NP-MRD: Showing NP-Card for [(1s,2s,4s,5s,6r,10s)-5-hydroxy-10-{[(2s,3r,4s,5s,6r)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}-3,9-dioxatricyclo[4.4.0.0²,⁴]decan-2-yl]methyl (2e)-3-phenylprop-2-enoate (NP0205569)

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Record Information

Version

2.0

Created at

2022-09-05 01:30:30 UTC

Updated at

2022-09-05 01:30:30 UTC

NP-MRD ID

NP0205569

Secondary Accession Numbers

None

Natural Product Identification

Common Name

[(1s,2s,4s,5s,6r,10s)-5-hydroxy-10-{[(2s,3r,4s,5s,6r)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}-3,9-dioxatricyclo[4.4.0.0²,⁴]decan-2-yl]methyl (2e)-3-phenylprop-2-enoate

Description

Globularidin belongs to the class of organic compounds known as o-glycosyl compounds. These are glycoside in which a sugar group is bonded through one carbon to another group via a O-glycosidic bond. [(1s,2s,4s,5s,6r,10s)-5-hydroxy-10-{[(2s,3r,4s,5s,6r)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}-3,9-dioxatricyclo[4.4.0.0²,⁴]decan-2-yl]methyl (2e)-3-phenylprop-2-enoate is found in Globularia alypum, Globularia arabica and Globularia trichosantha. [(1s,2s,4s,5s,6r,10s)-5-hydroxy-10-{[(2s,3r,4s,5s,6r)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}-3,9-dioxatricyclo[4.4.0.0²,⁴]decan-2-yl]methyl (2e)-3-phenylprop-2-enoate was first documented in 2006 (PMID: 16394555). Based on a literature review very few articles have been published on Globularidin.

Structure

MOL 3D MOL SDF PDB SMILES InChI


  Mrv1652309052203302D          

 35 39  0  0  1  0            999 V2000
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M  END

     RDKit          3D

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M  END


  Mrv1652309052203302D          

 35 39  0  0  1  0            999 V2000
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 33 34  1  1  0  0  0
 22 35  1  0  0  0  0
 18 35  1  0  0  0  0
 35 13  1  6  0  0  0
M  END
> <DATABASE_ID>
NP0205569

> <DATABASE_NAME>
NP-MRD

> <SMILES>
OC[C@H]1O[C@@H](O[C@@H]2OCC[C@H]3[C@H](O)[C@@H]4O[C@]4(COC(=O)\C=C\C4=CC=CC=C4)[C@@H]23)[C@H](O)[C@@H](O)[C@@H]1O

> <INCHI_IDENTIFIER>
InChI=1S/C24H30O11/c25-10-14-18(28)19(29)20(30)23(33-14)34-22-16-13(8-9-31-22)17(27)21-24(16,35-21)11-32-15(26)7-6-12-4-2-1-3-5-12/h1-7,13-14,16-23,25,27-30H,8-11H2/b7-6+/t13-,14-,16-,17+,18-,19+,20-,21+,22+,23+,24-/m1/s1

> <INCHI_KEY>
CPHCYIDKOAOKCL-LUVHZPKESA-N

> <FORMULA>
C24H30O11

> <MOLECULAR_WEIGHT>
494.493

> <EXACT_MASS>
494.178811786

> <JCHEM_ACCEPTOR_COUNT>
10

> <JCHEM_ATOM_COUNT>
65

> <JCHEM_AVERAGE_POLARIZABILITY>
48.22762523246557

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
5

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
[(1S,2S,4S,5S,6R,10S)-5-hydroxy-10-{[(2S,3R,4S,5S,6R)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}-3,9-dioxatricyclo[4.4.0.0^{2,4}]decan-2-yl]methyl (2E)-3-phenylprop-2-enoate

> <JCHEM_LOGP>
-0.4098919366666669

> <JCHEM_MDDR_LIKE_RULE>
1

> <JCHEM_NUMBER_OF_RINGS>
5

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
13.11756999366619

> <JCHEM_PKA_STRONGEST_ACIDIC>
12.196798712456609

> <JCHEM_PKA_STRONGEST_BASIC>
-2.9810847586749727

> <JCHEM_POLAR_SURFACE_AREA>
167.67000000000002

> <JCHEM_REFRACTIVITY>
116.66610000000001

> <JCHEM_ROTATABLE_BOND_COUNT>
8

> <JCHEM_RULE_OF_FIVE>
1

> <JCHEM_TRADITIONAL_IUPAC>
[(1S,2S,4S,5S,6R,10S)-5-hydroxy-10-{[(2S,3R,4S,5S,6R)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}-3,9-dioxatricyclo[4.4.0.0^{2,4}]decan-2-yl]methyl (2E)-3-phenylprop-2-enoate

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 05-SEP-22   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   05-SEP-22         0                                  
HETATM    1  O   UNK     0       4.490   5.932   0.000  0.00  0.00           O+0
HETATM    2  C   UNK     0       5.799   5.122   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       7.156   5.850   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       7.203   7.390   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       8.560   8.118   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       8.607   9.658   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       9.964  10.386   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0      11.274   9.576   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0      11.226   8.036   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0       9.870   7.308   0.000  0.00  0.00           C+0
HETATM   11  O   UNK     0       5.752   3.582   0.000  0.00  0.00           O+0
HETATM   12  C   UNK     0       4.395   2.854   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0       4.348   1.314   0.000  0.00  0.00           C+0
HETATM   14  O   UNK     0       5.874   1.107   0.000  0.00  0.00           O+0
HETATM   15  C   UNK     0       4.931  -0.111   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0       3.755  -1.106   0.000  0.00  0.00           C+0
HETATM   17  O   UNK     0       3.869  -2.642   0.000  0.00  0.00           O+0
HETATM   18  C   UNK     0       2.446  -0.295   0.000  0.00  0.00           C+0
HETATM   19  C   UNK     0       0.967  -0.726   0.000  0.00  0.00           C+0
HETATM   20  C   UNK     0      -0.145   0.339   0.000  0.00  0.00           C+0
HETATM   21  O   UNK     0       0.221   1.835   0.000  0.00  0.00           O+0
HETATM   22  C   UNK     0       1.700   2.266   0.000  0.00  0.00           C+0
HETATM   23  O   UNK     0       2.066   3.762   0.000  0.00  0.00           O+0
HETATM   24  C   UNK     0       0.954   4.827   0.000  0.00  0.00           C+0
HETATM   25  O   UNK     0      -0.524   4.396   0.000  0.00  0.00           O+0
HETATM   26  C   UNK     0      -1.637   5.461   0.000  0.00  0.00           C+0
HETATM   27  C   UNK     0      -3.115   5.031   0.000  0.00  0.00           C+0
HETATM   28  O   UNK     0      -3.482   3.535   0.000  0.00  0.00           O+0
HETATM   29  C   UNK     0      -1.270   6.957   0.000  0.00  0.00           C+0
HETATM   30  O   UNK     0      -2.383   8.022   0.000  0.00  0.00           O+0
HETATM   31  C   UNK     0       0.208   7.388   0.000  0.00  0.00           C+0
HETATM   32  O   UNK     0       0.575   8.883   0.000  0.00  0.00           O+0
HETATM   33  C   UNK     0       1.320   6.323   0.000  0.00  0.00           C+0
HETATM   34  O   UNK     0       2.799   6.753   0.000  0.00  0.00           O+0
HETATM   35  C   UNK     0       2.812   1.201   0.000  0.00  0.00           C+0
CONECT    1    2                                                            
CONECT    2    1    3   11                                                  
CONECT    3    2    4                                                       
CONECT    4    3    5                                                       
CONECT    5    4    6   10                                                  
CONECT    6    5    7                                                       
CONECT    7    6    8                                                       
CONECT    8    7    9                                                       
CONECT    9    8   10                                                       
CONECT   10    9    5                                                       
CONECT   11    2   12                                                       
CONECT   12   11   13                                                       
CONECT   13   12   14   15   35                                             
CONECT   14   13   15                                                       
CONECT   15   14   13   16                                                  
CONECT   16   15   17   18                                                  
CONECT   17   16                                                            
CONECT   18   16   19   35                                                  
CONECT   19   18   20                                                       
CONECT   20   19   21                                                       
CONECT   21   20   22                                                       
CONECT   22   21   23   35                                                  
CONECT   23   22   24                                                       
CONECT   24   23   25   33                                                  
CONECT   25   24   26                                                       
CONECT   26   25   27   29                                                  
CONECT   27   26   28                                                       
CONECT   28   27                                                            
CONECT   29   26   30   31                                                  
CONECT   30   29                                                            
CONECT   31   29   32   33                                                  
CONECT   32   31                                                            
CONECT   33   31   24   34                                                  
CONECT   34   33                                                            
CONECT   35   22   18   13                                                  
MASTER        0    0    0    0    0    0    0    0   35    0   78    0
END

View in JSmol

Synonyms

Not Available

Chemical Formula

C₂₄H₃₀O₁₁

Average Mass

494.4930 Da

Monoisotopic Mass

494.17881 Da

IUPAC Name

[(1S,2S,4S,5S,6R,10S)-5-hydroxy-10-{[(2S,3R,4S,5S,6R)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}-3,9-dioxatricyclo[4.4.0.0^{2,4}]decan-2-yl]methyl (2E)-3-phenylprop-2-enoate

Traditional Name

[(1S,2S,4S,5S,6R,10S)-5-hydroxy-10-{[(2S,3R,4S,5S,6R)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}-3,9-dioxatricyclo[4.4.0.0^{2,4}]decan-2-yl]methyl (2E)-3-phenylprop-2-enoate

CAS Registry Number

Not Available

SMILES

OC[C@H]1O[C@@H](O[C@@H]2OCC[C@H]3[C@H](O)[C@@H]4O[C@]4(COC(=O)\C=C\C4=CC=CC=C4)[C@@H]23)[C@H](O)[C@@H](O)[C@@H]1O

InChI Identifier

InChI=1S/C24H30O11/c25-10-14-18(28)19(29)20(30)23(33-14)34-22-16-13(8-9-31-22)17(27)21-24(16,35-21)11-32-15(26)7-6-12-4-2-1-3-5-12/h1-7,13-14,16-23,25,27-30H,8-11H2/b7-6+/t13-,14-,16-,17+,18-,19+,20-,21+,22+,23+,24-/m1/s1

InChI Key

CPHCYIDKOAOKCL-LUVHZPKESA-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

Species Name	Source	Reference
Globularia alypum	LOTUS Database	35616633
Globularia arabica	LOTUS Database	35616633
Globularia trichosantha	LOTUS Database	35616633

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as o-glycosyl compounds. These are glycoside in which a sugar group is bonded through one carbon to another group via a O-glycosidic bond.

Kingdom

Organic compounds

Super Class

Organic oxygen compounds

Class

Organooxygen compounds

Sub Class

Carbohydrates and carbohydrate conjugates

Direct Parent

O-glycosyl compounds

Alternative Parents

Substituents

Cinnamic acid or derivatives
Hexose monosaccharide
Cinnamic acid ester
O-glycosyl compound
Styrene
Fatty acid ester
Fatty acyl
Monocyclic benzene moiety
Benzenoid
Oxane
Monosaccharide
Alpha,beta-unsaturated carboxylic ester
Enoate ester
Cyclic alcohol
Carboxylic acid ester
Secondary alcohol
Oxacycle
Organoheterocyclic compound
Carboxylic acid derivative
Acetal
Dialkyl ether
Oxirane
Monocarboxylic acid or derivatives
Polyol
Ether
Carbonyl group
Organic oxide
Hydrocarbon derivative
Alcohol
Primary 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	-0.41	ChemAxon
pKa (Strongest Acidic)	12.2	ChemAxon
pKa (Strongest Basic)	-3	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	10	ChemAxon
Hydrogen Donor Count	5	ChemAxon
Polar Surface Area	167.67 Å²	ChemAxon
Rotatable Bond Count	8	ChemAxon
Refractivity	116.67 m³·mol⁻¹	ChemAxon
Polarizability	48.23 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	Yes	ChemAxon

External Links

HMDB ID

Not Available

DrugBank ID

Not Available

Phenol Explorer Compound ID

Not Available

FoodDB ID

Not Available

KNApSAcK ID

C00010512

Chemspider ID

10235037

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

21603203

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

Es-Safi NE, Khlifi S, Kollmann A, Kerhoas L, El Abbouyi A, Ducrot PH: Iridoid glucosides from the aerial parts of Globularia alypum L. (Globulariaceae). Chem Pharm Bull (Tokyo). 2006 Jan;54(1):85-8. doi: 10.1248/cpb.54.85. [PubMed:16394555 ]
LOTUS database [Link]

Showing NP-Card for [(1s,2s,4s,5s,6r,10s)-5-hydroxy-10-{[(2s,3r,4s,5s,6r)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}-3,9-dioxatricyclo[4.4.0.0²,⁴]decan-2-yl]methyl (2e)-3-phenylprop-2-enoate (NP0205569)

MOL for NP0205569 ([(1s,2s,4s,5s,6r,10s)-5-hydroxy-10-{[(2s,3r,4s,5s,6r)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}-3,9-dioxatricyclo[4.4.0.0²,⁴]decan-2-yl]methyl (2e)-3-phenylprop-2-enoate)

3D MOL for NP0205569 ([(1s,2s,4s,5s,6r,10s)-5-hydroxy-10-{[(2s,3r,4s,5s,6r)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}-3,9-dioxatricyclo[4.4.0.0²,⁴]decan-2-yl]methyl (2e)-3-phenylprop-2-enoate)

3D SDF for NP0205569 ([(1s,2s,4s,5s,6r,10s)-5-hydroxy-10-{[(2s,3r,4s,5s,6r)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}-3,9-dioxatricyclo[4.4.0.0²,⁴]decan-2-yl]methyl (2e)-3-phenylprop-2-enoate)

3D-SDF for NP0205569 ([(1s,2s,4s,5s,6r,10s)-5-hydroxy-10-{[(2s,3r,4s,5s,6r)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}-3,9-dioxatricyclo[4.4.0.0²,⁴]decan-2-yl]methyl (2e)-3-phenylprop-2-enoate)

PDB for NP0205569 ([(1s,2s,4s,5s,6r,10s)-5-hydroxy-10-{[(2s,3r,4s,5s,6r)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}-3,9-dioxatricyclo[4.4.0.0²,⁴]decan-2-yl]methyl (2e)-3-phenylprop-2-enoate)

3D PDB for NP0205569 ([(1s,2s,4s,5s,6r,10s)-5-hydroxy-10-{[(2s,3r,4s,5s,6r)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}-3,9-dioxatricyclo[4.4.0.0²,⁴]decan-2-yl]methyl (2e)-3-phenylprop-2-enoate)

SMILES for NP0205569 ([(1s,2s,4s,5s,6r,10s)-5-hydroxy-10-{[(2s,3r,4s,5s,6r)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}-3,9-dioxatricyclo[4.4.0.0²,⁴]decan-2-yl]methyl (2e)-3-phenylprop-2-enoate)

INCHI for NP0205569 ([(1s,2s,4s,5s,6r,10s)-5-hydroxy-10-{[(2s,3r,4s,5s,6r)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}-3,9-dioxatricyclo[4.4.0.0²,⁴]decan-2-yl]methyl (2e)-3-phenylprop-2-enoate)

Structure for NP0205569 ([(1s,2s,4s,5s,6r,10s)-5-hydroxy-10-{[(2s,3r,4s,5s,6r)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}-3,9-dioxatricyclo[4.4.0.0²,⁴]decan-2-yl]methyl (2e)-3-phenylprop-2-enoate)

3D Structure for NP0205569 ([(1s,2s,4s,5s,6r,10s)-5-hydroxy-10-{[(2s,3r,4s,5s,6r)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}-3,9-dioxatricyclo[4.4.0.0²,⁴]decan-2-yl]methyl (2e)-3-phenylprop-2-enoate)