NP-MRD: Showing NP-Card for Goshonoside F1 (NP0137087)

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Record Information

Version

1.0

Created at

2022-05-30 16:41:18 UTC

Updated at

2022-05-30 16:41:18 UTC

NP-MRD ID

NP0137087

Secondary Accession Numbers

None

Natural Product Identification

Common Name

Goshonoside F1

Description

Goshonoside F1 belongs to the class of organic compounds known as diterpene glycosides. These are diterpenoids in which an isoprene unit is glycosylated. Goshonoside F1 is an extremely weak basic (essentially neutral) compound (based on its pKa). Outside of the human body, Goshonoside F1 has been detected, but not quantified in, fruits. It was first documented in 2000 (PMID: 11413487). This could make goshonoside F1 a potential biomarker for the consumption of these foods (PMID: 16902246) (PMID: 17374880) (PMID: 20044567).

Structure

MOL 3D MOL SDF PDB SMILES InChI


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 29 20  1  0  0  0  0
 30 21  1  0  0  0  0
 31 22  1  0  0  0  0
 32 23  1  0  0  0  0
 33 12  1  0  0  0  0
 33 24  1  0  0  0  0
 34 18  1  0  0  0  0
 34 24  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0137087

> <DATABASE_NAME>
NP-MRD

> <SMILES>
C\C(CCC1C(=C)CCC2C(C)(CO)C(O)CCC12C)=C/COC1OC(CO)C(O)C(O)C1O

> <INCHI_IDENTIFIER>
InChI=1S/C26H44O8/c1-15(10-12-33-24-23(32)22(31)21(30)18(13-27)34-24)5-7-17-16(2)6-8-19-25(17,3)11-9-20(29)26(19,4)14-28/h10,17-24,27-32H,2,5-9,11-14H2,1,3-4H3/b15-10+

> <INCHI_KEY>
JAFZKPLEKRHFFD-XNTDXEJSSA-N

> <FORMULA>
C26H44O8

> <MOLECULAR_WEIGHT>
484.6228

> <EXACT_MASS>
484.303618384

> <JCHEM_ACCEPTOR_COUNT>
8

> <JCHEM_AVERAGE_POLARIZABILITY>
54.351789073265905

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
6

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
2-{[(2E)-5-[6-hydroxy-5-(hydroxymethyl)-5,8a-dimethyl-2-methylidene-decahydronaphthalen-1-yl]-3-methylpent-2-en-1-yl]oxy}-6-(hydroxymethyl)oxane-3,4,5-triol

> <ALOGPS_LOGP>
0.82

> <JCHEM_LOGP>
0.8768925769999991

> <ALOGPS_LOGS>
-3.08

> <JCHEM_MDDR_LIKE_RULE>
1

> <JCHEM_NUMBER_OF_RINGS>
3

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
13.180429661213452

> <JCHEM_PKA_STRONGEST_ACIDIC>
12.208226344469162

> <JCHEM_PKA_STRONGEST_BASIC>
-2.785455403536962

> <JCHEM_POLAR_SURFACE_AREA>
139.84

> <JCHEM_REFRACTIVITY>
127.75729999999996

> <JCHEM_ROTATABLE_BOND_COUNT>
8

> <JCHEM_RULE_OF_FIVE>
0

> <ALOGPS_SOLUBILITY>
4.05e-01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
2-{[(2E)-5-[6-hydroxy-5-(hydroxymethyl)-5,8a-dimethyl-2-methylidene-hexahydro-1H-naphthalen-1-yl]-3-methylpent-2-en-1-yl]oxy}-6-(hydroxymethyl)oxane-3,4,5-triol

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 06-MAY-13   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   06-MAY-13         0                                  
HETATM    1  C   UNK     0       1.334   6.930   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       1.334   2.310   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       5.335   3.080   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       5.679  -1.950   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       2.667   4.620   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       2.667   0.000   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       4.001   3.850   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0       4.001  -0.770   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0       8.002   1.540   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0       4.001   6.930   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0       6.668   2.310   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0       4.001   8.470   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0       8.002  13.860   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0       7.658  -1.950   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0       2.667   6.160   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0       2.667   1.540   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0       4.001   2.310   0.000  0.00  0.00           C+0
HETATM   18  C   UNK     0       6.668  13.090   0.000  0.00  0.00           C+0
HETATM   19  C   UNK     0       5.335   0.000   0.000  0.00  0.00           C+0
HETATM   20  C   UNK     0       8.002   0.000   0.000  0.00  0.00           C+0
HETATM   21  C   UNK     0       5.335  13.860   0.000  0.00  0.00           C+0
HETATM   22  C   UNK     0       4.001  13.090   0.000  0.00  0.00           C+0
HETATM   23  C   UNK     0       4.001  11.550   0.000  0.00  0.00           C+0
HETATM   24  C   UNK     0       5.335  10.780   0.000  0.00  0.00           C+0
HETATM   25  C   UNK     0       5.335   1.540   0.000  0.00  0.00           C+0
HETATM   26  C   UNK     0       6.668  -0.770   0.000  0.00  0.00           C+0
HETATM   27  O   UNK     0       8.002  15.400   0.000  0.00  0.00           O+0
HETATM   28  O   UNK     0       7.132  -3.397   0.000  0.00  0.00           O+0
HETATM   29  O   UNK     0       9.336  -0.770   0.000  0.00  0.00           O+0
HETATM   30  O   UNK     0       5.335  15.400   0.000  0.00  0.00           O+0
HETATM   31  O   UNK     0       2.667  13.860   0.000  0.00  0.00           O+0
HETATM   32  O   UNK     0       2.667  10.780   0.000  0.00  0.00           O+0
HETATM   33  O   UNK     0       5.335   9.240   0.000  0.00  0.00           O+0
HETATM   34  O   UNK     0       6.668  11.550   0.000  0.00  0.00           O+0
CONECT    1   15                                                            
CONECT    2   16                                                            
CONECT    3   25                                                            
CONECT    4   26                                                            
CONECT    5    7   15                                                       
CONECT    6    8   16                                                       
CONECT    7    5   17                                                       
CONECT    8    6   19                                                       
CONECT    9   11   20                                                       
CONECT   10   12   15                                                       
CONECT   11    9   25                                                       
CONECT   12   10   33                                                       
CONECT   13   18   27                                                       
CONECT   14   26   28                                                       
CONECT   15    1    5   10                                                  
CONECT   16    2    6   17                                                  
CONECT   17    7   16   25                                                  
CONECT   18   13   21   34                                                  
CONECT   19    8   25   26                                                  
CONECT   20    9   26   29                                                  
CONECT   21   18   22   30                                                  
CONECT   22   21   23   31                                                  
CONECT   23   22   24   32                                                  
CONECT   24   23   33   34                                                  
CONECT   25    3   11   17   19                                             
CONECT   26    4   14   19   20                                             
CONECT   27   13                                                            
CONECT   28   14                                                            
CONECT   29   20                                                            
CONECT   30   21                                                            
CONECT   31   22                                                            
CONECT   32   23                                                            
CONECT   33   12   24                                                       
CONECT   34   18   24                                                       
MASTER        0    0    0    0    0    0    0    0   34    0   72    0
END

View in JSmol

Synonyms

Not Available

Chemical Formula

C₂₆H₄₄O₈

Average Mass

484.6228 Da

Monoisotopic Mass

484.30362 Da

IUPAC Name

2-{[(2E)-5-[6-hydroxy-5-(hydroxymethyl)-5,8a-dimethyl-2-methylidene-decahydronaphthalen-1-yl]-3-methylpent-2-en-1-yl]oxy}-6-(hydroxymethyl)oxane-3,4,5-triol

Traditional Name

2-{[(2E)-5-[6-hydroxy-5-(hydroxymethyl)-5,8a-dimethyl-2-methylidene-hexahydro-1H-naphthalen-1-yl]-3-methylpent-2-en-1-yl]oxy}-6-(hydroxymethyl)oxane-3,4,5-triol

CAS Registry Number

Not Available

SMILES

C\C(CCC1C(=C)CCC2C(C)(CO)C(O)CCC12C)=C/COC1OC(CO)C(O)C(O)C1O

InChI Identifier

InChI=1S/C26H44O8/c1-15(10-12-33-24-23(32)22(31)21(30)18(13-27)34-24)5-7-17-16(2)6-8-19-25(17,3)11-9-20(29)26(19,4)14-28/h10,17-24,27-32H,2,5-9,11-14H2,1,3-4H3/b15-10+

InChI Key

JAFZKPLEKRHFFD-XNTDXEJSSA-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

Not Available

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as diterpene glycosides. These are diterpenoids in which an isoprene unit is glycosylated.

Kingdom

Organic compounds

Super Class

Lipids and lipid-like molecules

Class

Prenol lipids

Sub Class

Terpene glycosides

Direct Parent

Diterpene glycosides

Alternative Parents

Substituents

Diterpene glycoside
Labdane diterpenoid
Diterpenoid
Fatty acyl glycoside
Fatty acyl glycoside of mono- or disaccharide
Alkyl glycoside
Hexose monosaccharide
Glycosyl compound
O-glycosyl compound
Fatty acyl
Monosaccharide
Oxane
Cyclic alcohol
Secondary alcohol
Polyol
Organoheterocyclic compound
Acetal
Oxacycle
Primary alcohol
Hydrocarbon derivative
Organic oxygen compound
Alcohol
Organooxygen compound
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	0.82	ALOGPS
logP	0.88	ChemAxon
logS	-3.1	ALOGPS
pKa (Strongest Acidic)	12.21	ChemAxon
pKa (Strongest Basic)	-2.8	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	8	ChemAxon
Hydrogen Donor Count	6	ChemAxon
Polar Surface Area	139.84 Å²	ChemAxon
Rotatable Bond Count	8	ChemAxon
Refractivity	127.76 m³·mol⁻¹	ChemAxon
Polarizability	54.35 Å³	ChemAxon
Number of Rings	3	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

HMDB0038539

DrugBank ID

Not Available

Phenol Explorer Compound ID

Not Available

FoodDB ID

FDB017925

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

13855760

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

Simons K, Toomre D: Lipid rafts and signal transduction. Nat Rev Mol Cell Biol. 2000 Oct;1(1):31-9. [PubMed:11413487 ]
Watson AD: Thematic review series: systems biology approaches to metabolic and cardiovascular disorders. Lipidomics: a global approach to lipid analysis in biological systems. J Lipid Res. 2006 Oct;47(10):2101-11. Epub 2006 Aug 10. [PubMed:16902246 ]
Sethi JK, Vidal-Puig AJ: Thematic review series: adipocyte biology. Adipose tissue function and plasticity orchestrate nutritional adaptation. J Lipid Res. 2007 Jun;48(6):1253-62. Epub 2007 Mar 20. [PubMed:17374880 ]
Lingwood D, Simons K: Lipid rafts as a membrane-organizing principle. Science. 2010 Jan 1;327(5961):46-50. doi: 10.1126/science.1174621. [PubMed:20044567 ]

Showing NP-Card for Goshonoside F1 (NP0137087)

MOL for NP0137087 (Goshonoside F1)

3D MOL for NP0137087 (Goshonoside F1)

3D SDF for NP0137087 (Goshonoside F1)

3D-SDF for NP0137087 (Goshonoside F1)

PDB for NP0137087 (Goshonoside F1)

3D PDB for NP0137087 (Goshonoside F1)

SMILES for NP0137087 (Goshonoside F1)

INCHI for NP0137087 (Goshonoside F1)

Structure for NP0137087 (Goshonoside F1)

3D Structure for NP0137087 (Goshonoside F1)