NP-MRD: Showing NP-Card for 3-oxo-3-[(3,4,5-trihydroxy-6-{5,7,11,19-tetraoxapentacyclo[10.8.0.0²,¹⁰.0⁴,⁸.0¹³,¹⁸]icosa-2,4(8),9,13,15,17-hexaen-16-yloxy}oxan-2-yl)methoxy]propanoic acid (NP0227511)

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Record Information

Version

2.0

Created at

2022-09-06 06:51:10 UTC

Updated at

2022-09-06 06:51:11 UTC

NP-MRD ID

NP0227511

Secondary Accession Numbers

None

Natural Product Identification

Common Name

3-oxo-3-[(3,4,5-trihydroxy-6-{5,7,11,19-tetraoxapentacyclo[10.8.0.0²,¹⁰.0⁴,⁸.0¹³,¹⁸]icosa-2,4(8),9,13,15,17-hexaen-16-yloxy}oxan-2-yl)methoxy]propanoic acid

Description

2'-Hydroxygenistein 7-(6''-malonylglucoside) belongs to the class of organic compounds known as isoflavonoid o-glycosides. These are o-glycosylated derivatives of isoflavonoids, which are natural products derived from 3-phenylchromen-4-one. 2'-Hydroxygenistein 7-(6''-malonylglucoside) is an extremely weak basic (essentially neutral) compound (based on its pKa). Outside of the human body, 2'-Hydroxygenistein 7-(6''-malonylglucoside) has been detected, but not quantified in, pulses and white lupines. 3-oxo-3-[(3,4,5-trihydroxy-6-{5,7,11,19-tetraoxapentacyclo[10.8.0.0²,¹⁰.0⁴,⁸.0¹³,¹⁸]icosa-2,4(8),9,13,15,17-hexaen-16-yloxy}oxan-2-yl)methoxy]propanoic acid is found in Cicer judaicum, Maackia amurensis and Sophora flavescens. This could make 2'-hydroxygenistein 7-(6''-malonylglucoside) a potential biomarker for the consumption of these foods.

Structure

MOL 3D MOL SDF PDB SMILES InChI


  Mrv0541 05061310572D          

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M  END

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M  END


  Mrv0541 05061310572D          

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 28 20  2  0  0  0  0
 29 21  1  0  0  0  0
 30 22  1  0  0  0  0
 31 23  1  0  0  0  0
 32  7  1  0  0  0  0
 32 14  1  0  0  0  0
 33  8  1  0  0  0  0
 33 20  1  0  0  0  0
 34  9  1  0  0  0  0
 34 16  1  0  0  0  0
 35  9  1  0  0  0  0
 35 17  1  0  0  0  0
 36 10  1  0  0  0  0
 36 25  1  0  0  0  0
 37 15  1  0  0  0  0
 37 24  1  0  0  0  0
 38 18  1  0  0  0  0
 38 25  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0227511

> <DATABASE_NAME>
NP-MRD

> <SMILES>
OC1C(COC(=O)CC(O)=O)OC(OC2=CC3=C(C=C2)C2OC4=CC5=C(OCO5)C=C4C2CO3)C(O)C1O

> <INCHI_IDENTIFIER>
InChI=1S/C25H24O13/c26-19(27)6-20(28)33-8-18-21(29)22(30)23(31)25(38-18)36-10-1-2-11-14(3-10)32-7-13-12-4-16-17(35-9-34-16)5-15(12)37-24(11)13/h1-5,13,18,21-25,29-31H,6-9H2,(H,26,27)

> <INCHI_KEY>
ZHXRWFOBROFZAC-UHFFFAOYSA-N

> <FORMULA>
C25H24O13

> <MOLECULAR_WEIGHT>
532.4503

> <EXACT_MASS>
532.121690854

> <JCHEM_ACCEPTOR_COUNT>
12

> <JCHEM_AVERAGE_POLARIZABILITY>
50.96406814622962

> <JCHEM_BIOAVAILABILITY>
0

> <JCHEM_DONOR_COUNT>
4

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
3-oxo-3-[(3,4,5-trihydroxy-6-{5,7,11,19-tetraoxapentacyclo[10.8.0.0²,¹⁰.0⁴,⁸.0¹³,¹⁸]icosa-2,4(8),9,13(18),14,16-hexaen-16-yloxy}oxan-2-yl)methoxy]propanoic acid

> <ALOGPS_LOGP>
0.36

> <JCHEM_LOGP>
0.35541389266666695

> <ALOGPS_LOGS>
-2.83

> <JCHEM_MDDR_LIKE_RULE>
1

> <JCHEM_NUMBER_OF_RINGS>
6

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-1

> <JCHEM_PKA>
12.201707345883293

> <JCHEM_PKA_STRONGEST_ACIDIC>
3.399538612934885

> <JCHEM_PKA_STRONGEST_BASIC>
-3.64910302537729

> <JCHEM_POLAR_SURFACE_AREA>
179.66999999999996

> <JCHEM_REFRACTIVITY>
120.00479999999995

> <JCHEM_ROTATABLE_BOND_COUNT>
7

> <JCHEM_RULE_OF_FIVE>
0

> <ALOGPS_SOLUBILITY>
7.92e-01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
3-oxo-3-[(3,4,5-trihydroxy-6-{5,7,11,19-tetraoxapentacyclo[10.8.0.0²,¹⁰.0⁴,⁸.0¹³,¹⁸]icosa-2,4(8),9,13(18),14,16-hexaen-16-yloxy}oxan-2-yl)methoxy]propanoic acid

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 06-MAY-13   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   06-MAY-13         0                                  
HETATM    1  C   UNK     0       1.807   4.357   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       3.343   4.464   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       1.992   1.696   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       9.387   1.625   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       9.495   4.703   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0      -7.716  -2.991   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       5.925   0.633   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0      -4.829  -0.116   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0      13.142   3.034   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0       1.131   2.973   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0       4.204   3.187   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0       8.081   2.441   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0       6.601   2.017   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0       3.528   1.803   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0       8.135   3.980   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0      10.747   2.348   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0      10.801   3.887   0.000  0.00  0.00           C+0
HETATM   18  C   UNK     0      -3.292  -0.009   0.000  0.00  0.00           C+0
HETATM   19  C   UNK     0      -9.252  -3.098   0.000  0.00  0.00           C+0
HETATM   20  C   UNK     0      -7.040  -1.607   0.000  0.00  0.00           C+0
HETATM   21  C   UNK     0      -2.431  -1.286   0.000  0.00  0.00           C+0
HETATM   22  C   UNK     0      -0.895  -1.179   0.000  0.00  0.00           C+0
HETATM   23  C   UNK     0      -0.220   0.205   0.000  0.00  0.00           C+0
HETATM   24  C   UNK     0       5.740   3.294   0.000  0.00  0.00           C+0
HETATM   25  C   UNK     0      -1.081   1.482   0.000  0.00  0.00           C+0
HETATM   26  O   UNK     0      -9.927  -4.482   0.000  0.00  0.00           O+0
HETATM   27  O   UNK     0     -10.113  -1.821   0.000  0.00  0.00           O+0
HETATM   28  O   UNK     0      -7.901  -0.330   0.000  0.00  0.00           O+0
HETATM   29  O   UNK     0      -3.107  -2.670   0.000  0.00  0.00           O+0
HETATM   30  O   UNK     0      -0.034  -2.456   0.000  0.00  0.00           O+0
HETATM   31  O   UNK     0       1.317   0.312   0.000  0.00  0.00           O+0
HETATM   32  O   UNK     0       4.389   0.526   0.000  0.00  0.00           O+0
HETATM   33  O   UNK     0      -5.504  -1.500   0.000  0.00  0.00           O+0
HETATM   34  O   UNK     0      12.194   1.821   0.000  0.00  0.00           O+0
HETATM   35  O   UNK     0      12.282   4.311   0.000  0.00  0.00           O+0
HETATM   36  O   UNK     0      -0.405   2.866   0.000  0.00  0.00           O+0
HETATM   37  O   UNK     0       6.688   4.507   0.000  0.00  0.00           O+0
HETATM   38  O   UNK     0      -2.617   1.375   0.000  0.00  0.00           O+0
CONECT    1    2   10                                                       
CONECT    2    1   11                                                       
CONECT    3   10   14                                                       
CONECT    4   12   16                                                       
CONECT    5   15   17                                                       
CONECT    6   19   20                                                       
CONECT    7   13   32                                                       
CONECT    8   18   33                                                       
CONECT    9   34   35                                                       
CONECT   10    1    3   36                                                  
CONECT   11    2   14   24                                                  
CONECT   12    4   13   15                                                  
CONECT   13    7   12   24                                                  
CONECT   14    3   11   32                                                  
CONECT   15    5   12   37                                                  
CONECT   16    4   17   34                                                  
CONECT   17    5   16   35                                                  
CONECT   18    8   21   38                                                  
CONECT   19    6   26   27                                                  
CONECT   20    6   28   33                                                  
CONECT   21   18   22   29                                                  
CONECT   22   21   23   30                                                  
CONECT   23   22   25   31                                                  
CONECT   24   11   13   37                                                  
CONECT   25   23   36   38                                                  
CONECT   26   19                                                            
CONECT   27   19                                                            
CONECT   28   20                                                            
CONECT   29   21                                                            
CONECT   30   22                                                            
CONECT   31   23                                                            
CONECT   32    7   14                                                       
CONECT   33    8   20                                                       
CONECT   34    9   16                                                       
CONECT   35    9   17                                                       
CONECT   36   10   25                                                       
CONECT   37   15   24                                                       
CONECT   38   18   25                                                       
MASTER        0    0    0    0    0    0    0    0   38    0   86    0
END

View in JSmol

Synonyms

Value	Source
2'-Hydroxygenistein 7-O-(6''-malonylglucoside)	HMDB
5,7,2',4'-Tetrahydroxyisoflavone 7-O-(6''-malonylglucoside)	HMDB
Ethyl oxo(2-(trifluoromethyl)anilino)acetate	HMDB
Maackiain 3-O-glucosyl-6''-malonate	HMDB
Trifolirhizin 6'-O-malonate	HMDB
3-oxo-3-[(3,4,5-Trihydroxy-6-{5,7,11,19-tetraoxapentacyclo[10.8.0.0²,¹⁰.0⁴,⁸.0¹³,¹⁸]icosa-2,4(8),9,13(18),14,16-hexaen-16-yloxy}oxan-2-yl)methoxy]propanoate	Generator

Chemical Formula

C₂₅H₂₄O₁₃

Average Mass

532.4503 Da

Monoisotopic Mass

532.12169 Da

IUPAC Name

3-oxo-3-[(3,4,5-trihydroxy-6-{5,7,11,19-tetraoxapentacyclo[10.8.0.0²,¹⁰.0⁴,⁸.0¹³,¹⁸]icosa-2,4(8),9,13(18),14,16-hexaen-16-yloxy}oxan-2-yl)methoxy]propanoic acid

Traditional Name

3-oxo-3-[(3,4,5-trihydroxy-6-{5,7,11,19-tetraoxapentacyclo[10.8.0.0²,¹⁰.0⁴,⁸.0¹³,¹⁸]icosa-2,4(8),9,13(18),14,16-hexaen-16-yloxy}oxan-2-yl)methoxy]propanoic acid

CAS Registry Number

Not Available

SMILES

OC1C(COC(=O)CC(O)=O)OC(OC2=CC3=C(C=C2)C2OC4=CC5=C(OCO5)C=C4C2CO3)C(O)C1O

InChI Identifier

InChI=1S/C25H24O13/c26-19(27)6-20(28)33-8-18-21(29)22(30)23(31)25(38-18)36-10-1-2-11-14(3-10)32-7-13-12-4-16-17(35-9-34-16)5-15(12)37-24(11)13/h1-5,13,18,21-25,29-31H,6-9H2,(H,26,27)

InChI Key

ZHXRWFOBROFZAC-UHFFFAOYSA-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
Cicer judaicum	LOTUS Database	35616633
Maackia amurensis	LOTUS Database	35616633
Sophora flavescens	LOTUS Database	35616633

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as isoflavonoid o-glycosides. These are o-glycosylated derivatives of isoflavonoids, which are natural products derived from 3-phenylchromen-4-one.

Kingdom

Organic compounds

Super Class

Phenylpropanoids and polyketides

Class

Isoflavonoids

Sub Class

Isoflavonoid O-glycosides

Direct Parent

Isoflavonoid O-glycosides

Alternative Parents

Substituents

Isoflavonoid o-glycoside
Isoflavonoid-7-o-glycoside
Isoflavone
Hydroxyisoflavonoid
Phenolic glycoside
Chromone
Glycosyl compound
O-glycosyl compound
Benzopyran
1-benzopyran
Resorcinol
1-hydroxy-4-unsubstituted benzenoid
1-hydroxy-2-unsubstituted benzenoid
Phenol
Pyranone
Benzenoid
Pyran
Monocyclic benzene moiety
1,3-dicarbonyl compound
Oxane
Monosaccharide
Dicarboxylic acid or derivatives
Vinylogous acid
Heteroaromatic compound
Secondary alcohol
Carboxylic acid ester
Organoheterocyclic compound
Polyol
Acetal
Carboxylic acid derivative
Oxacycle
Carboxylic acid
Organooxygen compound
Carbonyl group
Alcohol
Hydrocarbon derivative
Organic oxygen 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	0.36	ALOGPS
logP	0.36	ChemAxon
logS	-2.8	ALOGPS
pKa (Strongest Acidic)	3.4	ChemAxon
pKa (Strongest Basic)	-3.6	ChemAxon
Physiological Charge	-1	ChemAxon
Hydrogen Acceptor Count	12	ChemAxon
Hydrogen Donor Count	4	ChemAxon
Polar Surface Area	179.67 Å²	ChemAxon
Rotatable Bond Count	7	ChemAxon
Refractivity	120 m³·mol⁻¹	ChemAxon
Polarizability	50.96 Å³	ChemAxon
Number of Rings	6	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

HMDB0039247

DrugBank ID

Not Available

Phenol Explorer Compound ID

Not Available

FoodDB ID

FDB018785

KNApSAcK ID

C00019704

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

131752588

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

LOTUS database [Link]

Showing NP-Card for 3-oxo-3-[(3,4,5-trihydroxy-6-{5,7,11,19-tetraoxapentacyclo[10.8.0.0²,¹⁰.0⁴,⁸.0¹³,¹⁸]icosa-2,4(8),9,13,15,17-hexaen-16-yloxy}oxan-2-yl)methoxy]propanoic acid (NP0227511)

MOL for NP0227511 (3-oxo-3-[(3,4,5-trihydroxy-6-{5,7,11,19-tetraoxapentacyclo[10.8.0.0²,¹⁰.0⁴,⁸.0¹³,¹⁸]icosa-2,4(8),9,13,15,17-hexaen-16-yloxy}oxan-2-yl)methoxy]propanoic acid)

3D MOL for NP0227511 (3-oxo-3-[(3,4,5-trihydroxy-6-{5,7,11,19-tetraoxapentacyclo[10.8.0.0²,¹⁰.0⁴,⁸.0¹³,¹⁸]icosa-2,4(8),9,13,15,17-hexaen-16-yloxy}oxan-2-yl)methoxy]propanoic acid)

3D SDF for NP0227511 (3-oxo-3-[(3,4,5-trihydroxy-6-{5,7,11,19-tetraoxapentacyclo[10.8.0.0²,¹⁰.0⁴,⁸.0¹³,¹⁸]icosa-2,4(8),9,13,15,17-hexaen-16-yloxy}oxan-2-yl)methoxy]propanoic acid)

3D-SDF for NP0227511 (3-oxo-3-[(3,4,5-trihydroxy-6-{5,7,11,19-tetraoxapentacyclo[10.8.0.0²,¹⁰.0⁴,⁸.0¹³,¹⁸]icosa-2,4(8),9,13,15,17-hexaen-16-yloxy}oxan-2-yl)methoxy]propanoic acid)

PDB for NP0227511 (3-oxo-3-[(3,4,5-trihydroxy-6-{5,7,11,19-tetraoxapentacyclo[10.8.0.0²,¹⁰.0⁴,⁸.0¹³,¹⁸]icosa-2,4(8),9,13,15,17-hexaen-16-yloxy}oxan-2-yl)methoxy]propanoic acid)

3D PDB for NP0227511 (3-oxo-3-[(3,4,5-trihydroxy-6-{5,7,11,19-tetraoxapentacyclo[10.8.0.0²,¹⁰.0⁴,⁸.0¹³,¹⁸]icosa-2,4(8),9,13,15,17-hexaen-16-yloxy}oxan-2-yl)methoxy]propanoic acid)

SMILES for NP0227511 (3-oxo-3-[(3,4,5-trihydroxy-6-{5,7,11,19-tetraoxapentacyclo[10.8.0.0²,¹⁰.0⁴,⁸.0¹³,¹⁸]icosa-2,4(8),9,13,15,17-hexaen-16-yloxy}oxan-2-yl)methoxy]propanoic acid)

INCHI for NP0227511 (3-oxo-3-[(3,4,5-trihydroxy-6-{5,7,11,19-tetraoxapentacyclo[10.8.0.0²,¹⁰.0⁴,⁸.0¹³,¹⁸]icosa-2,4(8),9,13,15,17-hexaen-16-yloxy}oxan-2-yl)methoxy]propanoic acid)

Structure for NP0227511 (3-oxo-3-[(3,4,5-trihydroxy-6-{5,7,11,19-tetraoxapentacyclo[10.8.0.0²,¹⁰.0⁴,⁸.0¹³,¹⁸]icosa-2,4(8),9,13,15,17-hexaen-16-yloxy}oxan-2-yl)methoxy]propanoic acid)

3D Structure for NP0227511 (3-oxo-3-[(3,4,5-trihydroxy-6-{5,7,11,19-tetraoxapentacyclo[10.8.0.0²,¹⁰.0⁴,⁸.0¹³,¹⁸]icosa-2,4(8),9,13,15,17-hexaen-16-yloxy}oxan-2-yl)methoxy]propanoic acid)