NP-MRD: Showing NP-Card for (-)-Cucurbitoside D (NP0072031)

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Record Information

Version

2.0

Created at

2022-04-28 17:24:46 UTC

Updated at

2022-04-28 17:24:47 UTC

NP-MRD ID

NP0072031

Secondary Accession Numbers

None

Natural Product Identification

Common Name

(-)-Cucurbitoside D

Description

[(3S,4R,5S)-5-{[(2S,3R,4S,5R,6R)-4,5-dihydroxy-6-(hydroxymethyl)-2-[4-(hydroxymethyl)phenoxy]oxan-3-yl]oxy}-3,4-dihydroxyoxolan-3-yl]methyl 4-hydroxybenzoate belongs to the class of organic compounds known as phenolic glycosides. These are organic compounds containing a phenolic structure attached to a glycosyl moiety. Some examples of phenolic structures include lignans, and flavonoids. Among the sugar units found in natural glycosides are D-glucose, L-Fructose, and L rhamnose. (-)-Cucurbitoside D is found in Cucurbita moschata . Based on a literature review very few articles have been published on [(3S,4R,5S)-5-{[(2S,3R,4S,5R,6R)-4,5-dihydroxy-6-(hydroxymethyl)-2-[4-(hydroxymethyl)phenoxy]oxan-3-yl]oxy}-3,4-dihydroxyoxolan-3-yl]methyl 4-hydroxybenzoate.

Structure

MOL 3D MOL SDF PDB SMILES InChI


  Mrv1652304282219242D          

 38 41  0  0  1  0            999 V2000
    3.0625   -5.4804    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    2.2420   -5.5667    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    1.9065   -6.3203    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    2.3914   -6.9878    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    3.2119   -6.9015    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.5474   -6.1479    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    4.3679   -6.0616    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.8528   -6.7291    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.6733   -6.6428    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.1582   -7.3103    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.8227   -8.0639    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.0022   -8.1502    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.5173   -7.4827    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
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  1  2  1  0  0  0  0
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  4  5  1  0  0  0  0
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  4 16  1  6  0  0  0
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  3 18  1  6  0  0  0
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  1 20  1  1  0  0  0
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 31 36  1  0  0  0  0
 34 37  1  0  0  0  0
 24 38  1  1  0  0  0
M  END

     RDKit          3D

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M  END


  Mrv1652304282219242D          

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  2 19  1  6  0  0  0
  1 20  1  1  0  0  0
 21 20  1  6  0  0  0
 21 22  1  0  0  0  0
 22 23  1  0  0  0  0
 23 24  1  0  0  0  0
 24 25  1  0  0  0  0
 21 25  1  0  0  0  0
 25 26  1  1  0  0  0
 24 27  1  6  0  0  0
 27 28  1  0  0  0  0
 28 29  1  0  0  0  0
 29 30  2  0  0  0  0
 29 31  1  0  0  0  0
 31 32  2  0  0  0  0
 32 33  1  0  0  0  0
 33 34  2  0  0  0  0
 34 35  1  0  0  0  0
 35 36  2  0  0  0  0
 31 36  1  0  0  0  0
 34 37  1  0  0  0  0
 24 38  1  1  0  0  0
M  END
> <DATABASE_ID>
NP0072031

> <DATABASE_NAME>
NP-MRD

> <SMILES>
OC[C@H]1O[C@@H](OC2=CC=C(CO)C=C2)[C@H](O[C@@H]2OC[C@](O)(COC(=O)C3=CC=C(O)C=C3)[C@H]2O)[C@@H](O)[C@H]1O

> <INCHI_IDENTIFIER>
InChI=1S/C25H30O13/c26-9-13-1-7-16(8-2-13)36-23-20(19(30)18(29)17(10-27)37-23)38-24-21(31)25(33,12-35-24)11-34-22(32)14-3-5-15(28)6-4-14/h1-8,17-21,23-24,26-31,33H,9-12H2/t17-,18+,19+,20-,21+,23-,24+,25-/m1/s1

> <INCHI_KEY>
WIMAHNFFARKNJF-LZMGOZBSSA-N

> <FORMULA>
C25H30O13

> <MOLECULAR_WEIGHT>
538.502

> <EXACT_MASS>
538.168641026

> <JCHEM_ACCEPTOR_COUNT>
12

> <JCHEM_ATOM_COUNT>
68

> <JCHEM_AVERAGE_POLARIZABILITY>
52.702821395896464

> <JCHEM_BIOAVAILABILITY>
0

> <JCHEM_DONOR_COUNT>
7

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
[(3S,4R,5S)-5-{[(2S,3R,4S,5R,6R)-4,5-dihydroxy-6-(hydroxymethyl)-2-[4-(hydroxymethyl)phenoxy]oxan-3-yl]oxy}-3,4-dihydroxyoxolan-3-yl]methyl 4-hydroxybenzoate

> <ALOGPS_LOGP>
-0.22

> <JCHEM_LOGP>
-0.45050189933333273

> <ALOGPS_LOGS>
-2.59

> <JCHEM_MDDR_LIKE_RULE>
1

> <JCHEM_NUMBER_OF_RINGS>
4

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
11.79294719655997

> <JCHEM_PKA_STRONGEST_ACIDIC>
8.497251151035867

> <JCHEM_PKA_STRONGEST_BASIC>
-2.79515604190041

> <JCHEM_POLAR_SURFACE_AREA>
204.82999999999998

> <JCHEM_REFRACTIVITY>
125.47229999999998

> <JCHEM_ROTATABLE_BOND_COUNT>
10

> <JCHEM_RULE_OF_FIVE>
0

> <ALOGPS_SOLUBILITY>
1.39e+00 g/l

> <JCHEM_TRADITIONAL_IUPAC>
[(3S,4R,5S)-5-{[(2S,3R,4S,5R,6R)-4,5-dihydroxy-6-(hydroxymethyl)-2-[4-(hydroxymethyl)phenoxy]oxan-3-yl]oxy}-3,4-dihydroxyoxolan-3-yl]methyl 4-hydroxybenzoate

> <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       5.717 -10.230   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       4.185 -10.391   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       3.559 -11.798   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       4.464 -13.044   0.000  0.00  0.00           C+0
HETATM    5  O   UNK     0       5.996 -12.883   0.000  0.00  0.00           O+0
HETATM    6  C   UNK     0       6.622 -11.476   0.000  0.00  0.00           C+0
HETATM    7  O   UNK     0       8.153 -11.315   0.000  0.00  0.00           O+0
HETATM    8  C   UNK     0       9.059 -12.561   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0      10.590 -12.400   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0      11.495 -13.646   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0      10.869 -15.053   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0       9.337 -15.214   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0       8.432 -13.968   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0      11.774 -16.299   0.000  0.00  0.00           C+0
HETATM   15  O   UNK     0      11.148 -17.705   0.000  0.00  0.00           O+0
HETATM   16  C   UNK     0       3.838 -14.451   0.000  0.00  0.00           C+0
HETATM   17  O   UNK     0       4.743 -15.697   0.000  0.00  0.00           O+0
HETATM   18  O   UNK     0       2.027 -11.959   0.000  0.00  0.00           O+0
HETATM   19  O   UNK     0       3.280  -9.145   0.000  0.00  0.00           O+0
HETATM   20  O   UNK     0       6.343  -8.823   0.000  0.00  0.00           O+0
HETATM   21  C   UNK     0       5.438  -7.577   0.000  0.00  0.00           C+0
HETATM   22  O   UNK     0       3.898  -7.577   0.000  0.00  0.00           O+0
HETATM   23  C   UNK     0       3.422  -6.113   0.000  0.00  0.00           C+0
HETATM   24  C   UNK     0       4.668  -5.208   0.000  0.00  0.00           C+0
HETATM   25  C   UNK     0       5.914  -6.113   0.000  0.00  0.00           C+0
HETATM   26  O   UNK     0       7.378  -5.637   0.000  0.00  0.00           O+0
HETATM   27  C   UNK     0       3.912  -3.866   0.000  0.00  0.00           C+0
HETATM   28  O   UNK     0       4.696  -2.540   0.000  0.00  0.00           O+0
HETATM   29  C   UNK     0       3.940  -1.199   0.000  0.00  0.00           C+0
HETATM   30  O   UNK     0       2.400  -1.183   0.000  0.00  0.00           O+0
HETATM   31  C   UNK     0       4.724   0.127   0.000  0.00  0.00           C+0
HETATM   32  C   UNK     0       3.968   1.469   0.000  0.00  0.00           C+0
HETATM   33  C   UNK     0       4.752   2.794   0.000  0.00  0.00           C+0
HETATM   34  C   UNK     0       6.292   2.778   0.000  0.00  0.00           C+0
HETATM   35  C   UNK     0       7.048   1.436   0.000  0.00  0.00           C+0
HETATM   36  C   UNK     0       6.264   0.111   0.000  0.00  0.00           C+0
HETATM   37  O   UNK     0       7.076   4.103   0.000  0.00  0.00           O+0
HETATM   38  O   UNK     0       5.424  -3.866   0.000  0.00  0.00           O+0
CONECT    1    2    6   20                                                  
CONECT    2    1    3   19                                                  
CONECT    3    2    4   18                                                  
CONECT    4    3    5   16                                                  
CONECT    5    4    6                                                       
CONECT    6    5    1    7                                                  
CONECT    7    6    8                                                       
CONECT    8    7    9   13                                                  
CONECT    9    8   10                                                       
CONECT   10    9   11                                                       
CONECT   11   10   12   14                                                  
CONECT   12   11   13                                                       
CONECT   13   12    8                                                       
CONECT   14   11   15                                                       
CONECT   15   14                                                            
CONECT   16    4   17                                                       
CONECT   17   16                                                            
CONECT   18    3                                                            
CONECT   19    2                                                            
CONECT   20    1   21                                                       
CONECT   21   20   22   25                                                  
CONECT   22   21   23                                                       
CONECT   23   22   24                                                       
CONECT   24   23   25   27   38                                             
CONECT   25   24   21   26                                                  
CONECT   26   25                                                            
CONECT   27   24   28                                                       
CONECT   28   27   29                                                       
CONECT   29   28   30   31                                                  
CONECT   30   29                                                            
CONECT   31   29   32   36                                                  
CONECT   32   31   33                                                       
CONECT   33   32   34                                                       
CONECT   34   33   35   37                                                  
CONECT   35   34   36                                                       
CONECT   36   35   31                                                       
CONECT   37   34                                                            
CONECT   38   24                                                            
MASTER        0    0    0    0    0    0    0    0   38    0   82    0
END

View in JSmol

Synonyms

Value	Source
[(3S,4R,5S)-5-{[(2S,3R,4S,5R,6R)-4,5-dihydroxy-6-(hydroxymethyl)-2-[4-(hydroxymethyl)phenoxy]oxan-3-yl]oxy}-3,4-dihydroxyoxolan-3-yl]methyl 4-hydroxybenzoic acid	Generator

Chemical Formula

C₂₅H₃₀O₁₃

Average Mass

538.5020 Da

Monoisotopic Mass

538.16864 Da

IUPAC Name

[(3S,4R,5S)-5-{[(2S,3R,4S,5R,6R)-4,5-dihydroxy-6-(hydroxymethyl)-2-[4-(hydroxymethyl)phenoxy]oxan-3-yl]oxy}-3,4-dihydroxyoxolan-3-yl]methyl 4-hydroxybenzoate

Traditional Name

[(3S,4R,5S)-5-{[(2S,3R,4S,5R,6R)-4,5-dihydroxy-6-(hydroxymethyl)-2-[4-(hydroxymethyl)phenoxy]oxan-3-yl]oxy}-3,4-dihydroxyoxolan-3-yl]methyl 4-hydroxybenzoate

CAS Registry Number

Not Available

SMILES

OC[C@H]1O[C@@H](OC2=CC=C(CO)C=C2)[C@H](O[C@@H]2OC[C@](O)(COC(=O)C3=CC=C(O)C=C3)[C@H]2O)[C@@H](O)[C@H]1O

InChI Identifier

InChI=1S/C25H30O13/c26-9-13-1-7-16(8-2-13)36-23-20(19(30)18(29)17(10-27)37-23)38-24-21(31)25(33,12-35-24)11-34-22(32)14-3-5-15(28)6-4-14/h1-8,17-21,23-24,26-31,33H,9-12H2/t17-,18+,19+,20-,21+,23-,24+,25-/m1/s1

InChI Key

WIMAHNFFARKNJF-LZMGOZBSSA-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
Cucurbita moschata	Plant	KNApSAcK

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as phenolic glycosides. These are organic compounds containing a phenolic structure attached to a glycosyl moiety. Some examples of phenolic structures include lignans, and flavonoids. Among the sugar units found in natural glycosides are D-glucose, L-Fructose, and L rhamnose.

Kingdom

Organic compounds

Super Class

Organic oxygen compounds

Class

Organooxygen compounds

Sub Class

Carbohydrates and carbohydrate conjugates

Direct Parent

Phenolic glycosides

Alternative Parents

Substituents

Phenolic glycoside
P-hydroxybenzoic acid alkyl ester
P-hydroxybenzoic acid ester
O-glycosyl compound
Disaccharide
Benzoate ester
Benzoic acid or derivatives
Phenoxy compound
Phenol ether
Benzyl alcohol
Benzoyl
1-hydroxy-2-unsubstituted benzenoid
Phenol
Benzenoid
Oxane
Monocyclic benzene moiety
Tetrahydrofuran
Tertiary alcohol
Secondary alcohol
Carboxylic acid ester
Oxacycle
Organoheterocyclic compound
Monocarboxylic acid or derivatives
Carboxylic acid derivative
Acetal
Organic oxide
Hydrocarbon derivative
Aromatic alcohol
Primary alcohol
Alcohol
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	-0.22	ALOGPS
logP	-0.45	ChemAxon
logS	-2.6	ALOGPS
pKa (Strongest Acidic)	8.5	ChemAxon
pKa (Strongest Basic)	-2.8	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	12	ChemAxon
Hydrogen Donor Count	7	ChemAxon
Polar Surface Area	204.83 Å²	ChemAxon
Rotatable Bond Count	10	ChemAxon
Refractivity	125.47 m³·mol⁻¹	ChemAxon
Polarizability	52.7 Å³	ChemAxon
Number of Rings	4	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

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

162932651

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

Not Available

Showing NP-Card for (-)-Cucurbitoside D (NP0072031)

MOL for NP0072031 ((-)-Cucurbitoside D)

3D MOL for NP0072031 ((-)-Cucurbitoside D)

3D SDF for NP0072031 ((-)-Cucurbitoside D)

3D-SDF for NP0072031 ((-)-Cucurbitoside D)

PDB for NP0072031 ((-)-Cucurbitoside D)

3D PDB for NP0072031 ((-)-Cucurbitoside D)

SMILES for NP0072031 ((-)-Cucurbitoside D)

INCHI for NP0072031 ((-)-Cucurbitoside D)

Structure for NP0072031 ((-)-Cucurbitoside D)

3D Structure for NP0072031 ((-)-Cucurbitoside D)