NP-MRD: Showing NP-Card for (-)-Pharboside F (NP0081463)

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Record Information

Version

2.0

Created at

2022-04-29 02:28:16 UTC

Updated at

2022-04-29 02:28:16 UTC

NP-MRD ID

NP0081463

Secondary Accession Numbers

None

Natural Product Identification

Common Name

(-)-Pharboside F

Description

(1R,2R,3S,4S,5R,9S,10S,13R,14R)-2,3-dihydroxy-14-(hydroxymethyl)-5,9-dimethyl-14-{[(2S,3R,4S,5S,6R)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}tetracyclo[11.2.1.0¹,¹⁰.0⁴,⁹]Hexadecane-5-carboxylic acid belongs to the class of organic compounds known as diterpene glycosides. These are diterpenoids in which an isoprene unit is glycosylated. (-)-Pharboside F is found in Pharbitis nil . Based on a literature review very few articles have been published on (1R,2R,3S,4S,5R,9S,10S,13R,14R)-2,3-dihydroxy-14-(hydroxymethyl)-5,9-dimethyl-14-{[(2S,3R,4S,5S,6R)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}tetracyclo[11.2.1.0¹,¹⁰.0⁴,⁹]Hexadecane-5-carboxylic acid.

Structure

MOL 3D MOL SDF PDB SMILES InChI


  Mrv1652304292204282D          

 37 41  0  0  1  0            999 V2000
    1.7100    2.6497    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.9554    1.8050    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
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   -0.8537    1.6514    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
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  3 23  1  0  0  0  0
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 26 35  1  1  0  0  0
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 23 37  1  6  0  0  0
M  END

     RDKit          3D

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M  END


  Mrv1652304292204282D          

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    4.4199    0.0610    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.2147    0.2822    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.2140   -0.7379    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.6813   -0.1726    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.5371    2.3926    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.7294   -0.5860    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.1290   -0.2656    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  2  1  1  1  0  0  0
  2  3  1  0  0  0  0
  3  4  1  1  0  0  0
  5  4  1  1  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
  3  8  1  0  0  0  0
  7  9  1  6  0  0  0
  9 10  1  0  0  0  0
  7 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  6  0  0  0
 14 21  1  1  0  0  0
 13 22  1  6  0  0  0
  3 23  1  0  0  0  0
 23 24  1  0  0  0  0
 25 24  1  1  0  0  0
 25 26  1  0  0  0  0
  2 26  1  0  0  0  0
 26 27  1  0  0  0  0
 27 28  1  0  0  0  0
 28 29  1  0  0  0  0
 29 30  1  0  0  0  0
 25 30  1  0  0  0  0
 30 31  1  1  0  0  0
 31 32  2  0  0  0  0
 31 33  1  0  0  0  0
 30 34  1  6  0  0  0
 26 35  1  1  0  0  0
 24 36  1  6  0  0  0
 23 37  1  6  0  0  0
M  END
> <DATABASE_ID>
NP0081463

> <DATABASE_NAME>
NP-MRD

> <SMILES>
C[C@@]12CCC[C@](C)([C@H]1[C@H](O)[C@H](O)[C@@]13C[C@@H](CC[C@@H]21)[C@@](CO)(C3)O[C@@H]1O[C@H](CO)[C@@H](O)[C@H](O)[C@H]1O)C(O)=O

> <INCHI_IDENTIFIER>
InChI=1S/C26H42O11/c1-23-6-3-7-24(2,22(34)35)19(23)18(32)20(33)25-8-12(4-5-14(23)25)26(10-25,11-28)37-21-17(31)16(30)15(29)13(9-27)36-21/h12-21,27-33H,3-11H2,1-2H3,(H,34,35)/t12-,13-,14+,15-,16+,17-,18+,19+,20+,21+,23+,24-,25-,26+/m1/s1

> <INCHI_KEY>
QUCGBWQRLWOVBR-WSNGDQLASA-N

> <FORMULA>
C26H42O11

> <MOLECULAR_WEIGHT>
530.611

> <EXACT_MASS>
530.272712172

> <JCHEM_ACCEPTOR_COUNT>
11

> <JCHEM_ATOM_COUNT>
79

> <JCHEM_AVERAGE_POLARIZABILITY>
54.89504148497776

> <JCHEM_BIOAVAILABILITY>
0

> <JCHEM_DONOR_COUNT>
8

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(1R,2R,3S,4S,5R,9S,10S,13R,14R)-2,3-dihydroxy-14-(hydroxymethyl)-5,9-dimethyl-14-{[(2S,3R,4S,5S,6R)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}tetracyclo[11.2.1.0^{1,10}.0^{4,9}]hexadecane-5-carboxylic acid

> <ALOGPS_LOGP>
-0.94

> <JCHEM_LOGP>
-1.2052372060000005

> <ALOGPS_LOGS>
-2.08

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
5

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-1

> <JCHEM_PKA>
12.186278761119887

> <JCHEM_PKA_STRONGEST_ACIDIC>
4.272449089643423

> <JCHEM_PKA_STRONGEST_BASIC>
-2.98108368520617

> <JCHEM_POLAR_SURFACE_AREA>
197.36999999999998

> <JCHEM_REFRACTIVITY>
126.02519999999997

> <JCHEM_ROTATABLE_BOND_COUNT>
5

> <JCHEM_RULE_OF_FIVE>
0

> <ALOGPS_SOLUBILITY>
4.42e+00 g/l

> <JCHEM_TRADITIONAL_IUPAC>
(1R,2R,3S,4S,5R,9S,10S,13R,14R)-2,3-dihydroxy-14-(hydroxymethyl)-5,9-dimethyl-14-{[(2S,3R,4S,5S,6R)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}tetracyclo[11.2.1.0^{1,10}.0^{4,9}]hexadecane-5-carboxylic acid

> <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       3.192   4.946   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       3.650   3.369   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       2.532   2.148   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       1.644   3.143   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       0.568   4.012   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       1.614   5.242   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0      -0.143   2.566   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0       1.020   1.434   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0      -1.594   3.083   0.000  0.00  0.00           C+0
HETATM   10  O   UNK     0      -2.766   2.085   0.000  0.00  0.00           O+0
HETATM   11  O   UNK     0      -1.336   1.593   0.000  0.00  0.00           O+0
HETATM   12  C   UNK     0      -1.091   0.073   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0       0.349  -0.475   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0       0.595  -1.995   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0      -0.599  -2.968   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0      -2.039  -2.421   0.000  0.00  0.00           C+0
HETATM   17  O   UNK     0      -2.284  -0.900   0.000  0.00  0.00           O+0
HETATM   18  C   UNK     0      -3.232  -3.394   0.000  0.00  0.00           C+0
HETATM   19  O   UNK     0      -2.986  -4.914   0.000  0.00  0.00           O+0
HETATM   20  O   UNK     0      -0.353  -4.488   0.000  0.00  0.00           O+0
HETATM   21  O   UNK     0       2.034  -2.542   0.000  0.00  0.00           O+0
HETATM   22  O   UNK     0       1.542   0.498   0.000  0.00  0.00           O+0
HETATM   23  C   UNK     0       3.102   0.680   0.000  0.00  0.00           C+0
HETATM   24  C   UNK     0       4.613   0.369   0.000  0.00  0.00           C+0
HETATM   25  C   UNK     0       5.647   1.524   0.000  0.00  0.00           C+0
HETATM   26  C   UNK     0       5.183   2.993   0.000  0.00  0.00           C+0
HETATM   27  C   UNK     0       6.222   4.129   0.000  0.00  0.00           C+0
HETATM   28  C   UNK     0       7.726   3.797   0.000  0.00  0.00           C+0
HETATM   29  C   UNK     0       8.190   2.329   0.000  0.00  0.00           C+0
HETATM   30  C   UNK     0       7.151   1.192   0.000  0.00  0.00           C+0
HETATM   31  C   UNK     0       8.250   0.114   0.000  0.00  0.00           C+0
HETATM   32  O   UNK     0       9.734   0.527   0.000  0.00  0.00           O+0
HETATM   33  O   UNK     0       7.866  -1.377   0.000  0.00  0.00           O+0
HETATM   34  C   UNK     0       6.872  -0.322   0.000  0.00  0.00           C+0
HETATM   35  C   UNK     0       4.736   4.466   0.000  0.00  0.00           C+0
HETATM   36  O   UNK     0       5.095  -1.094   0.000  0.00  0.00           O+0
HETATM   37  O   UNK     0       2.107  -0.496   0.000  0.00  0.00           O+0
CONECT    1    2    6                                                       
CONECT    2    1    3   26                                                  
CONECT    3    2    4    8   23                                             
CONECT    4    3    5                                                       
CONECT    5    4    6    7                                                  
CONECT    6    5    1                                                       
CONECT    7    5    8    9   11                                             
CONECT    8    7    3                                                       
CONECT    9    7   10                                                       
CONECT   10    9                                                            
CONECT   11    7   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    3   24   37                                                  
CONECT   24   23   25   36                                                  
CONECT   25   24   26   30                                                  
CONECT   26   25    2   27   35                                             
CONECT   27   26   28                                                       
CONECT   28   27   29                                                       
CONECT   29   28   30                                                       
CONECT   30   29   25   31   34                                             
CONECT   31   30   32   33                                                  
CONECT   32   31                                                            
CONECT   33   31                                                            
CONECT   34   30                                                            
CONECT   35   26                                                            
CONECT   36   24                                                            
CONECT   37   23                                                            
MASTER        0    0    0    0    0    0    0    0   37    0   82    0
END

View in JSmol

Synonyms

Value	Source
(1R,2R,3S,4S,5R,9S,10S,13R,14R)-2,3-Dihydroxy-14-(hydroxymethyl)-5,9-dimethyl-14-{[(2S,3R,4S,5S,6R)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}tetracyclo[11.2.1.0,.0,]hexadecane-5-carboxylate	Generator

Chemical Formula

C₂₆H₄₂O₁₁

Average Mass

530.6110 Da

Monoisotopic Mass

530.27271 Da

IUPAC Name

Traditional Name

CAS Registry Number

Not Available

SMILES

C[C@@]12CCC[C@](C)([C@H]1[C@H](O)[C@H](O)[C@@]13C[C@@H](CC[C@@H]21)[C@@](CO)(C3)O[C@@H]1O[C@H](CO)[C@@H](O)[C@H](O)[C@H]1O)C(O)=O

InChI Identifier

InChI=1S/C26H42O11/c1-23-6-3-7-24(2,22(34)35)19(23)18(32)20(33)25-8-12(4-5-14(23)25)26(10-25,11-28)37-21-17(31)16(30)15(29)13(9-27)36-21/h12-21,27-33H,3-11H2,1-2H3,(H,34,35)/t12-,13-,14+,15-,16+,17-,18+,19+,20+,21+,23+,24-,25-,26+/m1/s1

InChI Key

QUCGBWQRLWOVBR-WSNGDQLASA-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
Ipomoea nil	Plant	KNApSAcK

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
Diterpenoid
Kaurane diterpenoid
Fatty acyl glycoside
Fatty acyl glycoside of mono- or disaccharide
Hexose monosaccharide
Glycosyl compound
O-glycosyl compound
Fatty acyl
Monosaccharide
Oxane
Cyclic alcohol
Secondary alcohol
Polyol
Monocarboxylic acid or derivatives
Organoheterocyclic compound
Oxacycle
Acetal
Carboxylic acid
Carboxylic acid derivative
Primary alcohol
Alcohol
Organic oxygen compound
Organic oxide
Carbonyl group
Hydrocarbon derivative
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	-0.94	ALOGPS
logP	-1.2	ChemAxon
logS	-2.1	ALOGPS
pKa (Strongest Acidic)	4.27	ChemAxon
pKa (Strongest Basic)	-3	ChemAxon
Physiological Charge	-1	ChemAxon
Hydrogen Acceptor Count	11	ChemAxon
Hydrogen Donor Count	8	ChemAxon
Polar Surface Area	197.37 Å²	ChemAxon
Rotatable Bond Count	5	ChemAxon
Refractivity	126.03 m³·mol⁻¹	ChemAxon
Polarizability	54.9 Å³	ChemAxon
Number of Rings	5	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

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

44179026

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

Not Available

Showing NP-Card for (-)-Pharboside F (NP0081463)

MOL for NP0081463 ((-)-Pharboside F)

3D MOL for NP0081463 ((-)-Pharboside F)

3D SDF for NP0081463 ((-)-Pharboside F)

3D-SDF for NP0081463 ((-)-Pharboside F)

PDB for NP0081463 ((-)-Pharboside F)

3D PDB for NP0081463 ((-)-Pharboside F)

SMILES for NP0081463 ((-)-Pharboside F)

INCHI for NP0081463 ((-)-Pharboside F)

Structure for NP0081463 ((-)-Pharboside F)

3D Structure for NP0081463 ((-)-Pharboside F)