NP-MRD: Showing NP-Card for (2r,3s)-3-(hydroxymethyl)-7-methoxy-2-(3-methoxy-4-{[(2s,3r,4s,5s,6r)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}phenyl)-2,3-dihydro-1-benzofuran-5-carboxylic acid (NP0153911)

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Record Information

Version

2.0

Created at

2022-09-02 10:38:43 UTC

Updated at

2022-09-02 10:38:44 UTC

NP-MRD ID

NP0153911

Secondary Accession Numbers

None

Natural Product Identification

Common Name

(2r,3s)-3-(hydroxymethyl)-7-methoxy-2-(3-methoxy-4-{[(2s,3r,4s,5s,6r)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}phenyl)-2,3-dihydro-1-benzofuran-5-carboxylic acid

Description

(2R,3S)-3-(hydroxymethyl)-7-methoxy-2-(3-methoxy-4-{[(2S,3R,4S,5S,6R)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}phenyl)-2,3-dihydro-1-benzofuran-5-carboxylic acid belongs to the class of organic compounds known as hydrolyzable tannins. These are tannins with a structure characterized by either of the following models. In model 1, the structure contains galloyl units (in some cases, shikimic acid units) that are linked to diverse polyol carbohydrate-, catechin-, or triterpenoid units. In model 2, contains at least two galloyl units C-C coupled to each other, and do not contain a glycosidically linked catechin unit. (2r,3s)-3-(hydroxymethyl)-7-methoxy-2-(3-methoxy-4-{[(2s,3r,4s,5s,6r)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}phenyl)-2,3-dihydro-1-benzofuran-5-carboxylic acid is found in Urena lobata. Based on a literature review very few articles have been published on (2R,3S)-3-(hydroxymethyl)-7-methoxy-2-(3-methoxy-4-{[(2S,3R,4S,5S,6R)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}phenyl)-2,3-dihydro-1-benzofuran-5-carboxylic acid.

Structure

MOL 3D MOL SDF PDB SMILES InChI


  Mrv1652309022212392D          

 36 39  0  0  1  0            999 V2000
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M  END

     RDKit          3D

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M  END


  Mrv1652309022212392D          

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 26 27  1  0  0  0  0
 27 28  1  0  0  0  0
 28 29  1  1  0  0  0
 29 30  1  0  0  0  0
 28 31  1  0  0  0  0
 31 32  1  6  0  0  0
 31 33  1  0  0  0  0
 33 34  1  1  0  0  0
 33 35  1  0  0  0  0
 26 35  1  0  0  0  0
 35 36  1  6  0  0  0
M  END
> <DATABASE_ID>
NP0153911

> <DATABASE_NAME>
NP-MRD

> <SMILES>
COC1=C2O[C@H]([C@H](CO)C2=CC(=C1)C(O)=O)C1=CC=C(O[C@@H]2O[C@H](CO)[C@@H](O)[C@H](O)[C@H]2O)C(OC)=C1

> <INCHI_IDENTIFIER>
InChI=1S/C24H28O12/c1-32-15-6-10(3-4-14(15)34-24-20(29)19(28)18(27)17(9-26)35-24)21-13(8-25)12-5-11(23(30)31)7-16(33-2)22(12)36-21/h3-7,13,17-21,24-29H,8-9H2,1-2H3,(H,30,31)/t13-,17-,18-,19+,20-,21+,24-/m1/s1

> <INCHI_KEY>
IRPPUVUWTSBWMV-IVOJZKDFSA-N

> <FORMULA>
C24H28O12

> <MOLECULAR_WEIGHT>
508.476

> <EXACT_MASS>
508.158076342

> <JCHEM_ACCEPTOR_COUNT>
12

> <JCHEM_ATOM_COUNT>
64

> <JCHEM_AVERAGE_POLARIZABILITY>
50.870750808713275

> <JCHEM_BIOAVAILABILITY>
0

> <JCHEM_DONOR_COUNT>
6

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(2R,3S)-3-(hydroxymethyl)-7-methoxy-2-(3-methoxy-4-{[(2S,3R,4S,5S,6R)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}phenyl)-2,3-dihydro-1-benzofuran-5-carboxylic acid

> <ALOGPS_LOGP>
0.13

> <JCHEM_LOGP>
-0.6198388576666664

> <ALOGPS_LOGS>
-2.95

> <JCHEM_MDDR_LIKE_RULE>
1

> <JCHEM_NUMBER_OF_RINGS>
4

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-1

> <JCHEM_PKA>
12.19957822876137

> <JCHEM_PKA_STRONGEST_ACIDIC>
4.104034330470917

> <JCHEM_PKA_STRONGEST_BASIC>
-2.7295485153287142

> <JCHEM_POLAR_SURFACE_AREA>
184.6

> <JCHEM_REFRACTIVITY>
120.723

> <JCHEM_ROTATABLE_BOND_COUNT>
8

> <JCHEM_RULE_OF_FIVE>
0

> <ALOGPS_SOLUBILITY>
5.76e-01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
(2R,3S)-3-(hydroxymethyl)-7-methoxy-2-(3-methoxy-4-{[(2S,3R,4S,5S,6R)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}phenyl)-2,3-dihydro-1-benzofuran-5-carboxylic acid

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 02-SEP-22   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   02-SEP-22         0                                  
HETATM    1  C   UNK     0      -2.630   2.698   0.000  0.00  0.00           C+0
HETATM    2  O   UNK     0      -3.400   1.365   0.000  0.00  0.00           O+0
HETATM    3  C   UNK     0      -2.630   0.031   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0      -1.090   0.031   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0      -0.320  -1.303   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       1.220  -1.303   0.000  0.00  0.00           C+0
HETATM    7  O   UNK     0       2.126  -0.057   0.000  0.00  0.00           O+0
HETATM    8  C   UNK     0       3.590  -0.533   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0       4.924   0.237   0.000  0.00  0.00           C+0
HETATM   10  O   UNK     0       4.924   1.777   0.000  0.00  0.00           O+0
HETATM   11  C   UNK     0       6.258   2.547   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0       6.258  -0.533   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0       6.258  -2.073   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0       7.591  -2.843   0.000  0.00  0.00           C+0
HETATM   15  O   UNK     0       8.925  -2.073   0.000  0.00  0.00           O+0
HETATM   16  O   UNK     0       7.591  -4.383   0.000  0.00  0.00           O+0
HETATM   17  C   UNK     0       4.924  -2.843   0.000  0.00  0.00           C+0
HETATM   18  C   UNK     0       3.590  -2.073   0.000  0.00  0.00           C+0
HETATM   19  C   UNK     0       2.126  -2.549   0.000  0.00  0.00           C+0
HETATM   20  C   UNK     0       1.650  -4.013   0.000  0.00  0.00           C+0
HETATM   21  O   UNK     0       0.143  -4.334   0.000  0.00  0.00           O+0
HETATM   22  C   UNK     0      -1.090  -2.637   0.000  0.00  0.00           C+0
HETATM   23  C   UNK     0      -2.630  -2.637   0.000  0.00  0.00           C+0
HETATM   24  C   UNK     0      -3.400  -1.303   0.000  0.00  0.00           C+0
HETATM   25  O   UNK     0      -4.940  -1.303   0.000  0.00  0.00           O+0
HETATM   26  C   UNK     0      -5.710   0.031   0.000  0.00  0.00           C+0
HETATM   27  O   UNK     0      -4.940   1.365   0.000  0.00  0.00           O+0
HETATM   28  C   UNK     0      -5.710   2.698   0.000  0.00  0.00           C+0
HETATM   29  C   UNK     0      -4.940   4.032   0.000  0.00  0.00           C+0
HETATM   30  O   UNK     0      -3.400   4.032   0.000  0.00  0.00           O+0
HETATM   31  C   UNK     0      -7.250   2.698   0.000  0.00  0.00           C+0
HETATM   32  O   UNK     0      -8.020   4.032   0.000  0.00  0.00           O+0
HETATM   33  C   UNK     0      -8.020   1.365   0.000  0.00  0.00           C+0
HETATM   34  O   UNK     0      -9.560   1.365   0.000  0.00  0.00           O+0
HETATM   35  C   UNK     0      -7.250   0.031   0.000  0.00  0.00           C+0
HETATM   36  O   UNK     0      -8.020  -1.303   0.000  0.00  0.00           O+0
CONECT    1    2                                                            
CONECT    2    1    3                                                       
CONECT    3    2    4   24                                                  
CONECT    4    3    5                                                       
CONECT    5    4    6   22                                                  
CONECT    6    5    7   19                                                  
CONECT    7    6    8                                                       
CONECT    8    7    9   18                                                  
CONECT    9    8   10   12                                                  
CONECT   10    9   11                                                       
CONECT   11   10                                                            
CONECT   12    9   13                                                       
CONECT   13   12   14   17                                                  
CONECT   14   13   15   16                                                  
CONECT   15   14                                                            
CONECT   16   14                                                            
CONECT   17   13   18                                                       
CONECT   18   17    8   19                                                  
CONECT   19   18    6   20                                                  
CONECT   20   19   21                                                       
CONECT   21   20                                                            
CONECT   22    5   23                                                       
CONECT   23   22   24                                                       
CONECT   24   23    3   25                                                  
CONECT   25   24   26                                                       
CONECT   26   25   27   35                                                  
CONECT   27   26   28                                                       
CONECT   28   27   29   31                                                  
CONECT   29   28   30                                                       
CONECT   30   29                                                            
CONECT   31   28   32   33                                                  
CONECT   32   31                                                            
CONECT   33   31   34   35                                                  
CONECT   34   33                                                            
CONECT   35   33   26   36                                                  
CONECT   36   35                                                            
MASTER        0    0    0    0    0    0    0    0   36    0   78    0
END

View in JSmol

Synonyms

Value	Source
(2R,3S)-3-(Hydroxymethyl)-7-methoxy-2-(3-methoxy-4-{[(2S,3R,4S,5S,6R)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}phenyl)-2,3-dihydro-1-benzofuran-5-carboxylate	Generator

Chemical Formula

C₂₄H₂₈O₁₂

Average Mass

508.4760 Da

Monoisotopic Mass

508.15808 Da

IUPAC Name

(2R,3S)-3-(hydroxymethyl)-7-methoxy-2-(3-methoxy-4-{[(2S,3R,4S,5S,6R)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}phenyl)-2,3-dihydro-1-benzofuran-5-carboxylic acid

Traditional Name

(2R,3S)-3-(hydroxymethyl)-7-methoxy-2-(3-methoxy-4-{[(2S,3R,4S,5S,6R)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}phenyl)-2,3-dihydro-1-benzofuran-5-carboxylic acid

CAS Registry Number

Not Available

SMILES

COC1=C2O[C@H]([C@H](CO)C2=CC(=C1)C(O)=O)C1=CC=C(O[C@@H]2O[C@H](CO)[C@@H](O)[C@H](O)[C@H]2O)C(OC)=C1

InChI Identifier

InChI=1S/C24H28O12/c1-32-15-6-10(3-4-14(15)34-24-20(29)19(28)18(27)17(9-26)35-24)21-13(8-25)12-5-11(23(30)31)7-16(33-2)22(12)36-21/h3-7,13,17-21,24-29H,8-9H2,1-2H3,(H,30,31)/t13-,17-,18-,19+,20-,21+,24-/m1/s1

InChI Key

IRPPUVUWTSBWMV-IVOJZKDFSA-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
Urena lobata	LOTUS Database	35616633

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as hydrolyzable tannins. These are tannins with a structure characterized by either of the following models. In model 1, the structure contains galloyl units (in some cases, shikimic acid units) that are linked to diverse polyol carbohydrate-, catechin-, or triterpenoid units. In model 2, contains at least two galloyl units C-C coupled to each other, and do not contain a glycosidically linked catechin unit.

Kingdom

Organic compounds

Super Class

Phenylpropanoids and polyketides

Class

Tannins

Sub Class

Hydrolyzable tannins

Direct Parent

Hydrolyzable tannins

Alternative Parents

Substituents

2-arylbenzofuran flavonoid
Lignan glycoside
Hydrolyzable tannin
Neolignan skeleton
Phenolic glycoside
Hexose monosaccharide
Glycosyl compound
M-methoxybenzoic acid or derivatives
O-glycosyl compound
Coumaran
Phenoxy compound
Anisole
Methoxybenzene
Phenol ether
Alkyl aryl ether
Monocyclic benzene moiety
Benzenoid
Monosaccharide
Oxane
Secondary alcohol
Monocarboxylic acid or derivatives
Organoheterocyclic compound
Oxacycle
Ether
Carboxylic acid
Carboxylic acid derivative
Acetal
Polyol
Primary alcohol
Alcohol
Hydrocarbon derivative
Organic oxygen compound
Organooxygen compound
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	0.13	ALOGPS
logP	-0.62	ChemAxon
logS	-3	ALOGPS
pKa (Strongest Acidic)	4.1	ChemAxon
pKa (Strongest Basic)	-2.7	ChemAxon
Physiological Charge	-1	ChemAxon
Hydrogen Acceptor Count	12	ChemAxon
Hydrogen Donor Count	6	ChemAxon
Polar Surface Area	184.6 Å²	ChemAxon
Rotatable Bond Count	8	ChemAxon
Refractivity	120.72 m³·mol⁻¹	ChemAxon
Polarizability	50.87 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

162915878

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

LOTUS database [Link]

Showing NP-Card for (2r,3s)-3-(hydroxymethyl)-7-methoxy-2-(3-methoxy-4-{[(2s,3r,4s,5s,6r)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}phenyl)-2,3-dihydro-1-benzofuran-5-carboxylic acid (NP0153911)

MOL for NP0153911 ((2r,3s)-3-(hydroxymethyl)-7-methoxy-2-(3-methoxy-4-{[(2s,3r,4s,5s,6r)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}phenyl)-2,3-dihydro-1-benzofuran-5-carboxylic acid)

3D MOL for NP0153911 ((2r,3s)-3-(hydroxymethyl)-7-methoxy-2-(3-methoxy-4-{[(2s,3r,4s,5s,6r)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}phenyl)-2,3-dihydro-1-benzofuran-5-carboxylic acid)

3D SDF for NP0153911 ((2r,3s)-3-(hydroxymethyl)-7-methoxy-2-(3-methoxy-4-{[(2s,3r,4s,5s,6r)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}phenyl)-2,3-dihydro-1-benzofuran-5-carboxylic acid)

3D-SDF for NP0153911 ((2r,3s)-3-(hydroxymethyl)-7-methoxy-2-(3-methoxy-4-{[(2s,3r,4s,5s,6r)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}phenyl)-2,3-dihydro-1-benzofuran-5-carboxylic acid)

PDB for NP0153911 ((2r,3s)-3-(hydroxymethyl)-7-methoxy-2-(3-methoxy-4-{[(2s,3r,4s,5s,6r)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}phenyl)-2,3-dihydro-1-benzofuran-5-carboxylic acid)

3D PDB for NP0153911 ((2r,3s)-3-(hydroxymethyl)-7-methoxy-2-(3-methoxy-4-{[(2s,3r,4s,5s,6r)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}phenyl)-2,3-dihydro-1-benzofuran-5-carboxylic acid)

SMILES for NP0153911 ((2r,3s)-3-(hydroxymethyl)-7-methoxy-2-(3-methoxy-4-{[(2s,3r,4s,5s,6r)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}phenyl)-2,3-dihydro-1-benzofuran-5-carboxylic acid)

INCHI for NP0153911 ((2r,3s)-3-(hydroxymethyl)-7-methoxy-2-(3-methoxy-4-{[(2s,3r,4s,5s,6r)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}phenyl)-2,3-dihydro-1-benzofuran-5-carboxylic acid)

Structure for NP0153911 ((2r,3s)-3-(hydroxymethyl)-7-methoxy-2-(3-methoxy-4-{[(2s,3r,4s,5s,6r)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}phenyl)-2,3-dihydro-1-benzofuran-5-carboxylic acid)

3D Structure for NP0153911 ((2r,3s)-3-(hydroxymethyl)-7-methoxy-2-(3-methoxy-4-{[(2s,3r,4s,5s,6r)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}phenyl)-2,3-dihydro-1-benzofuran-5-carboxylic acid)