NP-MRD: Showing NP-Card for (3,4,5-trihydroxy-6-{[6-hydroxy-2-(hydroxymethyl)-8-methyl-9,10-dioxatetracyclo[4.3.1.0²,⁵.0³,⁸]decan-3-yl]oxy}oxan-2-yl)methyl benzoate (NP0195770)

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Record Information

Version

2.0

Created at

2022-09-04 13:42:04 UTC

Updated at

2022-09-04 13:42:04 UTC

NP-MRD ID

NP0195770

Secondary Accession Numbers

None

Natural Product Identification

Common Name

(3,4,5-trihydroxy-6-{[6-hydroxy-2-(hydroxymethyl)-8-methyl-9,10-dioxatetracyclo[4.3.1.0²,⁵.0³,⁸]decan-3-yl]oxy}oxan-2-yl)methyl benzoate

Description

(3,4,5-Trihydroxy-6-{[6-hydroxy-2-(hydroxymethyl)-8-methyl-9,10-dioxatetracyclo[4.3.1.0²,⁵.0³,⁸]Decan-3-yl]oxy}oxan-2-yl)methyl benzoate belongs to the class of organic compounds known as terpene glycosides. (3,4,5-trihydroxy-6-{[6-hydroxy-2-(hydroxymethyl)-8-methyl-9,10-dioxatetracyclo[4.3.1.0²,⁵.0³,⁸]decan-3-yl]oxy}oxan-2-yl)methyl benzoate is found in Paeonia suffruticosa. These are prenol lipids containing a carbohydrate moiety glycosidically bound to a terpene backbone (3,4,5-trihydroxy-6-{[6-hydroxy-2-(hydroxymethyl)-8-methyl-9,10-dioxatetracyclo[4.3.1.0²,⁵.0³,⁸]Decan-3-yl]oxy}oxan-2-yl)methyl benzoate is an extremely weak basic (essentially neutral) compound (based on its pKa).

Structure

MOL 3D MOL SDF PDB SMILES InChI


  Mrv1533004241504362D          

 34 39  0  0  0  0            999 V2000
    2.1764    1.6493    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
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    2.2273   -0.8550    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.4587    0.0289    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
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M  END

     RDKit          3D

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M  END


  Mrv1533004241504362D          

 34 39  0  0  0  0            999 V2000
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M  END
> <DATABASE_ID>
NP0195770

> <DATABASE_NAME>
NP-MRD

> <SMILES>
CC12CC3(O)OC(O1)C1(CO)C3CC21OC1OC(COC(=O)C2=CC=CC=C2)C(O)C(O)C1O

> <INCHI_IDENTIFIER>
InChI=1S/C23H28O11/c1-20-9-22(29)13-7-23(20,21(13,10-24)19(33-20)34-22)32-18-16(27)15(26)14(25)12(31-18)8-30-17(28)11-5-3-2-4-6-11/h2-6,12-16,18-19,24-27,29H,7-10H2,1H3

> <INCHI_KEY>
XPSPAXSLPOGEEE-UHFFFAOYSA-N

> <FORMULA>
C23H28O11

> <MOLECULAR_WEIGHT>
480.466

> <EXACT_MASS>
480.163161722

> <JCHEM_ACCEPTOR_COUNT>
10

> <JCHEM_ATOM_COUNT>
62

> <JCHEM_AVERAGE_POLARIZABILITY>
46.42051453485935

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
5

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(3,4,5-trihydroxy-6-{[6-hydroxy-2-(hydroxymethyl)-8-methyl-9,10-dioxatetracyclo[4.3.1.0²,⁵.0³,⁸]decan-3-yl]oxy}oxan-2-yl)methyl benzoate

> <ALOGPS_LOGP>
-0.80

> <JCHEM_LOGP>
-0.38654997533333335

> <ALOGPS_LOGS>
-1.91

> <JCHEM_MDDR_LIKE_RULE>
1

> <JCHEM_NUMBER_OF_RINGS>
6

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
12.304078293151179

> <JCHEM_PKA_STRONGEST_ACIDIC>
11.54397619228127

> <JCHEM_PKA_STRONGEST_BASIC>
-2.8674330465628213

> <JCHEM_POLAR_SURFACE_AREA>
164.37

> <JCHEM_REFRACTIVITY>
109.30370000000003

> <JCHEM_ROTATABLE_BOND_COUNT>
7

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
5.98e+00 g/l

> <JCHEM_TRADITIONAL_IUPAC>
(3,4,5-trihydroxy-6-{[6-hydroxy-2-(hydroxymethyl)-8-methyl-9,10-dioxatetracyclo[4.3.1.0²,⁵.0³,⁸]decan-3-yl]oxy}oxan-2-yl)methyl benzoate

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 24-APR-15   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   24-APR-15         0                                  
HETATM    1  C   UNK     0       4.063   3.079   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       4.251   1.550   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       5.762   0.987   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       5.424  -0.621   0.000  0.00  0.00           C+0
HETATM    5  O   UNK     0       6.962  -0.691   0.000  0.00  0.00           O+0
HETATM    6  O   UNK     0       5.608  -2.184   0.000  0.00  0.00           O+0
HETATM    7  C   UNK     0       4.158  -1.596   0.000  0.00  0.00           C+0
HETATM    8  O   UNK     0       4.590   0.054   0.000  0.00  0.00           O+0
HETATM    9  C   UNK     0       2.584  -1.184   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0       1.287  -2.014   0.000  0.00  0.00           C+0
HETATM   11  O   UNK     0       1.358  -3.552   0.000  0.00  0.00           O+0
HETATM   12  C   UNK     0       3.632  -0.388   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0       1.840  -0.259   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0       2.905   0.624   0.000  0.00  0.00           C+0
HETATM   15  O   UNK     0       1.977   1.853   0.000  0.00  0.00           O+0
HETATM   16  C   UNK     0       0.448   1.662   0.000  0.00  0.00           C+0
HETATM   17  O   UNK     0      -0.151   0.244   0.000  0.00  0.00           O+0
HETATM   18  C   UNK     0      -1.679   0.054   0.000  0.00  0.00           C+0
HETATM   19  C   UNK     0      -2.279  -1.365   0.000  0.00  0.00           C+0
HETATM   20  O   UNK     0      -3.807  -1.555   0.000  0.00  0.00           O+0
HETATM   21  C   UNK     0      -4.406  -2.974   0.000  0.00  0.00           C+0
HETATM   22  O   UNK     0      -3.477  -4.202   0.000  0.00  0.00           O+0
HETATM   23  C   UNK     0      -5.934  -3.164   0.000  0.00  0.00           C+0
HETATM   24  C   UNK     0      -6.534  -4.582   0.000  0.00  0.00           C+0
HETATM   25  C   UNK     0      -8.062  -4.773   0.000  0.00  0.00           C+0
HETATM   26  C   UNK     0      -8.991  -3.544   0.000  0.00  0.00           C+0
HETATM   27  C   UNK     0      -8.391  -2.126   0.000  0.00  0.00           C+0
HETATM   28  C   UNK     0      -6.863  -1.936   0.000  0.00  0.00           C+0
HETATM   29  C   UNK     0      -2.608   1.282   0.000  0.00  0.00           C+0
HETATM   30  O   UNK     0      -4.136   1.092   0.000  0.00  0.00           O+0
HETATM   31  C   UNK     0      -2.009   2.701   0.000  0.00  0.00           C+0
HETATM   32  O   UNK     0      -2.937   3.929   0.000  0.00  0.00           O+0
HETATM   33  C   UNK     0      -0.480   2.891   0.000  0.00  0.00           C+0
HETATM   34  O   UNK     0       0.119   4.309   0.000  0.00  0.00           O+0
CONECT    1    2                                                            
CONECT    2    1    3    8   14                                             
CONECT    3    2    4                                                       
CONECT    4    3    5    6   12                                             
CONECT    5    4                                                            
CONECT    6    4    7                                                       
CONECT    7    6    8    9                                                  
CONECT    8    7    2                                                       
CONECT    9    7   10   12   14                                             
CONECT   10    9   11                                                       
CONECT   11   10                                                            
CONECT   12    9    4   13                                                  
CONECT   13   12   14                                                       
CONECT   14   13    2    9   15                                             
CONECT   15   14   16                                                       
CONECT   16   15   17   33                                                  
CONECT   17   16   18                                                       
CONECT   18   17   19   29                                                  
CONECT   19   18   20                                                       
CONECT   20   19   21                                                       
CONECT   21   20   22   23                                                  
CONECT   22   21                                                            
CONECT   23   21   24   28                                                  
CONECT   24   23   25                                                       
CONECT   25   24   26                                                       
CONECT   26   25   27                                                       
CONECT   27   26   28                                                       
CONECT   28   27   23                                                       
CONECT   29   18   30   31                                                  
CONECT   30   29                                                            
CONECT   31   29   32   33                                                  
CONECT   32   31                                                            
CONECT   33   31   16   34                                                  
CONECT   34   33                                                            
MASTER        0    0    0    0    0    0    0    0   34    0   78    0
END

View in JSmol

Synonyms

Value	Source
(3,4,5-Trihydroxy-6-{[6-hydroxy-2-(hydroxymethyl)-8-methyl-9,10-dioxatetracyclo[4.3.1.0,.0,]decan-3-yl]oxy}oxan-2-yl)methyl benzoic acid	Generator
(3,4,5-Trihydroxy-6-{[6-hydroxy-2-(hydroxymethyl)-8-methyl-9,10-dioxatetracyclo[4.3.1.0²,⁵.0³,⁸]decan-3-yl]oxy}oxan-2-yl)methyl benzoic acid	Generator

Chemical Formula

C₂₃H₂₈O₁₁

Average Mass

480.4660 Da

Monoisotopic Mass

480.16316 Da

IUPAC Name

(3,4,5-trihydroxy-6-{[6-hydroxy-2-(hydroxymethyl)-8-methyl-9,10-dioxatetracyclo[4.3.1.0²,⁵.0³,⁸]decan-3-yl]oxy}oxan-2-yl)methyl benzoate

Traditional Name

(3,4,5-trihydroxy-6-{[6-hydroxy-2-(hydroxymethyl)-8-methyl-9,10-dioxatetracyclo[4.3.1.0²,⁵.0³,⁸]decan-3-yl]oxy}oxan-2-yl)methyl benzoate

CAS Registry Number

Not Available

SMILES

CC12CC3(O)OC(O1)C1(CO)C3CC21OC1OC(COC(=O)C2=CC=CC=C2)C(O)C(O)C1O

InChI Identifier

InChI=1S/C23H28O11/c1-20-9-22(29)13-7-23(20,21(13,10-24)19(33-20)34-22)32-18-16(27)15(26)14(25)12(31-18)8-30-17(28)11-5-3-2-4-6-11/h2-6,12-16,18-19,24-27,29H,7-10H2,1H3

InChI Key

XPSPAXSLPOGEEE-UHFFFAOYSA-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
Paeonia suffruticosa	LOTUS Database	35616633

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as terpene glycosides. These are prenol lipids containing a carbohydrate moiety glycosidically bound to a terpene backbone.

Kingdom

Organic compounds

Super Class

Lipids and lipid-like molecules

Class

Prenol lipids

Sub Class

Terpene glycosides

Direct Parent

Terpene glycosides

Alternative Parents

Substituents

Terpene glycoside
Glycosyl compound
O-glycosyl compound
Aromatic monoterpenoid
Benzoate ester
Pinane monoterpenoid
Nopinane monoterpenoid
Monoterpenoid
Benzoic acid or derivatives
Benzoyl
Furofuran
Oxepane
Meta-dioxane
Monocyclic benzene moiety
Benzenoid
Monosaccharide
Oxane
Tetrahydrofuran
Cyclic alcohol
Secondary alcohol
Carboxylic acid ester
Hemiacetal
Polyol
Acetal
Oxacycle
Organoheterocyclic compound
Carboxylic acid derivative
Monocarboxylic acid or derivatives
Organic oxide
Hydrocarbon derivative
Organic oxygen compound
Primary alcohol
Organooxygen compound
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	-0.8	ALOGPS
logP	-0.39	ChemAxon
logS	-1.9	ALOGPS
pKa (Strongest Acidic)	11.54	ChemAxon
pKa (Strongest Basic)	-2.9	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	10	ChemAxon
Hydrogen Donor Count	5	ChemAxon
Polar Surface Area	164.37 Å²	ChemAxon
Rotatable Bond Count	7	ChemAxon
Refractivity	109.3 m³·mol⁻¹	ChemAxon
Polarizability	46.42 Å³	ChemAxon
Number of Rings	6	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

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

85191720

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

LOTUS database [Link]

Showing NP-Card for (3,4,5-trihydroxy-6-{[6-hydroxy-2-(hydroxymethyl)-8-methyl-9,10-dioxatetracyclo[4.3.1.0²,⁵.0³,⁸]decan-3-yl]oxy}oxan-2-yl)methyl benzoate (NP0195770)

MOL for NP0195770 ((3,4,5-trihydroxy-6-{[6-hydroxy-2-(hydroxymethyl)-8-methyl-9,10-dioxatetracyclo[4.3.1.0²,⁵.0³,⁸]decan-3-yl]oxy}oxan-2-yl)methyl benzoate)

3D MOL for NP0195770 ((3,4,5-trihydroxy-6-{[6-hydroxy-2-(hydroxymethyl)-8-methyl-9,10-dioxatetracyclo[4.3.1.0²,⁵.0³,⁸]decan-3-yl]oxy}oxan-2-yl)methyl benzoate)

3D SDF for NP0195770 ((3,4,5-trihydroxy-6-{[6-hydroxy-2-(hydroxymethyl)-8-methyl-9,10-dioxatetracyclo[4.3.1.0²,⁵.0³,⁸]decan-3-yl]oxy}oxan-2-yl)methyl benzoate)

3D-SDF for NP0195770 ((3,4,5-trihydroxy-6-{[6-hydroxy-2-(hydroxymethyl)-8-methyl-9,10-dioxatetracyclo[4.3.1.0²,⁵.0³,⁸]decan-3-yl]oxy}oxan-2-yl)methyl benzoate)

PDB for NP0195770 ((3,4,5-trihydroxy-6-{[6-hydroxy-2-(hydroxymethyl)-8-methyl-9,10-dioxatetracyclo[4.3.1.0²,⁵.0³,⁸]decan-3-yl]oxy}oxan-2-yl)methyl benzoate)

3D PDB for NP0195770 ((3,4,5-trihydroxy-6-{[6-hydroxy-2-(hydroxymethyl)-8-methyl-9,10-dioxatetracyclo[4.3.1.0²,⁵.0³,⁸]decan-3-yl]oxy}oxan-2-yl)methyl benzoate)

SMILES for NP0195770 ((3,4,5-trihydroxy-6-{[6-hydroxy-2-(hydroxymethyl)-8-methyl-9,10-dioxatetracyclo[4.3.1.0²,⁵.0³,⁸]decan-3-yl]oxy}oxan-2-yl)methyl benzoate)

INCHI for NP0195770 ((3,4,5-trihydroxy-6-{[6-hydroxy-2-(hydroxymethyl)-8-methyl-9,10-dioxatetracyclo[4.3.1.0²,⁵.0³,⁸]decan-3-yl]oxy}oxan-2-yl)methyl benzoate)

Structure for NP0195770 ((3,4,5-trihydroxy-6-{[6-hydroxy-2-(hydroxymethyl)-8-methyl-9,10-dioxatetracyclo[4.3.1.0²,⁵.0³,⁸]decan-3-yl]oxy}oxan-2-yl)methyl benzoate)

3D Structure for NP0195770 ((3,4,5-trihydroxy-6-{[6-hydroxy-2-(hydroxymethyl)-8-methyl-9,10-dioxatetracyclo[4.3.1.0²,⁵.0³,⁸]decan-3-yl]oxy}oxan-2-yl)methyl benzoate)