NP-MRD: Showing NP-Card for 3,7-dimethyl-1-{[3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}octa-2,6-dien-4-yl 3,4,5-trihydroxybenzoate (NP0252898)

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Record Information

Version

2.0

Created at

2022-09-07 16:35:08 UTC

Updated at

2022-09-07 16:35:08 UTC

NP-MRD ID

NP0252898

Secondary Accession Numbers

None

Natural Product Identification

Common Name

3,7-dimethyl-1-{[3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}octa-2,6-dien-4-yl 3,4,5-trihydroxybenzoate

Description

3,7-Dimethyl-1-{[3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}octa-2,6-dien-4-yl 3,4,5-trihydroxybenzoate 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. 3,7-dimethyl-1-{[3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}octa-2,6-dien-4-yl 3,4,5-trihydroxybenzoate is found in Rhodiola rosea and Rhodiola sachalinensis. 3,7-Dimethyl-1-{[3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}octa-2,6-dien-4-yl 3,4,5-trihydroxybenzoate is an extremely weak basic (essentially neutral) compound (based on its pKa).

Structure

MOL 3D MOL SDF PDB SMILES InChI


  Mrv1533004241512592D          

 34 35  0  0  0  0            999 V2000
    0.7145   -1.2375    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
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    1.4289   -4.1250    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


  Mrv1533004241512592D          

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M  END
> <DATABASE_ID>
NP0252898

> <DATABASE_NAME>
NP-MRD

> <SMILES>
CC(C)=CCC(OC(=O)C1=CC(O)=C(O)C(O)=C1)C(C)=CCOC1OC(CO)C(O)C(O)C1O

> <INCHI_IDENTIFIER>
InChI=1S/C23H32O11/c1-11(2)4-5-16(33-22(31)13-8-14(25)18(27)15(26)9-13)12(3)6-7-32-23-21(30)20(29)19(28)17(10-24)34-23/h4,6,8-9,16-17,19-21,23-30H,5,7,10H2,1-3H3

> <INCHI_KEY>
DMMHQBFBNBLSMS-UHFFFAOYSA-N

> <FORMULA>
C23H32O11

> <MOLECULAR_WEIGHT>
484.498

> <EXACT_MASS>
484.19446185

> <JCHEM_ACCEPTOR_COUNT>
10

> <JCHEM_ATOM_COUNT>
66

> <JCHEM_AVERAGE_POLARIZABILITY>
49.644469239241246

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
7

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
3,7-dimethyl-1-{[3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}octa-2,6-dien-4-yl 3,4,5-trihydroxybenzoate

> <ALOGPS_LOGP>
0.92

> <JCHEM_LOGP>
1.0853404670000006

> <ALOGPS_LOGS>
-2.97

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
2

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
11.237448930034185

> <JCHEM_PKA_STRONGEST_ACIDIC>
8.103338539229474

> <JCHEM_PKA_STRONGEST_BASIC>
-2.9810835511357814

> <JCHEM_POLAR_SURFACE_AREA>
186.37

> <JCHEM_REFRACTIVITY>
120.8756

> <JCHEM_ROTATABLE_BOND_COUNT>
10

> <JCHEM_RULE_OF_FIVE>
0

> <ALOGPS_SOLUBILITY>
5.17e-01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
3,7-dimethyl-1-{[3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}octa-2,6-dien-4-yl 3,4,5-trihydroxybenzoate

> <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       1.334  -2.310   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       0.000  -3.080   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       0.000  -4.620   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       1.334  -5.390   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       1.334  -6.930   0.000  0.00  0.00           C+0
HETATM    6  O   UNK     0       2.667  -7.700   0.000  0.00  0.00           O+0
HETATM    7  C   UNK     0       4.001  -6.930   0.000  0.00  0.00           C+0
HETATM    8  O   UNK     0       4.001  -5.390   0.000  0.00  0.00           O+0
HETATM    9  C   UNK     0       5.335  -7.700   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0       6.668  -6.930   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0       8.002  -7.700   0.000  0.00  0.00           C+0
HETATM   12  O   UNK     0       9.336  -6.930   0.000  0.00  0.00           O+0
HETATM   13  C   UNK     0       8.002  -9.240   0.000  0.00  0.00           C+0
HETATM   14  O   UNK     0       9.336 -10.010   0.000  0.00  0.00           O+0
HETATM   15  C   UNK     0       6.668 -10.010   0.000  0.00  0.00           C+0
HETATM   16  O   UNK     0       6.668 -11.550   0.000  0.00  0.00           O+0
HETATM   17  C   UNK     0       5.335  -9.240   0.000  0.00  0.00           C+0
HETATM   18  C   UNK     0       0.000  -7.700   0.000  0.00  0.00           C+0
HETATM   19  C   UNK     0      -1.334  -6.930   0.000  0.00  0.00           C+0
HETATM   20  C   UNK     0      -2.667  -7.700   0.000  0.00  0.00           C+0
HETATM   21  O   UNK     0      -2.667  -9.240   0.000  0.00  0.00           O+0
HETATM   22  C   UNK     0      -4.001 -10.010   0.000  0.00  0.00           C+0
HETATM   23  O   UNK     0      -4.001 -11.550   0.000  0.00  0.00           O+0
HETATM   24  C   UNK     0      -5.335 -12.320   0.000  0.00  0.00           C+0
HETATM   25  C   UNK     0      -5.335 -13.860   0.000  0.00  0.00           C+0
HETATM   26  O   UNK     0      -6.668 -14.630   0.000  0.00  0.00           O+0
HETATM   27  C   UNK     0      -6.668 -11.550   0.000  0.00  0.00           C+0
HETATM   28  O   UNK     0      -8.002 -12.320   0.000  0.00  0.00           O+0
HETATM   29  C   UNK     0      -6.668 -10.010   0.000  0.00  0.00           C+0
HETATM   30  O   UNK     0      -8.002  -9.240   0.000  0.00  0.00           O+0
HETATM   31  C   UNK     0      -5.335  -9.240   0.000  0.00  0.00           C+0
HETATM   32  O   UNK     0      -5.335  -7.700   0.000  0.00  0.00           O+0
HETATM   33  C   UNK     0       0.000  -9.240   0.000  0.00  0.00           C+0
HETATM   34  C   UNK     0      -1.334  -2.310   0.000  0.00  0.00           C+0
CONECT    1    2                                                            
CONECT    2    1    3   34                                                  
CONECT    3    2    4                                                       
CONECT    4    3    5                                                       
CONECT    5    4    6   18                                                  
CONECT    6    5    7                                                       
CONECT    7    6    8    9                                                  
CONECT    8    7                                                            
CONECT    9    7   10   17                                                  
CONECT   10    9   11                                                       
CONECT   11   10   12   13                                                  
CONECT   12   11                                                            
CONECT   13   11   14   15                                                  
CONECT   14   13                                                            
CONECT   15   13   16   17                                                  
CONECT   16   15                                                            
CONECT   17   15    9                                                       
CONECT   18    5   19   33                                                  
CONECT   19   18   20                                                       
CONECT   20   19   21                                                       
CONECT   21   20   22                                                       
CONECT   22   21   23   31                                                  
CONECT   23   22   24                                                       
CONECT   24   23   25   27                                                  
CONECT   25   24   26                                                       
CONECT   26   25                                                            
CONECT   27   24   28   29                                                  
CONECT   28   27                                                            
CONECT   29   27   30   31                                                  
CONECT   30   29                                                            
CONECT   31   29   22   32                                                  
CONECT   32   31                                                            
CONECT   33   18                                                            
CONECT   34    2                                                            
MASTER        0    0    0    0    0    0    0    0   34    0   70    0
END

View in JSmol

Synonyms

Value	Source
3,7-Dimethyl-1-{[3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}octa-2,6-dien-4-yl 3,4,5-trihydroxybenzoic acid	Generator

Chemical Formula

C₂₃H₃₂O₁₁

Average Mass

484.4980 Da

Monoisotopic Mass

484.19446 Da

IUPAC Name

3,7-dimethyl-1-{[3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}octa-2,6-dien-4-yl 3,4,5-trihydroxybenzoate

Traditional Name

3,7-dimethyl-1-{[3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}octa-2,6-dien-4-yl 3,4,5-trihydroxybenzoate

CAS Registry Number

Not Available

SMILES

CC(C)=CCC(OC(=O)C1=CC(O)=C(O)C(O)=C1)C(C)=CCOC1OC(CO)C(O)C(O)C1O

InChI Identifier

InChI=1S/C23H32O11/c1-11(2)4-5-16(33-22(31)13-8-14(25)18(27)15(26)9-13)12(3)6-7-32-23-21(30)20(29)19(28)17(10-24)34-23/h4,6,8-9,16-17,19-21,23-30H,5,7,10H2,1-3H3

InChI Key

DMMHQBFBNBLSMS-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
Rhodiola rosea	LOTUS Database	35616633
Rhodiola sachalinensis	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
Fatty acyl glycoside of mono- or disaccharide
Fatty acyl glycoside
Galloyl ester
Hexose monosaccharide
Gallic acid or derivatives
Alkyl glycoside
O-glycosyl compound
P-hydroxybenzoic acid alkyl ester
Glycosyl compound
M-hydroxybenzoic acid ester
P-hydroxybenzoic acid ester
Monoterpenoid
Monocyclic monoterpenoid
Aromatic monoterpenoid
Benzoate ester
Pyrogallol derivative
Benzoic acid or derivatives
Benzenetriol
Benzoyl
1-hydroxy-2-unsubstituted benzenoid
1-hydroxy-4-unsubstituted benzenoid
Phenol
Monocyclic benzene moiety
Fatty acyl
Benzenoid
Oxane
Monosaccharide
Secondary alcohol
Carboxylic acid ester
Carboxylic acid derivative
Organoheterocyclic compound
Oxacycle
Acetal
Polyol
Monocarboxylic acid or derivatives
Primary alcohol
Organic oxygen compound
Alcohol
Hydrocarbon derivative
Organooxygen compound
Organic oxide
Aromatic heteromonocyclic compound

Molecular Framework

Aromatic heteromonocyclic 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	0.92	ALOGPS
logP	1.09	ChemAxon
logS	-3	ALOGPS
pKa (Strongest Acidic)	8.1	ChemAxon
pKa (Strongest Basic)	-3	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	10	ChemAxon
Hydrogen Donor Count	7	ChemAxon
Polar Surface Area	186.37 Å²	ChemAxon
Rotatable Bond Count	10	ChemAxon
Refractivity	120.88 m³·mol⁻¹	ChemAxon
Polarizability	49.64 Å³	ChemAxon
Number of Rings	2	ChemAxon
Bioavailability	Yes	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

Not Available

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

LOTUS database [Link]

Showing NP-Card for 3,7-dimethyl-1-{[3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}octa-2,6-dien-4-yl 3,4,5-trihydroxybenzoate (NP0252898)

MOL for NP0252898 (3,7-dimethyl-1-{[3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}octa-2,6-dien-4-yl 3,4,5-trihydroxybenzoate)

3D MOL for NP0252898 (3,7-dimethyl-1-{[3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}octa-2,6-dien-4-yl 3,4,5-trihydroxybenzoate)

3D SDF for NP0252898 (3,7-dimethyl-1-{[3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}octa-2,6-dien-4-yl 3,4,5-trihydroxybenzoate)

3D-SDF for NP0252898 (3,7-dimethyl-1-{[3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}octa-2,6-dien-4-yl 3,4,5-trihydroxybenzoate)

PDB for NP0252898 (3,7-dimethyl-1-{[3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}octa-2,6-dien-4-yl 3,4,5-trihydroxybenzoate)

3D PDB for NP0252898 (3,7-dimethyl-1-{[3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}octa-2,6-dien-4-yl 3,4,5-trihydroxybenzoate)

SMILES for NP0252898 (3,7-dimethyl-1-{[3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}octa-2,6-dien-4-yl 3,4,5-trihydroxybenzoate)

INCHI for NP0252898 (3,7-dimethyl-1-{[3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}octa-2,6-dien-4-yl 3,4,5-trihydroxybenzoate)

Structure for NP0252898 (3,7-dimethyl-1-{[3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}octa-2,6-dien-4-yl 3,4,5-trihydroxybenzoate)

3D Structure for NP0252898 (3,7-dimethyl-1-{[3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}octa-2,6-dien-4-yl 3,4,5-trihydroxybenzoate)