-2-yl)-2,9,11,14,19,19-hexamethyl-5-oxapentacyclo[12.8.0.0^{2,11}.0^{4,10}.0^{15,20}]docosa-16,20-diene-8,13,18-trione

Traditional Name

(1S,2S,4R,6S,9S,10R,11R,14R,15R)-17-hydroxy-6-(2-hydroxypropan-2-yl)-2,9,11,14,19,19-hexamethyl-5-oxapentacyclo[12.8.0.0^{2,11}.0^{4,10}.0^{15,20}]docosa-16,20-diene-8,13,18-trione

CAS Registry Number

Not Available

SMILES

C[C@H]1[C@H]2[C@@H](C[C@@]3(C)[C@@H]4CC=C5[C@@H](C=C(O)C(=O)C5(C)C)[C@]4(C)C(=O)C[C@]23C)O[C@@H](CC1=O)C(C)(C)O

InChI Identifier

InChI=1S/C30H42O6/c1-15-18(31)12-23(27(4,5)35)36-20-13-28(6)21-10-9-16-17(11-19(32)25(34)26(16,2)3)30(21,8)22(33)14-29(28,7)24(15)20/h9,11,15,17,20-21,23-24,32,35H,10,12-14H2,1-8H3/t15-,17-,20-,21+,23+,24+,28+,29-,30+/m1/s1

InChI Key

MBYLRWSUZLFUTO-PQNVQGKDSA-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
Bryonia dioica	Plant	KNApSAcK
Cucurbita foetidissima	LOTUS Database	35616633

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as 11-oxosteroids. These are steroid derivatives carrying a C=O group at the 11-position of the steroid skeleton.

Kingdom

Organic compounds

Super Class

Lipids and lipid-like molecules

Class

Steroids and steroid derivatives

Sub Class

Oxosteroids

Direct Parent

11-oxosteroids

Alternative Parents

Substituents

3-oxo-delta-1-steroid
3-oxosteroid
14-alpha-methylsteroid
2-hydroxysteroid
Hydroxysteroid
11-oxosteroid
Delta-1-steroid
Cyclohexenone
Oxepane
Tertiary alcohol
Cyclic ketone
Ketone
Dialkyl ether
Enol
Ether
Oxacycle
Organoheterocyclic compound
Organic oxygen compound
Hydrocarbon derivative
Organic oxide
Alcohol
Carbonyl group
Organooxygen compound
Aliphatic heteropolycyclic compound

Molecular Framework

Aliphatic heteropolycyclic compounds

External Descriptors

11-oxo steroid (CHEBI:3953 )
Cholesterol and derivatives (C08806 )
Cycloartane (C08806 )
Cholesterol and derivatives (LMST01010116 )

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	3.61	ALOGPS
logP	4.07	ChemAxon
logS	-5.2	ALOGPS
pKa (Strongest Acidic)	9.12	ChemAxon
pKa (Strongest Basic)	-3.1	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	6	ChemAxon
Hydrogen Donor Count	2	ChemAxon
Polar Surface Area	100.9 Å²	ChemAxon
Rotatable Bond Count	1	ChemAxon
Refractivity	138.69 m³·mol⁻¹	ChemAxon
Polarizability	56.09 Å³	ChemAxon
Number of Rings	5	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

C00003694

Chemspider ID

106553

KEGG Compound ID

C08806

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

119287

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

Kaya GI, Melzig MF: Quantitative determination of cucurbitacin E and cucurbitacin I in homoeopathic mother tincture of Gratiola officinalis L. by HPLC. Pharmazie. 2008 Dec;63(12):851-3. [PubMed:19177898 ]

Showing NP-Card for Cucurbitacin S (NP0052182)

MOL for NP0052182 (Cucurbitacin S)

3D MOL for NP0052182 (Cucurbitacin S)

3D SDF for NP0052182 (Cucurbitacin S)

3D-SDF for NP0052182 (Cucurbitacin S)

PDB for NP0052182 (Cucurbitacin S)

3D PDB for NP0052182 (Cucurbitacin S)

SMILES for NP0052182 (Cucurbitacin S)

INCHI for NP0052182 (Cucurbitacin S)

Structure for NP0052182 (Cucurbitacin S)

3D Structure for NP0052182 (Cucurbitacin S)