NP-MRD: Showing NP-Card for (2r,3s,4r,5r,6r)-6-{[(3r,3as,4s,5s,6as)-4-hydroxy-4-(hydroxymethyl)-5-methyl-2-oxo-tetrahydro-3h-cyclopenta[b]furan-3-yl]methoxy}-4,5-dihydroxy-2-(hydroxymethyl)oxan-3-yl (2e)-3-(4-hydroxyphenyl)prop-2-enoate (NP0285763)

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Record Information

Version

2.0

Created at

2022-09-09 14:04:20 UTC

Updated at

2022-09-09 14:04:20 UTC

NP-MRD ID

NP0285763

Secondary Accession Numbers

None

Natural Product Identification

Common Name

(2r,3s,4r,5r,6r)-6-{[(3r,3as,4s,5s,6as)-4-hydroxy-4-(hydroxymethyl)-5-methyl-2-oxo-tetrahydro-3h-cyclopenta[b]furan-3-yl]methoxy}-4,5-dihydroxy-2-(hydroxymethyl)oxan-3-yl (2e)-3-(4-hydroxyphenyl)prop-2-enoate

Description

Verbenabraside B belongs to the class of organic compounds known as terpene glycosides. These are prenol lipids containing a carbohydrate moiety glycosidically bound to a terpene backbone. (2r,3s,4r,5r,6r)-6-{[(3r,3as,4s,5s,6as)-4-hydroxy-4-(hydroxymethyl)-5-methyl-2-oxo-tetrahydro-3h-cyclopenta[b]furan-3-yl]methoxy}-4,5-dihydroxy-2-(hydroxymethyl)oxan-3-yl (2e)-3-(4-hydroxyphenyl)prop-2-enoate is found in Verbena brasiliensis. (2r,3s,4r,5r,6r)-6-{[(3r,3as,4s,5s,6as)-4-hydroxy-4-(hydroxymethyl)-5-methyl-2-oxo-tetrahydro-3h-cyclopenta[b]furan-3-yl]methoxy}-4,5-dihydroxy-2-(hydroxymethyl)oxan-3-yl (2e)-3-(4-hydroxyphenyl)prop-2-enoate was first documented in 2006 (PMID: 17015981). Based on a literature review very few articles have been published on Verbenabraside B.

Structure

MOL 3D MOL SDF PDB SMILES InChI


  Mrv1652309092216042D          

 37 40  0  0  1  0            999 V2000
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M  END

     RDKit          3D

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M  END


  Mrv1652309092216042D          

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  6  7  2  0  0  0  0
  6  8  1  0  0  0  0
  8  9  1  1  0  0  0
  9 10  1  0  0  0  0
 11 10  1  6  0  0  0
 11 12  1  0  0  0  0
 12 13  1  0  0  0  0
 13 14  1  6  0  0  0
 14 15  1  0  0  0  0
 13 16  1  0  0  0  0
 16 17  1  1  0  0  0
 17 18  1  0  0  0  0
 18 19  2  0  0  0  0
 18 20  1  0  0  0  0
 20 21  2  0  0  0  0
 21 22  1  0  0  0  0
 22 23  2  0  0  0  0
 23 24  1  0  0  0  0
 24 25  2  0  0  0  0
 25 26  1  0  0  0  0
 25 27  1  0  0  0  0
 27 28  2  0  0  0  0
 22 28  1  0  0  0  0
 16 29  1  0  0  0  0
 29 30  1  6  0  0  0
 29 31  1  0  0  0  0
 11 31  1  0  0  0  0
 31 32  1  1  0  0  0
 33  8  1  6  0  0  0
  4 33  1  0  0  0  0
 33 34  1  0  0  0  0
  2 34  1  0  0  0  0
 34 35  1  1  0  0  0
 34 36  1  6  0  0  0
 36 37  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0285763

> <DATABASE_NAME>
NP-MRD

> <SMILES>
C[C@H]1C[C@@H]2OC(=O)[C@@H](CO[C@@H]3O[C@H](CO)[C@@H](OC(=O)\C=C\C4=CC=C(O)C=C4)[C@H](O)[C@H]3O)[C@@H]2[C@]1(O)CO

> <INCHI_IDENTIFIER>
InChI=1S/C25H32O12/c1-12-8-16-19(25(12,33)11-27)15(23(32)35-16)10-34-24-21(31)20(30)22(17(9-26)36-24)37-18(29)7-4-13-2-5-14(28)6-3-13/h2-7,12,15-17,19-22,24,26-28,30-31,33H,8-11H2,1H3/b7-4+/t12-,15-,16-,17+,19-,20+,21+,22+,24+,25-/m0/s1

> <INCHI_KEY>
PRCZUWUTPHKKKP-QUXYPBBGSA-N

> <FORMULA>
C25H32O12

> <MOLECULAR_WEIGHT>
524.519

> <EXACT_MASS>
524.18937647

> <JCHEM_ACCEPTOR_COUNT>
10

> <JCHEM_ATOM_COUNT>
69

> <JCHEM_AVERAGE_POLARIZABILITY>
52.42216403892889

> <JCHEM_BIOAVAILABILITY>
0

> <JCHEM_DONOR_COUNT>
6

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(2R,3S,4R,5R,6R)-6-{[(3R,3aS,4S,5S,6aS)-4-hydroxy-4-(hydroxymethyl)-5-methyl-2-oxo-hexahydro-2H-cyclopenta[b]furan-3-yl]methoxy}-4,5-dihydroxy-2-(hydroxymethyl)oxan-3-yl (2E)-3-(4-hydroxyphenyl)prop-2-enoate

> <JCHEM_LOGP>
-0.534921750666667

> <JCHEM_MDDR_LIKE_RULE>
1

> <JCHEM_NUMBER_OF_RINGS>
4

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
12.241826598606682

> <JCHEM_PKA_STRONGEST_ACIDIC>
9.397960141604413

> <JCHEM_PKA_STRONGEST_BASIC>
-2.9818075653428258

> <JCHEM_POLAR_SURFACE_AREA>
192.44

> <JCHEM_REFRACTIVITY>
124.45560000000003

> <JCHEM_ROTATABLE_BOND_COUNT>
9

> <JCHEM_RULE_OF_FIVE>
0

> <JCHEM_TRADITIONAL_IUPAC>
(2R,3S,4R,5R,6R)-6-{[(3R,3aS,4S,5S,6aS)-4-hydroxy-4-(hydroxymethyl)-5-methyl-2-oxo-tetrahydro-3H-cyclopenta[b]furan-3-yl]methoxy}-4,5-dihydroxy-2-(hydroxymethyl)oxan-3-yl (2E)-3-(4-hydroxyphenyl)prop-2-enoate

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 09-SEP-22   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   09-SEP-22         0                                  
HETATM    1  C   UNK     0      -0.075  -0.476   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       1.465  -0.476   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       2.370   0.770   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       3.834   0.294   0.000  0.00  0.00           C+0
HETATM    5  O   UNK     0       5.299   0.770   0.000  0.00  0.00           O+0
HETATM    6  C   UNK     0       6.204  -0.476   0.000  0.00  0.00           C+0
HETATM    7  O   UNK     0       7.744  -0.476   0.000  0.00  0.00           O+0
HETATM    8  C   UNK     0       5.299  -1.722   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0       5.775  -3.186   0.000  0.00  0.00           C+0
HETATM   10  O   UNK     0       7.281  -3.507   0.000  0.00  0.00           O+0
HETATM   11  C   UNK     0       7.757  -4.971   0.000  0.00  0.00           C+0
HETATM   12  O   UNK     0       9.264  -5.291   0.000  0.00  0.00           O+0
HETATM   13  C   UNK     0       9.739  -6.756   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0      11.246  -7.076   0.000  0.00  0.00           C+0
HETATM   15  O   UNK     0      12.276  -5.932   0.000  0.00  0.00           O+0
HETATM   16  C   UNK     0       8.709  -7.900   0.000  0.00  0.00           C+0
HETATM   17  O   UNK     0       9.185  -9.365   0.000  0.00  0.00           O+0
HETATM   18  C   UNK     0      10.691  -9.685   0.000  0.00  0.00           C+0
HETATM   19  O   UNK     0      11.167 -11.150   0.000  0.00  0.00           O+0
HETATM   20  C   UNK     0      11.722  -8.541   0.000  0.00  0.00           C+0
HETATM   21  C   UNK     0      13.228  -8.861   0.000  0.00  0.00           C+0
HETATM   22  C   UNK     0      14.258  -7.717   0.000  0.00  0.00           C+0
HETATM   23  C   UNK     0      13.783  -6.252   0.000  0.00  0.00           C+0
HETATM   24  C   UNK     0      14.813  -5.108   0.000  0.00  0.00           C+0
HETATM   25  C   UNK     0      16.319  -5.428   0.000  0.00  0.00           C+0
HETATM   26  O   UNK     0      17.350  -4.283   0.000  0.00  0.00           O+0
HETATM   27  C   UNK     0      16.795  -6.892   0.000  0.00  0.00           C+0
HETATM   28  C   UNK     0      15.765  -8.037   0.000  0.00  0.00           C+0
HETATM   29  C   UNK     0       7.203  -7.580   0.000  0.00  0.00           C+0
HETATM   30  O   UNK     0       6.172  -8.725   0.000  0.00  0.00           O+0
HETATM   31  C   UNK     0       6.727  -6.116   0.000  0.00  0.00           C+0
HETATM   32  O   UNK     0       5.220  -5.795   0.000  0.00  0.00           O+0
HETATM   33  C   UNK     0       3.834  -1.246   0.000  0.00  0.00           C+0
HETATM   34  C   UNK     0       2.370  -1.722   0.000  0.00  0.00           C+0
HETATM   35  O   UNK     0       2.674  -3.231   0.000  0.00  0.00           O+0
HETATM   36  C   UNK     0       1.236  -2.764   0.000  0.00  0.00           C+0
HETATM   37  O   UNK     0      -0.233  -2.304   0.000  0.00  0.00           O+0
CONECT    1    2                                                            
CONECT    2    1    3   34                                                  
CONECT    3    2    4                                                       
CONECT    4    3    5   33                                                  
CONECT    5    4    6                                                       
CONECT    6    5    7    8                                                  
CONECT    7    6                                                            
CONECT    8    6    9   33                                                  
CONECT    9    8   10                                                       
CONECT   10    9   11                                                       
CONECT   11   10   12   31                                                  
CONECT   12   11   13                                                       
CONECT   13   12   14   16                                                  
CONECT   14   13   15                                                       
CONECT   15   14                                                            
CONECT   16   13   17   29                                                  
CONECT   17   16   18                                                       
CONECT   18   17   19   20                                                  
CONECT   19   18                                                            
CONECT   20   18   21                                                       
CONECT   21   20   22                                                       
CONECT   22   21   23   28                                                  
CONECT   23   22   24                                                       
CONECT   24   23   25                                                       
CONECT   25   24   26   27                                                  
CONECT   26   25                                                            
CONECT   27   25   28                                                       
CONECT   28   27   22                                                       
CONECT   29   16   30   31                                                  
CONECT   30   29                                                            
CONECT   31   29   11   32                                                  
CONECT   32   31                                                            
CONECT   33    8    4   34                                                  
CONECT   34   33    2   35   36                                             
CONECT   35   34                                                            
CONECT   36   34   37                                                       
CONECT   37   36                                                            
MASTER        0    0    0    0    0    0    0    0   37    0   80    0
END

View in JSmol

Synonyms

Not Available

Chemical Formula

C₂₅H₃₂O₁₂

Average Mass

524.5190 Da

Monoisotopic Mass

524.18938 Da

IUPAC Name

Not Available

Traditional Name

Not Available

CAS Registry Number

Not Available

SMILES

C[C@H]1C[C@@H]2OC(=O)[C@@H](CO[C@@H]3O[C@H](CO)[C@@H](OC(=O)\C=C\C4=CC=C(O)C=C4)[C@H](O)[C@H]3O)[C@@H]2[C@]1(O)CO

InChI Identifier

InChI=1S/C25H32O12/c1-12-8-16-19(25(12,33)11-27)15(23(32)35-16)10-34-24-21(31)20(30)22(17(9-26)36-24)37-18(29)7-4-13-2-5-14(28)6-3-13/h2-7,12,15-17,19-22,24,26-28,30-31,33H,8-11H2,1H3/b7-4+/t12-,15-,16-,17+,19-,20+,21+,22+,24+,25-/m0/s1

InChI Key

PRCZUWUTPHKKKP-QUXYPBBGSA-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
Verbena brasiliensis	LOTUS Database	35616633

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as terpene glycosides. These are prenol lipids containing a carbohydrate moiety glycosidically bound to a terpene backbone.

Kingdom

Organic compounds

Super Class

Lipids and lipid-like molecules

Class

Prenol lipids

Sub Class

Terpene glycosides

Direct Parent

Terpene glycosides

Alternative Parents

Substituents

Terpene glycoside
Terpene lactone
Coumaric acid ester
Cinnamic acid or derivatives
Coumaric acid or derivatives
Hexose monosaccharide
Hydroxycinnamic acid or derivatives
Cinnamic acid ester
Glycosyl compound
O-glycosyl compound
Aromatic monoterpenoid
Monoterpenoid
Bicyclic monoterpenoid
Styrene
Fatty acid ester
Phenol
1-hydroxy-2-unsubstituted benzenoid
Gamma butyrolactone
Monocyclic benzene moiety
Dicarboxylic acid or derivatives
Monosaccharide
Oxane
Benzenoid
Fatty acyl
Tertiary alcohol
Cyclic alcohol
Enoate ester
Alpha,beta-unsaturated carboxylic ester
Tetrahydrofuran
Secondary alcohol
Carboxylic acid ester
Lactone
Acetal
Oxacycle
Carboxylic acid derivative
Organoheterocyclic compound
Alcohol
Primary alcohol
Carbonyl group
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

External Links

HMDB ID

Not Available

DrugBank ID

Not Available

Phenol Explorer Compound ID

Not Available

FoodDB ID

Not Available

KNApSAcK ID

C00032480

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

101412295

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

Ono M, Oishi K, Abe H, Masuoka C, Okawa M, Ikeda T, Nohara T: New iridoid glucosides from the aerial parts of Verbena brasiliensis. Chem Pharm Bull (Tokyo). 2006 Oct;54(10):1421-4. doi: 10.1248/cpb.54.1421. [PubMed:17015981 ]
LOTUS database [Link]

Showing NP-Card for (2r,3s,4r,5r,6r)-6-{[(3r,3as,4s,5s,6as)-4-hydroxy-4-(hydroxymethyl)-5-methyl-2-oxo-tetrahydro-3h-cyclopenta[b]furan-3-yl]methoxy}-4,5-dihydroxy-2-(hydroxymethyl)oxan-3-yl (2e)-3-(4-hydroxyphenyl)prop-2-enoate (NP0285763)

MOL for NP0285763 ((2r,3s,4r,5r,6r)-6-{[(3r,3as,4s,5s,6as)-4-hydroxy-4-(hydroxymethyl)-5-methyl-2-oxo-tetrahydro-3h-cyclopenta[b]furan-3-yl]methoxy}-4,5-dihydroxy-2-(hydroxymethyl)oxan-3-yl (2e)-3-(4-hydroxyphenyl)prop-2-enoate)

3D MOL for NP0285763 ((2r,3s,4r,5r,6r)-6-{[(3r,3as,4s,5s,6as)-4-hydroxy-4-(hydroxymethyl)-5-methyl-2-oxo-tetrahydro-3h-cyclopenta[b]furan-3-yl]methoxy}-4,5-dihydroxy-2-(hydroxymethyl)oxan-3-yl (2e)-3-(4-hydroxyphenyl)prop-2-enoate)

3D SDF for NP0285763 ((2r,3s,4r,5r,6r)-6-{[(3r,3as,4s,5s,6as)-4-hydroxy-4-(hydroxymethyl)-5-methyl-2-oxo-tetrahydro-3h-cyclopenta[b]furan-3-yl]methoxy}-4,5-dihydroxy-2-(hydroxymethyl)oxan-3-yl (2e)-3-(4-hydroxyphenyl)prop-2-enoate)

3D-SDF for NP0285763 ((2r,3s,4r,5r,6r)-6-{[(3r,3as,4s,5s,6as)-4-hydroxy-4-(hydroxymethyl)-5-methyl-2-oxo-tetrahydro-3h-cyclopenta[b]furan-3-yl]methoxy}-4,5-dihydroxy-2-(hydroxymethyl)oxan-3-yl (2e)-3-(4-hydroxyphenyl)prop-2-enoate)

PDB for NP0285763 ((2r,3s,4r,5r,6r)-6-{[(3r,3as,4s,5s,6as)-4-hydroxy-4-(hydroxymethyl)-5-methyl-2-oxo-tetrahydro-3h-cyclopenta[b]furan-3-yl]methoxy}-4,5-dihydroxy-2-(hydroxymethyl)oxan-3-yl (2e)-3-(4-hydroxyphenyl)prop-2-enoate)

3D PDB for NP0285763 ((2r,3s,4r,5r,6r)-6-{[(3r,3as,4s,5s,6as)-4-hydroxy-4-(hydroxymethyl)-5-methyl-2-oxo-tetrahydro-3h-cyclopenta[b]furan-3-yl]methoxy}-4,5-dihydroxy-2-(hydroxymethyl)oxan-3-yl (2e)-3-(4-hydroxyphenyl)prop-2-enoate)

SMILES for NP0285763 ((2r,3s,4r,5r,6r)-6-{[(3r,3as,4s,5s,6as)-4-hydroxy-4-(hydroxymethyl)-5-methyl-2-oxo-tetrahydro-3h-cyclopenta[b]furan-3-yl]methoxy}-4,5-dihydroxy-2-(hydroxymethyl)oxan-3-yl (2e)-3-(4-hydroxyphenyl)prop-2-enoate)

INCHI for NP0285763 ((2r,3s,4r,5r,6r)-6-{[(3r,3as,4s,5s,6as)-4-hydroxy-4-(hydroxymethyl)-5-methyl-2-oxo-tetrahydro-3h-cyclopenta[b]furan-3-yl]methoxy}-4,5-dihydroxy-2-(hydroxymethyl)oxan-3-yl (2e)-3-(4-hydroxyphenyl)prop-2-enoate)

Structure for NP0285763 ((2r,3s,4r,5r,6r)-6-{[(3r,3as,4s,5s,6as)-4-hydroxy-4-(hydroxymethyl)-5-methyl-2-oxo-tetrahydro-3h-cyclopenta[b]furan-3-yl]methoxy}-4,5-dihydroxy-2-(hydroxymethyl)oxan-3-yl (2e)-3-(4-hydroxyphenyl)prop-2-enoate)

3D Structure for NP0285763 ((2r,3s,4r,5r,6r)-6-{[(3r,3as,4s,5s,6as)-4-hydroxy-4-(hydroxymethyl)-5-methyl-2-oxo-tetrahydro-3h-cyclopenta[b]furan-3-yl]methoxy}-4,5-dihydroxy-2-(hydroxymethyl)oxan-3-yl (2e)-3-(4-hydroxyphenyl)prop-2-enoate)