NP-MRD: Showing NP-Card for [(3s,4r,5s)-5-{[(2s,3r,4s,5s,6r)-4,5-dihydroxy-2-[4-(2-hydroxyethyl)phenoxy]-6-(hydroxymethyl)oxan-3-yl]oxy}-3,4-dihydroxyoxolan-3-yl]methyl 4-aminobenzoate (NP0325557)

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Record Information

Version

2.0

Created at

2022-09-12 06:23:48 UTC

Updated at

2022-09-12 06:23:48 UTC

NP-MRD ID

NP0325557

Secondary Accession Numbers

None

Natural Product Identification

Common Name

[(3s,4r,5s)-5-{[(2s,3r,4s,5s,6r)-4,5-dihydroxy-2-[4-(2-hydroxyethyl)phenoxy]-6-(hydroxymethyl)oxan-3-yl]oxy}-3,4-dihydroxyoxolan-3-yl]methyl 4-aminobenzoate

Description

Cucurbitoside I 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. [(3s,4r,5s)-5-{[(2s,3r,4s,5s,6r)-4,5-dihydroxy-2-[4-(2-hydroxyethyl)phenoxy]-6-(hydroxymethyl)oxan-3-yl]oxy}-3,4-dihydroxyoxolan-3-yl]methyl 4-aminobenzoate is found in Cucurbita pepo. Based on a literature review very few articles have been published on Cucurbitoside I.

Structure

MOL 3D MOL SDF PDB SMILES InChI


  Mrv1652309122208232D          

 39 42  0  0  1  0            999 V2000
    0.8851    1.4368    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.6302    0.6522    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
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  5 38  1  0  0  0  0
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  2 39  1  0  0  0  0
M  END

     RDKit          3D

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M  END


  Mrv1652309122208232D          

 39 42  0  0  1  0            999 V2000
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    1.3819   -4.1974    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    2.1665   -3.9425    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4317   -0.3040    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1768    0.4806    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  2  3  2  0  0  0  0
  3  4  1  0  0  0  0
  4  5  2  0  0  0  0
  5  6  1  0  0  0  0
  6  7  2  0  0  0  0
  6  8  1  0  0  0  0
  8  9  1  0  0  0  0
 10  9  1  6  0  0  0
 10 11  1  1  0  0  0
 10 12  1  0  0  0  0
 12 13  1  0  0  0  0
 13 14  1  0  0  0  0
 14 15  1  6  0  0  0
 16 15  1  1  0  0  0
 16 17  1  0  0  0  0
 17 18  1  6  0  0  0
 18 19  1  0  0  0  0
 19 20  2  0  0  0  0
 20 21  1  0  0  0  0
 21 22  2  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
 22 26  1  0  0  0  0
 26 27  2  0  0  0  0
 19 27  1  0  0  0  0
 17 28  1  0  0  0  0
 28 29  1  0  0  0  0
 29 30  1  6  0  0  0
 30 31  1  0  0  0  0
 29 32  1  0  0  0  0
 32 33  1  1  0  0  0
 32 34  1  0  0  0  0
 16 34  1  0  0  0  0
 34 35  1  6  0  0  0
 14 36  1  0  0  0  0
 10 36  1  0  0  0  0
 36 37  1  1  0  0  0
  5 38  1  0  0  0  0
 38 39  2  0  0  0  0
  2 39  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0325557

> <DATABASE_NAME>
NP-MRD

> <SMILES>
NC1=CC=C(C=C1)C(=O)OC[C@@]1(O)CO[C@@H](O[C@@H]2[C@@H](O)[C@H](O)[C@@H](CO)O[C@H]2OC2=CC=C(CCO)C=C2)[C@@H]1O

> <INCHI_IDENTIFIER>
InChI=1S/C26H33NO12/c27-16-5-3-15(4-6-16)23(33)35-12-26(34)13-36-25(22(26)32)39-21-20(31)19(30)18(11-29)38-24(21)37-17-7-1-14(2-8-17)9-10-28/h1-8,18-22,24-25,28-32,34H,9-13,27H2/t18-,19-,20+,21-,22+,24-,25+,26-/m1/s1

> <INCHI_KEY>
ACOKXVSLVQCZRD-JUKYQPCLSA-N

> <FORMULA>
C26H33NO12

> <MOLECULAR_WEIGHT>
551.545

> <EXACT_MASS>
551.200275507

> <JCHEM_ACCEPTOR_COUNT>
12

> <JCHEM_ATOM_COUNT>
72

> <JCHEM_AVERAGE_POLARIZABILITY>
55.901896559307104

> <JCHEM_BIOAVAILABILITY>
0

> <JCHEM_DONOR_COUNT>
7

> <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)phenoxy]-6-(hydroxymethyl)oxan-3-yl]oxy}-3,4-dihydroxyoxolan-3-yl]methyl 4-aminobenzoate

> <JCHEM_LOGP>
-0.6872013266666661

> <JCHEM_MDDR_LIKE_RULE>
1

> <JCHEM_NUMBER_OF_RINGS>
4

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
12.645184810377248

> <JCHEM_PKA_STRONGEST_ACIDIC>
11.792988856784001

> <JCHEM_PKA_STRONGEST_BASIC>
2.6401075154786695

> <JCHEM_POLAR_SURFACE_AREA>
210.61999999999998

> <JCHEM_REFRACTIVITY>
132.94680000000002

> <JCHEM_ROTATABLE_BOND_COUNT>
11

> <JCHEM_RULE_OF_FIVE>
0

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

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 12-SEP-22   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   12-SEP-22         0                                  
HETATM    1  N   UNK     0       1.652   2.682   0.000  0.00  0.00           N+0
HETATM    2  C   UNK     0       1.176   1.217   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       2.207   0.073   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       1.731  -1.392   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       0.225  -1.712   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0      -0.251  -3.176   0.000  0.00  0.00           C+0
HETATM    7  O   UNK     0      -1.758  -3.497   0.000  0.00  0.00           O+0
HETATM    8  O   UNK     0       0.779  -4.321   0.000  0.00  0.00           O+0
HETATM    9  C   UNK     0       0.303  -5.786   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0       1.334  -6.930   0.000  0.00  0.00           C+0
HETATM   11  O   UNK     0       2.364  -5.786   0.000  0.00  0.00           O+0
HETATM   12  C   UNK     0       0.088  -7.835   0.000  0.00  0.00           C+0
HETATM   13  O   UNK     0       0.564  -9.300   0.000  0.00  0.00           O+0
HETATM   14  C   UNK     0       2.104  -9.300   0.000  0.00  0.00           C+0
HETATM   15  O   UNK     0       3.009 -10.546   0.000  0.00  0.00           O+0
HETATM   16  C   UNK     0       2.382 -11.953   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0       3.288 -13.198   0.000  0.00  0.00           C+0
HETATM   18  O   UNK     0       4.819 -13.037   0.000  0.00  0.00           O+0
HETATM   19  C   UNK     0       5.724 -14.283   0.000  0.00  0.00           C+0
HETATM   20  C   UNK     0       7.256 -14.122   0.000  0.00  0.00           C+0
HETATM   21  C   UNK     0       8.161 -15.368   0.000  0.00  0.00           C+0
HETATM   22  C   UNK     0       7.535 -16.775   0.000  0.00  0.00           C+0
HETATM   23  C   UNK     0       8.440 -18.021   0.000  0.00  0.00           C+0
HETATM   24  C   UNK     0       7.814 -19.428   0.000  0.00  0.00           C+0
HETATM   25  O   UNK     0       8.719 -20.674   0.000  0.00  0.00           O+0
HETATM   26  C   UNK     0       6.003 -16.936   0.000  0.00  0.00           C+0
HETATM   27  C   UNK     0       5.098 -15.690   0.000  0.00  0.00           C+0
HETATM   28  O   UNK     0       2.661 -14.605   0.000  0.00  0.00           O+0
HETATM   29  C   UNK     0       1.130 -14.766   0.000  0.00  0.00           C+0
HETATM   30  C   UNK     0       0.503 -16.173   0.000  0.00  0.00           C+0
HETATM   31  O   UNK     0      -1.028 -16.334   0.000  0.00  0.00           O+0
HETATM   32  C   UNK     0       0.225 -13.520   0.000  0.00  0.00           C+0
HETATM   33  O   UNK     0      -1.307 -13.681   0.000  0.00  0.00           O+0
HETATM   34  C   UNK     0       0.851 -12.114   0.000  0.00  0.00           C+0
HETATM   35  O   UNK     0      -0.054 -10.868   0.000  0.00  0.00           O+0
HETATM   36  C   UNK     0       2.580  -7.835   0.000  0.00  0.00           C+0
HETATM   37  O   UNK     0       4.044  -7.359   0.000  0.00  0.00           O+0
HETATM   38  C   UNK     0      -0.806  -0.567   0.000  0.00  0.00           C+0
HETATM   39  C   UNK     0      -0.330   0.897   0.000  0.00  0.00           C+0
CONECT    1    2                                                            
CONECT    2    1    3   39                                                  
CONECT    3    2    4                                                       
CONECT    4    3    5                                                       
CONECT    5    4    6   38                                                  
CONECT    6    5    7    8                                                  
CONECT    7    6                                                            
CONECT    8    6    9                                                       
CONECT    9    8   10                                                       
CONECT   10    9   11   12   36                                             
CONECT   11   10                                                            
CONECT   12   10   13                                                       
CONECT   13   12   14                                                       
CONECT   14   13   15   36                                                  
CONECT   15   14   16                                                       
CONECT   16   15   17   34                                                  
CONECT   17   16   18   28                                                  
CONECT   18   17   19                                                       
CONECT   19   18   20   27                                                  
CONECT   20   19   21                                                       
CONECT   21   20   22                                                       
CONECT   22   21   23   26                                                  
CONECT   23   22   24                                                       
CONECT   24   23   25                                                       
CONECT   25   24                                                            
CONECT   26   22   27                                                       
CONECT   27   26   19                                                       
CONECT   28   17   29                                                       
CONECT   29   28   30   32                                                  
CONECT   30   29   31                                                       
CONECT   31   30                                                            
CONECT   32   29   33   34                                                  
CONECT   33   32                                                            
CONECT   34   32   16   35                                                  
CONECT   35   34                                                            
CONECT   36   14   10   37                                                  
CONECT   37   36                                                            
CONECT   38    5   39                                                       
CONECT   39   38    2                                                       
MASTER        0    0    0    0    0    0    0    0   39    0   84    0
END

View in JSmol

Synonyms

Not Available

Chemical Formula

C₂₆H₃₃NO₁₂

Average Mass

551.5450 Da

Monoisotopic Mass

551.20028 Da

IUPAC Name

Not Available

Traditional Name

Not Available

CAS Registry Number

Not Available

SMILES

NC1=CC=C(C=C1)C(=O)OC[C@@]1(O)CO[C@@H](O[C@@H]2[C@@H](O)[C@H](O)[C@@H](CO)O[C@H]2OC2=CC=C(CCO)C=C2)[C@@H]1O

InChI Identifier

InChI=1S/C26H33NO12/c27-16-5-3-15(4-6-16)23(33)35-12-26(34)13-36-25(22(26)32)39-21-20(31)19(30)18(11-29)38-24(21)37-17-7-1-14(2-8-17)9-10-28/h1-8,18-22,24-25,28-32,34H,9-13,27H2/t18-,19-,20+,21-,22+,24-,25+,26-/m1/s1

InChI Key

ACOKXVSLVQCZRD-JUKYQPCLSA-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
Cucurbita pepo	LOTUS Database	35616633

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
Disaccharide
O-glycosyl compound
Aminobenzoic acid or derivatives
Benzoate ester
Tyrosol derivative
Benzoic acid or derivatives
Phenoxy compound
Benzoyl
Aniline or substituted anilines
Phenol ether
Monocyclic benzene moiety
Oxane
Benzenoid
Primary aromatic amine
Tertiary alcohol
Oxolane
Secondary alcohol
Amino acid or derivatives
Carboxylic acid ester
Acetal
Organoheterocyclic compound
Monocarboxylic acid or derivatives
Oxacycle
Carboxylic acid derivative
Primary alcohol
Hydrocarbon derivative
Organic oxide
Organopnictogen compound
Organonitrogen compound
Organic nitrogen compound
Primary amine
Alcohol
Amine
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

External Links

HMDB ID

Not Available

DrugBank ID

Not Available

Phenol Explorer Compound ID

Not Available

FoodDB ID

Not Available

KNApSAcK ID

C00042421

Chemspider ID

9730565

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

11555787

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

LOTUS database [Link]

Showing NP-Card for [(3s,4r,5s)-5-{[(2s,3r,4s,5s,6r)-4,5-dihydroxy-2-[4-(2-hydroxyethyl)phenoxy]-6-(hydroxymethyl)oxan-3-yl]oxy}-3,4-dihydroxyoxolan-3-yl]methyl 4-aminobenzoate (NP0325557)

MOL for NP0325557 ([(3s,4r,5s)-5-{[(2s,3r,4s,5s,6r)-4,5-dihydroxy-2-[4-(2-hydroxyethyl)phenoxy]-6-(hydroxymethyl)oxan-3-yl]oxy}-3,4-dihydroxyoxolan-3-yl]methyl 4-aminobenzoate)

3D MOL for NP0325557 ([(3s,4r,5s)-5-{[(2s,3r,4s,5s,6r)-4,5-dihydroxy-2-[4-(2-hydroxyethyl)phenoxy]-6-(hydroxymethyl)oxan-3-yl]oxy}-3,4-dihydroxyoxolan-3-yl]methyl 4-aminobenzoate)

3D SDF for NP0325557 ([(3s,4r,5s)-5-{[(2s,3r,4s,5s,6r)-4,5-dihydroxy-2-[4-(2-hydroxyethyl)phenoxy]-6-(hydroxymethyl)oxan-3-yl]oxy}-3,4-dihydroxyoxolan-3-yl]methyl 4-aminobenzoate)

3D-SDF for NP0325557 ([(3s,4r,5s)-5-{[(2s,3r,4s,5s,6r)-4,5-dihydroxy-2-[4-(2-hydroxyethyl)phenoxy]-6-(hydroxymethyl)oxan-3-yl]oxy}-3,4-dihydroxyoxolan-3-yl]methyl 4-aminobenzoate)

PDB for NP0325557 ([(3s,4r,5s)-5-{[(2s,3r,4s,5s,6r)-4,5-dihydroxy-2-[4-(2-hydroxyethyl)phenoxy]-6-(hydroxymethyl)oxan-3-yl]oxy}-3,4-dihydroxyoxolan-3-yl]methyl 4-aminobenzoate)

3D PDB for NP0325557 ([(3s,4r,5s)-5-{[(2s,3r,4s,5s,6r)-4,5-dihydroxy-2-[4-(2-hydroxyethyl)phenoxy]-6-(hydroxymethyl)oxan-3-yl]oxy}-3,4-dihydroxyoxolan-3-yl]methyl 4-aminobenzoate)

SMILES for NP0325557 ([(3s,4r,5s)-5-{[(2s,3r,4s,5s,6r)-4,5-dihydroxy-2-[4-(2-hydroxyethyl)phenoxy]-6-(hydroxymethyl)oxan-3-yl]oxy}-3,4-dihydroxyoxolan-3-yl]methyl 4-aminobenzoate)

INCHI for NP0325557 ([(3s,4r,5s)-5-{[(2s,3r,4s,5s,6r)-4,5-dihydroxy-2-[4-(2-hydroxyethyl)phenoxy]-6-(hydroxymethyl)oxan-3-yl]oxy}-3,4-dihydroxyoxolan-3-yl]methyl 4-aminobenzoate)

Structure for NP0325557 ([(3s,4r,5s)-5-{[(2s,3r,4s,5s,6r)-4,5-dihydroxy-2-[4-(2-hydroxyethyl)phenoxy]-6-(hydroxymethyl)oxan-3-yl]oxy}-3,4-dihydroxyoxolan-3-yl]methyl 4-aminobenzoate)

3D Structure for NP0325557 ([(3s,4r,5s)-5-{[(2s,3r,4s,5s,6r)-4,5-dihydroxy-2-[4-(2-hydroxyethyl)phenoxy]-6-(hydroxymethyl)oxan-3-yl]oxy}-3,4-dihydroxyoxolan-3-yl]methyl 4-aminobenzoate)