NP-MRD: Showing NP-Card for methyl 5-hydroxy-2-[(2s,3r,4r,5s,6r)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]-7-oxabicyclo[4.1.0]hepta-1,3,5-triene-3-carboxylate (NP0226914)

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Record Information

Version

2.0

Created at

2022-09-06 06:06:15 UTC

Updated at

2022-09-06 06:06:16 UTC

NP-MRD ID

NP0226914

Secondary Accession Numbers

None

Natural Product Identification

Common Name

methyl 5-hydroxy-2-[(2s,3r,4r,5s,6r)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]-7-oxabicyclo[4.1.0]hepta-1,3,5-triene-3-carboxylate

Description

Methyl 5-hydroxy-2-[(2S,3R,4R,5S,6R)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]-7-oxabicyclo[4.1.0]Hepta-1,3,5-triene-3-carboxylate 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. methyl 5-hydroxy-2-[(2s,3r,4r,5s,6r)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]-7-oxabicyclo[4.1.0]hepta-1,3,5-triene-3-carboxylate is found in Commelina communis. Based on a literature review very few articles have been published on methyl 5-hydroxy-2-[(2S,3R,4R,5S,6R)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]-7-oxabicyclo[4.1.0]Hepta-1,3,5-triene-3-carboxylate.

Structure

MOL SDF PDB SMILES InChI


  Mrv1652309062208062D          

 23 25  0  0  1  0            999 V2000
    4.2868    3.3000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.5724    2.8875    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.5724    2.0625    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.2868    1.6500    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.8579    1.6500    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8579    0.8250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.1434    0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.1434   -0.4125    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289    0.8250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289    1.6500    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.1434    2.0625    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.1434    2.8875    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    2.8579    3.3000    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.8579    4.1250    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    3.5724    4.5375    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.2868    4.1250    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.1434    4.5375    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    2.1434    5.3625    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289    4.1250    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    0.7145    4.5375    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289    3.3000    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    0.7145    2.8875    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145    1.2375    0.0000 O   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  2  0  0  0  0
  3  5  1  0  0  0  0
  5  6  2  0  0  0  0
  6  7  1  0  0  0  0
  7  8  1  0  0  0  0
  7  9  2  0  0  0  0
  9 10  1  0  0  0  0
 10 11  2  0  0  0  0
  5 11  1  0  0  0  0
 12 11  1  1  0  0  0
 12 13  1  0  0  0  0
 13 14  1  0  0  0  0
 14 15  1  1  0  0  0
 15 16  1  0  0  0  0
 14 17  1  0  0  0  0
 17 18  1  6  0  0  0
 17 19  1  0  0  0  0
 19 20  1  1  0  0  0
 19 21  1  0  0  0  0
 12 21  1  0  0  0  0
 21 22  1  6  0  0  0
 10 23  1  0  0  0  0
  9 23  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0226914

> <DATABASE_NAME>
NP-MRD

> <SMILES>
COC(=O)C1=CC(O)=C2OC2=C1[C@@H]1O[C@H](CO)[C@@H](O)[C@H](O)[C@H]1O

> <INCHI_IDENTIFIER>
InChI=1S/C14H16O9/c1-21-14(20)4-2-5(16)11-13(23-11)7(4)12-10(19)9(18)8(17)6(3-15)22-12/h2,6,8-10,12,15-19H,3H2,1H3/t6-,8-,9+,10-,12+/m1/s1

> <INCHI_KEY>
DNOYEWZAPJCUNS-QJCNDGQWSA-N

> <FORMULA>
C14H16O9

> <MOLECULAR_WEIGHT>
328.273

> <EXACT_MASS>
328.079432095

> <JCHEM_ACCEPTOR_COUNT>
7

> <JCHEM_ATOM_COUNT>
39

> <JCHEM_AVERAGE_POLARIZABILITY>
30.488201370036798

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
5

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
methyl 5-hydroxy-2-[(2S,3R,4R,5S,6R)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]-7-oxabicyclo[4.1.0]hepta-1,3,5-triene-3-carboxylate

> <JCHEM_LOGP>
-1.5571220796666665

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
3

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
12.538531986338096

> <JCHEM_PKA_STRONGEST_ACIDIC>
7.639664559545299

> <JCHEM_PKA_STRONGEST_BASIC>
-2.9791917733671447

> <JCHEM_POLAR_SURFACE_AREA>
149.21

> <JCHEM_REFRACTIVITY>
73.3653

> <JCHEM_ROTATABLE_BOND_COUNT>
4

> <JCHEM_RULE_OF_FIVE>
1

> <JCHEM_TRADITIONAL_IUPAC>
methyl 5-hydroxy-2-[(2S,3R,4R,5S,6R)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]-7-oxabicyclo[4.1.0]hepta-1,3,5-triene-3-carboxylate

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 06-SEP-22   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   06-SEP-22         0                                  
HETATM    1  C   UNK     0       8.002   6.160   0.000  0.00  0.00           C+0
HETATM    2  O   UNK     0       6.668   5.390   0.000  0.00  0.00           O+0
HETATM    3  C   UNK     0       6.668   3.850   0.000  0.00  0.00           C+0
HETATM    4  O   UNK     0       8.002   3.080   0.000  0.00  0.00           O+0
HETATM    5  C   UNK     0       5.335   3.080   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       5.335   1.540   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       4.001   0.770   0.000  0.00  0.00           C+0
HETATM    8  O   UNK     0       4.001  -0.770   0.000  0.00  0.00           O+0
HETATM    9  C   UNK     0       2.667   1.540   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0       2.667   3.080   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0       4.001   3.850   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0       4.001   5.390   0.000  0.00  0.00           C+0
HETATM   13  O   UNK     0       5.335   6.160   0.000  0.00  0.00           O+0
HETATM   14  C   UNK     0       5.335   7.700   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0       6.668   8.470   0.000  0.00  0.00           C+0
HETATM   16  O   UNK     0       8.002   7.700   0.000  0.00  0.00           O+0
HETATM   17  C   UNK     0       4.001   8.470   0.000  0.00  0.00           C+0
HETATM   18  O   UNK     0       4.001  10.010   0.000  0.00  0.00           O+0
HETATM   19  C   UNK     0       2.667   7.700   0.000  0.00  0.00           C+0
HETATM   20  O   UNK     0       1.334   8.470   0.000  0.00  0.00           O+0
HETATM   21  C   UNK     0       2.667   6.160   0.000  0.00  0.00           C+0
HETATM   22  O   UNK     0       1.334   5.390   0.000  0.00  0.00           O+0
HETATM   23  O   UNK     0       1.334   2.310   0.000  0.00  0.00           O+0
CONECT    1    2                                                            
CONECT    2    1    3                                                       
CONECT    3    2    4    5                                                  
CONECT    4    3                                                            
CONECT    5    3    6   11                                                  
CONECT    6    5    7                                                       
CONECT    7    6    8    9                                                  
CONECT    8    7                                                            
CONECT    9    7   10   23                                                  
CONECT   10    9   11   23                                                  
CONECT   11   10    5   12                                                  
CONECT   12   11   13   21                                                  
CONECT   13   12   14                                                       
CONECT   14   13   15   17                                                  
CONECT   15   14   16                                                       
CONECT   16   15                                                            
CONECT   17   14   18   19                                                  
CONECT   18   17                                                            
CONECT   19   17   20   21                                                  
CONECT   20   19                                                            
CONECT   21   19   12   22                                                  
CONECT   22   21                                                            
CONECT   23   10    9                                                       
MASTER        0    0    0    0    0    0    0    0   23    0   50    0
END

View in JSmol

Synonyms

Value	Source
Methyl 5-hydroxy-2-[(2S,3R,4R,5S,6R)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]-7-oxabicyclo[4.1.0]hepta-1,3,5-triene-3-carboxylic acid	Generator

Chemical Formula

C₁₄H₁₆O₉

Average Mass

328.2730 Da

Monoisotopic Mass

328.07943 Da

IUPAC Name

methyl 5-hydroxy-2-[(2S,3R,4R,5S,6R)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]-7-oxabicyclo[4.1.0]hepta-1,3,5-triene-3-carboxylate

Traditional Name

methyl 5-hydroxy-2-[(2S,3R,4R,5S,6R)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]-7-oxabicyclo[4.1.0]hepta-1,3,5-triene-3-carboxylate

CAS Registry Number

Not Available

SMILES

COC(=O)C1=CC(O)=C2OC2=C1[C@@H]1O[C@H](CO)[C@@H](O)[C@H](O)[C@H]1O

InChI Identifier

InChI=1S/C14H16O9/c1-21-14(20)4-2-5(16)11-13(23-11)7(4)12-10(19)9(18)8(17)6(3-15)22-12/h2,6,8-10,12,15-19H,3H2,1H3/t6-,8-,9+,10-,12+/m1/s1

InChI Key

DNOYEWZAPJCUNS-QJCNDGQWSA-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
Commelina communis	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
Hexose monosaccharide
C-glycosyl compound
Diaryl ether
1-hydroxy-2-unsubstituted benzenoid
Monosaccharide
Oxane
Benzenoid
Methyl ester
Secondary alcohol
Carboxylic acid ester
Polyol
Monocarboxylic acid or derivatives
Oxacycle
Ether
Dialkyl ether
Carboxylic acid derivative
Organoheterocyclic compound
Primary alcohol
Alcohol
Hydrocarbon derivative
Organic oxide
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	-1.6	ChemAxon
pKa (Strongest Acidic)	7.64	ChemAxon
pKa (Strongest Basic)	-3	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	7	ChemAxon
Hydrogen Donor Count	5	ChemAxon
Polar Surface Area	149.21 Å²	ChemAxon
Rotatable Bond Count	4	ChemAxon
Refractivity	73.37 m³·mol⁻¹	ChemAxon
Polarizability	30.49 Å³	ChemAxon
Number of Rings	3	ChemAxon
Bioavailability	Yes	ChemAxon
Rule of Five	Yes	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

28286130

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

163094846

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

LOTUS database [Link]

Showing NP-Card for methyl 5-hydroxy-2-[(2s,3r,4r,5s,6r)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]-7-oxabicyclo[4.1.0]hepta-1,3,5-triene-3-carboxylate (NP0226914)

MOL for NP0226914 (methyl 5-hydroxy-2-[(2s,3r,4r,5s,6r)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]-7-oxabicyclo[4.1.0]hepta-1,3,5-triene-3-carboxylate)

3D MOL for NP0226914 (methyl 5-hydroxy-2-[(2s,3r,4r,5s,6r)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]-7-oxabicyclo[4.1.0]hepta-1,3,5-triene-3-carboxylate)

3D SDF for NP0226914 (methyl 5-hydroxy-2-[(2s,3r,4r,5s,6r)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]-7-oxabicyclo[4.1.0]hepta-1,3,5-triene-3-carboxylate)

3D-SDF for NP0226914 (methyl 5-hydroxy-2-[(2s,3r,4r,5s,6r)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]-7-oxabicyclo[4.1.0]hepta-1,3,5-triene-3-carboxylate)

PDB for NP0226914 (methyl 5-hydroxy-2-[(2s,3r,4r,5s,6r)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]-7-oxabicyclo[4.1.0]hepta-1,3,5-triene-3-carboxylate)

3D PDB for NP0226914 (methyl 5-hydroxy-2-[(2s,3r,4r,5s,6r)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]-7-oxabicyclo[4.1.0]hepta-1,3,5-triene-3-carboxylate)

SMILES for NP0226914 (methyl 5-hydroxy-2-[(2s,3r,4r,5s,6r)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]-7-oxabicyclo[4.1.0]hepta-1,3,5-triene-3-carboxylate)

INCHI for NP0226914 (methyl 5-hydroxy-2-[(2s,3r,4r,5s,6r)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]-7-oxabicyclo[4.1.0]hepta-1,3,5-triene-3-carboxylate)

Structure for NP0226914 (methyl 5-hydroxy-2-[(2s,3r,4r,5s,6r)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]-7-oxabicyclo[4.1.0]hepta-1,3,5-triene-3-carboxylate)

3D Structure for NP0226914 (methyl 5-hydroxy-2-[(2s,3r,4r,5s,6r)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]-7-oxabicyclo[4.1.0]hepta-1,3,5-triene-3-carboxylate)