NP-MRD: Showing NP-Card for (-)-Tricalysioside I (NP0072500)

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Record Information

Version

2.0

Created at

2022-04-28 17:50:59 UTC

Updated at

2022-04-28 17:50:59 UTC

NP-MRD ID

NP0072500

Secondary Accession Numbers

None

Natural Product Identification

Common Name

(-)-Tricalysioside I

Description

Tricalysioside I belongs to the class of organic compounds known as diterpene glycosides. These are diterpenoids in which an isoprene unit is glycosylated. (-)-Tricalysioside I is found in Diplospora dubia and Tricalysia dubia OHWI. Based on a literature review very few articles have been published on Tricalysioside I.

Structure

MOL 3D MOL SDF PDB SMILES InChI


  Mrv1652304282219512D          

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M  END

     RDKit          3D

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M  END


  Mrv1652304282219512D          

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   -3.2290    1.6014    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -4.1551    2.6897    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.9322    2.9665    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -5.4117    1.6204    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -5.1140   -0.0025    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5597   -0.5561    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5370    0.2497    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.7161    1.7890    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.5988   -0.5427    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8603   -0.7762    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.4881   -1.3115    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.3723    0.4660    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  1  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  1  0  0  0
  8 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
  7 14  1  1  0  0  0
 12 15  1  0  0  0  0
 15 16  1  0  0  0  0
  8 16  1  0  0  0  0
 16 17  1  1  0  0  0
 17 18  1  0  0  0  0
 18 19  2  0  0  0  0
 18 20  1  0  0  0  0
 15 21  1  6  0  0  0
 21 22  1  0  0  0  0
 23 22  1  1  0  0  0
 23 24  1  0  0  0  0
 24 25  1  0  0  0  0
 25 26  1  0  0  0  0
 26 27  1  0  0  0  0
 27 28  1  0  0  0  0
 23 28  1  0  0  0  0
 27 29  1  1  0  0  0
 29 30  1  0  0  0  0
 26 31  1  6  0  0  0
 25 32  1  1  0  0  0
 24 33  1  6  0  0  0
 15 34  1  1  0  0  0
  5 35  1  1  0  0  0
  3 36  1  6  0  0  0
  3 37  1  1  0  0  0
 37 38  2  0  0  0  0
  2 39  1  1  0  0  0
M  END
> <DATABASE_ID>
NP0072500

> <DATABASE_NAME>
NP-MRD

> <SMILES>
CC(=O)O[C@H]1[C@](O)(CO[C@@H]2O[C@H](CO)[C@@H](O)[C@H](O)[C@H]2O)[C@H]2C[C@@]11CC[C@H]3[C@@](C)(CC[C@@H](O)[C@@]3(C)C=O)[C@@H]1CC2

> <INCHI_IDENTIFIER>
InChI=1S/C28H44O11/c1-14(31)38-24-27-9-6-17-25(2,8-7-19(32)26(17,3)12-30)18(27)5-4-15(10-27)28(24,36)13-37-23-22(35)21(34)20(33)16(11-29)39-23/h12,15-24,29,32-36H,4-11,13H2,1-3H3/t15-,16-,17+,18+,19-,20-,21+,22-,23-,24-,25-,26+,27-,28+/m1/s1

> <INCHI_KEY>
LUZSIDHOUJUSHA-HRSAQIEZSA-N

> <FORMULA>
C28H44O11

> <MOLECULAR_WEIGHT>
556.649

> <EXACT_MASS>
556.288362237

> <JCHEM_ACCEPTOR_COUNT>
10

> <JCHEM_ATOM_COUNT>
83

> <JCHEM_AVERAGE_POLARIZABILITY>
58.31415221556604

> <JCHEM_BIOAVAILABILITY>
0

> <JCHEM_DONOR_COUNT>
6

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(1R,4S,5S,6R,9S,10S,13R,14R,15R)-5-formyl-6,14-dihydroxy-5,9-dimethyl-14-({[(2R,3R,4S,5S,6R)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}methyl)tetracyclo[11.2.1.0^{1,10}.0^{4,9}]hexadecan-15-yl acetate

> <ALOGPS_LOGP>
-0.30

> <JCHEM_LOGP>
-0.844774318

> <ALOGPS_LOGS>
-2.80

> <JCHEM_MDDR_LIKE_RULE>
1

> <JCHEM_NUMBER_OF_RINGS>
5

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
12.767219138512544

> <JCHEM_PKA_STRONGEST_ACIDIC>
12.116984829224268

> <JCHEM_PKA_STRONGEST_BASIC>
-2.981083423676078

> <JCHEM_POLAR_SURFACE_AREA>
183.21

> <JCHEM_REFRACTIVITY>
134.1743

> <JCHEM_ROTATABLE_BOND_COUNT>
7

> <JCHEM_RULE_OF_FIVE>
0

> <ALOGPS_SOLUBILITY>
8.84e-01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
(1R,4S,5S,6R,9S,10S,13R,14R,15R)-5-formyl-6,14-dihydroxy-5,9-dimethyl-14-({[(2R,3R,4S,5S,6R)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}methyl)tetracyclo[11.2.1.0^{1,10}.0^{4,9}]hexadecan-15-yl 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       6.193   2.670   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       6.658   1.202   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       5.618   0.065   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       4.115   0.397   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       3.650   1.866   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       4.690   3.002   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       2.118   2.243   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0       0.999   1.022   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0       1.569  -0.447   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0       3.080  -0.758   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0       0.112   2.016   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0      -0.964   2.885   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0       0.081   4.116   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0       1.659   3.819   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0      -1.675   1.439   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0      -0.512   0.307   0.000  0.00  0.00           C+0
HETATM   17  O   UNK     0      -0.766  -1.212   0.000  0.00  0.00           O+0
HETATM   18  C   UNK     0       0.423  -2.191   0.000  0.00  0.00           C+0
HETATM   19  O   UNK     0       1.866  -1.651   0.000  0.00  0.00           O+0
HETATM   20  C   UNK     0       0.170  -3.710   0.000  0.00  0.00           C+0
HETATM   21  C   UNK     0      -3.126   1.956   0.000  0.00  0.00           C+0
HETATM   22  O   UNK     0      -4.299   0.958   0.000  0.00  0.00           O+0
HETATM   23  C   UNK     0      -5.750   1.475   0.000  0.00  0.00           C+0
HETATM   24  C   UNK     0      -6.923   0.477   0.000  0.00  0.00           C+0
HETATM   25  C   UNK     0      -8.373   0.993   0.000  0.00  0.00           C+0
HETATM   26  C   UNK     0      -8.651   2.508   0.000  0.00  0.00           C+0
HETATM   27  C   UNK     0      -7.478   3.506   0.000  0.00  0.00           C+0
HETATM   28  O   UNK     0      -6.028   2.989   0.000  0.00  0.00           O+0
HETATM   29  C   UNK     0      -7.756   5.021   0.000  0.00  0.00           C+0
HETATM   30  O   UNK     0      -9.207   5.538   0.000  0.00  0.00           O+0
HETATM   31  O   UNK     0     -10.102   3.025   0.000  0.00  0.00           O+0
HETATM   32  O   UNK     0      -9.546  -0.005   0.000  0.00  0.00           O+0
HETATM   33  O   UNK     0      -6.645  -1.038   0.000  0.00  0.00           O+0
HETATM   34  O   UNK     0      -2.869   0.466   0.000  0.00  0.00           O+0
HETATM   35  C   UNK     0       3.203   3.340   0.000  0.00  0.00           C+0
HETATM   36  C   UNK     0       6.718  -1.013   0.000  0.00  0.00           C+0
HETATM   37  C   UNK     0       5.339  -1.449   0.000  0.00  0.00           C+0
HETATM   38  O   UNK     0       6.511  -2.448   0.000  0.00  0.00           O+0
HETATM   39  O   UNK     0       8.162   0.870   0.000  0.00  0.00           O+0
CONECT    1    2    6                                                       
CONECT    2    1    3   39                                                  
CONECT    3    2    4   36   37                                             
CONECT    4    3    5   10                                                  
CONECT    5    4    6    7   35                                             
CONECT    6    5    1                                                       
CONECT    7    5    8   14                                                  
CONECT    8    7    9   11   16                                             
CONECT    9    8   10                                                       
CONECT   10    9    4                                                       
CONECT   11    8   12                                                       
CONECT   12   11   13   15                                                  
CONECT   13   12   14                                                       
CONECT   14   13    7                                                       
CONECT   15   12   16   21   34                                             
CONECT   16   15    8   17                                                  
CONECT   17   16   18                                                       
CONECT   18   17   19   20                                                  
CONECT   19   18                                                            
CONECT   20   18                                                            
CONECT   21   15   22                                                       
CONECT   22   21   23                                                       
CONECT   23   22   24   28                                                  
CONECT   24   23   25   33                                                  
CONECT   25   24   26   32                                                  
CONECT   26   25   27   31                                                  
CONECT   27   26   28   29                                                  
CONECT   28   27   23                                                       
CONECT   29   27   30                                                       
CONECT   30   29                                                            
CONECT   31   26                                                            
CONECT   32   25                                                            
CONECT   33   24                                                            
CONECT   34   15                                                            
CONECT   35    5                                                            
CONECT   36    3                                                            
CONECT   37    3   38                                                       
CONECT   38   37                                                            
CONECT   39    2                                                            
MASTER        0    0    0    0    0    0    0    0   39    0   86    0
END

View in JSmol

Synonyms

Not Available

Chemical Formula

C₂₈H₄₄O₁₁

Average Mass

556.6490 Da

Monoisotopic Mass

556.28836 Da

IUPAC Name

(1R,4S,5S,6R,9S,10S,13R,14R,15R)-5-formyl-6,14-dihydroxy-5,9-dimethyl-14-({[(2R,3R,4S,5S,6R)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}methyl)tetracyclo[11.2.1.0^{1,10}.0^{4,9}]hexadecan-15-yl acetate

Traditional Name

CAS Registry Number

Not Available

SMILES

CC(=O)O[C@H]1[C@](O)(CO[C@@H]2O[C@H](CO)[C@@H](O)[C@H](O)[C@H]2O)[C@H]2C[C@@]11CC[C@H]3[C@@](C)(CC[C@@H](O)[C@@]3(C)C=O)[C@@H]1CC2

InChI Identifier

InChI=1S/C28H44O11/c1-14(31)38-24-27-9-6-17-25(2,8-7-19(32)26(17,3)12-30)18(27)5-4-15(10-27)28(24,36)13-37-23-22(35)21(34)20(33)16(11-29)39-23/h12,15-24,29,32-36H,4-11,13H2,1-3H3/t15-,16-,17+,18+,19-,20-,21+,22-,23-,24-,25-,26+,27-,28+/m1/s1

InChI Key

LUZSIDHOUJUSHA-HRSAQIEZSA-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
Diplospora dubia	LOTUS Database	35616633
Tricalysia dubia OHWI	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
Steroid
Hexose monosaccharide
Glycosyl compound
O-glycosyl compound
Monosaccharide
Oxane
Cyclic alcohol
Tertiary alcohol
Secondary alcohol
Carboxylic acid ester
Polyol
Carboxylic acid derivative
Organoheterocyclic compound
Monocarboxylic acid or derivatives
Oxacycle
Acetal
Primary alcohol
Organic oxygen compound
Organic oxide
Hydrocarbon derivative
Alcohol
Carbonyl group
Aldehyde
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	-0.3	ALOGPS
logP	-0.84	ChemAxon
logS	-2.8	ALOGPS
pKa (Strongest Acidic)	12.12	ChemAxon
pKa (Strongest Basic)	-3	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	10	ChemAxon
Hydrogen Donor Count	6	ChemAxon
Polar Surface Area	183.21 Å²	ChemAxon
Rotatable Bond Count	7	ChemAxon
Refractivity	134.17 m³·mol⁻¹	ChemAxon
Polarizability	58.31 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	Yes	ChemAxon

External Links

HMDB ID

Not Available

DrugBank ID

Not Available

Phenol Explorer Compound ID

Not Available

FoodDB ID

Not Available

KNApSAcK ID

C00032396

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

101392257

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

Not Available

Showing NP-Card for (-)-Tricalysioside I (NP0072500)

MOL for NP0072500 ((-)-Tricalysioside I)

3D MOL for NP0072500 ((-)-Tricalysioside I)

3D SDF for NP0072500 ((-)-Tricalysioside I)

3D-SDF for NP0072500 ((-)-Tricalysioside I)

PDB for NP0072500 ((-)-Tricalysioside I)

3D PDB for NP0072500 ((-)-Tricalysioside I)

SMILES for NP0072500 ((-)-Tricalysioside I)

INCHI for NP0072500 ((-)-Tricalysioside I)

Structure for NP0072500 ((-)-Tricalysioside I)

3D Structure for NP0072500 ((-)-Tricalysioside I)