NP-MRD: Showing NP-Card for (-)-Cucurbitoside J (NP0078417)

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Record Information

Version

2.0

Created at

2022-04-28 23:30:15 UTC

Updated at

2022-04-28 23:30:15 UTC

NP-MRD ID

NP0078417

Secondary Accession Numbers

None

Natural Product Identification

Common Name

(-)-Cucurbitoside J

Description

Cucurbitoside J 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 J is found in Cucurbita pepo . Based on a literature review very few articles have been published on Cucurbitoside J.

Structure

MOL 3D MOL SDF PDB SMILES InChI


  Mrv1652304292201302D          

 38 40  0  0  1  0            999 V2000
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M  END

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  Mrv1652304292201302D          

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    5.4494   -5.7380    0.0000 C   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
  6  7  1  1  0  0  0
  7  8  1  0  0  0  0
  8  9  2  0  0  0  0
  9 10  1  0  0  0  0
 10 11  2  0  0  0  0
 11 12  1  0  0  0  0
 12 13  2  0  0  0  0
  8 13  1  0  0  0  0
 13 14  1  0  0  0  0
 14 15  1  0  0  0  0
 11 16  1  0  0  0  0
 16 17  1  0  0  0  0
 17 18  1  0  0  0  0
  4 19  1  1  0  0  0
 19 20  1  0  0  0  0
  3 21  1  6  0  0  0
  2 22  1  1  0  0  0
  1 23  1  6  0  0  0
 24 23  1  1  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
 24 28  1  0  0  0  0
 28 29  1  6  0  0  0
 27 30  1  6  0  0  0
 27 31  1  1  0  0  0
 31 32  1  0  0  0  0
 32 33  1  0  0  0  0
 33 34  2  0  0  0  0
 33 35  1  0  0  0  0
 35 36  1  6  0  0  0
 35 37  1  0  0  0  0
 37 38  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0078417

> <DATABASE_NAME>
NP-MRD

> <SMILES>
CC[C@H](C)C(=O)OC[C@@]1(O)CO[C@@H](O[C@H]2[C@H](OC3=CC=C(CCO)C=C3OC)O[C@H](CO)[C@@H](O)[C@@H]2O)[C@@H]1O

> <INCHI_IDENTIFIER>
InChI=1S/C25H38O13/c1-4-13(2)22(31)34-11-25(32)12-35-24(21(25)30)38-20-19(29)18(28)17(10-27)37-23(20)36-15-6-5-14(7-8-26)9-16(15)33-3/h5-6,9,13,17-21,23-24,26-30,32H,4,7-8,10-12H2,1-3H3/t13-,17+,18+,19-,20+,21-,23+,24-,25+/m0/s1

> <INCHI_KEY>
PSQDLUHLEIWGCS-UAGGHFOLSA-N

> <FORMULA>
C25H38O13

> <MOLECULAR_WEIGHT>
546.566

> <EXACT_MASS>
546.231241284

> <JCHEM_ACCEPTOR_COUNT>
12

> <JCHEM_ATOM_COUNT>
76

> <JCHEM_AVERAGE_POLARIZABILITY>
55.89062299412895

> <JCHEM_BIOAVAILABILITY>
0

> <JCHEM_DONOR_COUNT>
6

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

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

> <ALOGPS_LOGP>
-0.04

> <JCHEM_LOGP>
-0.382030286333334

> <ALOGPS_LOGS>
-2.45

> <JCHEM_MDDR_LIKE_RULE>
1

> <JCHEM_NUMBER_OF_RINGS>
3

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
12.645285174776472

> <JCHEM_PKA_STRONGEST_ACIDIC>
11.793278382370648

> <JCHEM_PKA_STRONGEST_BASIC>
-2.4137438428771656

> <JCHEM_POLAR_SURFACE_AREA>
193.82999999999998

> <JCHEM_REFRACTIVITY>
127.84149999999997

> <JCHEM_ROTATABLE_BOND_COUNT>
13

> <JCHEM_RULE_OF_FIVE>
0

> <ALOGPS_SOLUBILITY>
1.96e+00 g/l

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

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 29-APR-22   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   29-APR-22         0                                  
HETATM    1  C   UNK     0      -2.863  -9.715   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0      -3.008 -11.248   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0      -4.408 -11.889   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0      -5.663 -10.997   0.000  0.00  0.00           C+0
HETATM    5  O   UNK     0      -5.519  -9.464   0.000  0.00  0.00           O+0
HETATM    6  C   UNK     0      -4.118  -8.823   0.000  0.00  0.00           C+0
HETATM    7  O   UNK     0      -3.973  -7.289   0.000  0.00  0.00           O+0
HETATM    8  C   UNK     0      -5.229  -6.397   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0      -6.629  -7.038   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0      -7.884  -6.146   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0      -7.739  -4.613   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0      -6.339  -3.972   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0      -5.084  -4.864   0.000  0.00  0.00           C+0
HETATM   14  O   UNK     0      -3.684  -4.223   0.000  0.00  0.00           O+0
HETATM   15  C   UNK     0      -2.428  -5.115   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0      -8.995  -3.721   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0      -8.850  -2.188   0.000  0.00  0.00           C+0
HETATM   18  O   UNK     0     -10.105  -1.296   0.000  0.00  0.00           O+0
HETATM   19  C   UNK     0      -7.064 -11.638   0.000  0.00  0.00           C+0
HETATM   20  O   UNK     0      -8.319 -10.746   0.000  0.00  0.00           O+0
HETATM   21  O   UNK     0      -4.553 -13.422   0.000  0.00  0.00           O+0
HETATM   22  O   UNK     0      -1.753 -12.140   0.000  0.00  0.00           O+0
HETATM   23  O   UNK     0      -1.463  -9.074   0.000  0.00  0.00           O+0
HETATM   24  C   UNK     0      -0.208  -9.966   0.000  0.00  0.00           C+0
HETATM   25  O   UNK     0      -0.191 -11.506   0.000  0.00  0.00           O+0
HETATM   26  C   UNK     0       1.278 -11.966   0.000  0.00  0.00           C+0
HETATM   27  C   UNK     0       2.170 -10.711   0.000  0.00  0.00           C+0
HETATM   28  C   UNK     0       1.252  -9.475   0.000  0.00  0.00           C+0
HETATM   29  O   UNK     0       1.713  -8.005   0.000  0.00  0.00           O+0
HETATM   30  O   UNK     0       3.520 -11.453   0.000  0.00  0.00           O+0
HETATM   31  C   UNK     0       3.504  -9.941   0.000  0.00  0.00           C+0
HETATM   32  O   UNK     0       4.838 -10.711   0.000  0.00  0.00           O+0
HETATM   33  C   UNK     0       6.171  -9.941   0.000  0.00  0.00           C+0
HETATM   34  O   UNK     0       6.171  -8.401   0.000  0.00  0.00           O+0
HETATM   35  C   UNK     0       7.505 -10.711   0.000  0.00  0.00           C+0
HETATM   36  C   UNK     0       7.505 -12.251   0.000  0.00  0.00           C+0
HETATM   37  C   UNK     0       8.839  -9.941   0.000  0.00  0.00           C+0
HETATM   38  C   UNK     0      10.172 -10.711   0.000  0.00  0.00           C+0
CONECT    1    2    6   23                                                  
CONECT    2    1    3   22                                                  
CONECT    3    2    4   21                                                  
CONECT    4    3    5   19                                                  
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   16                                                  
CONECT   12   11   13                                                       
CONECT   13   12    8   14                                                  
CONECT   14   13   15                                                       
CONECT   15   14                                                            
CONECT   16   11   17                                                       
CONECT   17   16   18                                                       
CONECT   18   17                                                            
CONECT   19    4   20                                                       
CONECT   20   19                                                            
CONECT   21    3                                                            
CONECT   22    2                                                            
CONECT   23    1   24                                                       
CONECT   24   23   25   28                                                  
CONECT   25   24   26                                                       
CONECT   26   25   27                                                       
CONECT   27   26   28   30   31                                             
CONECT   28   27   24   29                                                  
CONECT   29   28                                                            
CONECT   30   27                                                            
CONECT   31   27   32                                                       
CONECT   32   31   33                                                       
CONECT   33   32   34   35                                                  
CONECT   34   33                                                            
CONECT   35   33   36   37                                                  
CONECT   36   35                                                            
CONECT   37   35   38                                                       
CONECT   38   37                                                            
MASTER        0    0    0    0    0    0    0    0   38    0   80    0
END

View in JSmol

Synonyms

Not Available

Chemical Formula

C₂₅H₃₈O₁₃

Average Mass

546.5660 Da

Monoisotopic Mass

546.23124 Da

IUPAC Name

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

Traditional Name

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

CAS Registry Number

Not Available

SMILES

CC[C@H](C)C(=O)OC[C@@]1(O)CO[C@@H](O[C@H]2[C@H](OC3=CC=C(CCO)C=C3OC)O[C@H](CO)[C@@H](O)[C@@H]2O)[C@@H]1O

InChI Identifier

InChI=1S/C25H38O13/c1-4-13(2)22(31)34-11-25(32)12-35-24(21(25)30)38-20-19(29)18(28)17(10-27)37-23(20)36-15-6-5-14(7-8-26)9-16(15)33-3/h5-6,9,13,17-21,23-24,26-30,32H,4,7-8,10-12H2,1-3H3/t13-,17+,18+,19-,20+,21-,23+,24-,25+/m0/s1

InChI Key

PSQDLUHLEIWGCS-UAGGHFOLSA-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 pepo	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
O-glycosyl compound
Disaccharide
Tyrosol derivative
Phenoxy compound
Anisole
Methoxybenzene
Phenol ether
Alkyl aryl ether
Fatty acid ester
Monocyclic benzene moiety
Fatty acyl
Oxane
Benzenoid
Oxolane
Tertiary alcohol
Carboxylic acid ester
Secondary alcohol
Acetal
Oxacycle
Carboxylic acid derivative
Organoheterocyclic compound
Ether
Monocarboxylic acid or derivatives
Carbonyl group
Organic oxide
Hydrocarbon derivative
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	-0.04	ALOGPS
logP	-0.38	ChemAxon
logS	-2.4	ALOGPS
pKa (Strongest Acidic)	11.79	ChemAxon
pKa (Strongest Basic)	-2.4	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	12	ChemAxon
Hydrogen Donor Count	6	ChemAxon
Polar Surface Area	193.83 Å²	ChemAxon
Rotatable Bond Count	13	ChemAxon
Refractivity	127.84 m³·mol⁻¹	ChemAxon
Polarizability	55.89 Å³	ChemAxon
Number of Rings	3	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

C00042422

Chemspider ID

9672420

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

11497614

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

Not Available

Showing NP-Card for (-)-Cucurbitoside J (NP0078417)

MOL for NP0078417 ((-)-Cucurbitoside J)

3D MOL for NP0078417 ((-)-Cucurbitoside J)

3D SDF for NP0078417 ((-)-Cucurbitoside J)

3D-SDF for NP0078417 ((-)-Cucurbitoside J)

PDB for NP0078417 ((-)-Cucurbitoside J)

3D PDB for NP0078417 ((-)-Cucurbitoside J)

SMILES for NP0078417 ((-)-Cucurbitoside J)

INCHI for NP0078417 ((-)-Cucurbitoside J)

Structure for NP0078417 ((-)-Cucurbitoside J)

3D Structure for NP0078417 ((-)-Cucurbitoside J)