NP-MRD: Showing NP-Card for (1s,3s,4r,5s)-1-{[(2e)-3-(3,4-dihydroxyphenyl)prop-2-enoyl]oxy}-3-{[(2z)-3-(3,4-dihydroxyphenyl)prop-2-enoyl]oxy}-4,5-dihydroxycyclohexane-1-carboxylic acid (NP0186771)

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Record Information

Version

2.0

Created at

2022-09-04 02:44:17 UTC

Updated at

2022-09-04 02:44:17 UTC

NP-MRD ID

NP0186771

Secondary Accession Numbers

None

Natural Product Identification

Common Name

(1s,3s,4r,5s)-1-{[(2e)-3-(3,4-dihydroxyphenyl)prop-2-enoyl]oxy}-3-{[(2z)-3-(3,4-dihydroxyphenyl)prop-2-enoyl]oxy}-4,5-dihydroxycyclohexane-1-carboxylic acid

Description

Cynarin, also known as cinarin or cynarix, belongs to the class of organic compounds known as quinic acids and derivatives. Quinic acids and derivatives are compounds containing a quinic acid moiety (or a derivative thereof), which is a cyclitol made up of a cyclohexane ring that bears four hydroxyl groups at positions 1,3.4, And 5, as well as a carboxylic acid at position 1. (1s,3s,4r,5s)-1-{[(2e)-3-(3,4-dihydroxyphenyl)prop-2-enoyl]oxy}-3-{[(2z)-3-(3,4-dihydroxyphenyl)prop-2-enoyl]oxy}-4,5-dihydroxycyclohexane-1-carboxylic acid was first documented in 2022 (PMID: 35409393). Based on a literature review a small amount of articles have been published on Cynarin (PMID: 35883710) (PMID: 35784390) (PMID: 35546047) (PMID: 35066016).

Structure

MOL 3D MOL SDF PDB SMILES InChI


  Mrv1652309042204442D          

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M  END

     RDKit          3D

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M  END


  Mrv1652309042204442D          

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M  END
> <DATABASE_ID>
NP0186771

> <DATABASE_NAME>
NP-MRD

> <SMILES>
O[C@H]1C[C@@](C[C@H](OC(=O)\C=C/C2=CC=C(O)C(O)=C2)[C@@H]1O)(OC(=O)\C=C\C1=CC=C(O)C(O)=C1)C(O)=O

> <INCHI_IDENTIFIER>
InChI=1S/C25H24O12/c26-15-5-1-13(9-17(15)28)3-7-21(31)36-20-12-25(24(34)35,11-19(30)23(20)33)37-22(32)8-4-14-2-6-16(27)18(29)10-14/h1-10,19-20,23,26-30,33H,11-12H2,(H,34,35)/b7-3-,8-4+/t19-,20-,23+,25-/m0/s1

> <INCHI_KEY>
YDDUMTOHNYZQPO-CZWHYVATSA-N

> <FORMULA>
C25H24O12

> <MOLECULAR_WEIGHT>
516.455

> <EXACT_MASS>
516.126776213

> <JCHEM_ACCEPTOR_COUNT>
10

> <JCHEM_ATOM_COUNT>
61

> <JCHEM_AVERAGE_POLARIZABILITY>
48.70106058616617

> <JCHEM_BIOAVAILABILITY>
0

> <JCHEM_DONOR_COUNT>
7

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(1S,3S,4R,5S)-1-{[(2E)-3-(3,4-dihydroxyphenyl)prop-2-enoyl]oxy}-3-{[(2Z)-3-(3,4-dihydroxyphenyl)prop-2-enoyl]oxy}-4,5-dihydroxycyclohexane-1-carboxylic acid

> <JCHEM_LOGP>
2.158230316666666

> <JCHEM_MDDR_LIKE_RULE>
1

> <JCHEM_NUMBER_OF_RINGS>
3

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-1

> <JCHEM_PKA>
8.907564069574317

> <JCHEM_PKA_STRONGEST_ACIDIC>
3.184533116763618

> <JCHEM_PKA_STRONGEST_BASIC>
-3.2325629248174694

> <JCHEM_POLAR_SURFACE_AREA>
211.27999999999997

> <JCHEM_REFRACTIVITY>
126.76419999999997

> <JCHEM_ROTATABLE_BOND_COUNT>
9

> <JCHEM_RULE_OF_FIVE>
0

> <JCHEM_TRADITIONAL_IUPAC>
(1S,3S,4R,5S)-1-{[(2E)-3-(3,4-dihydroxyphenyl)prop-2-enoyl]oxy}-3-{[(2Z)-3-(3,4-dihydroxyphenyl)prop-2-enoyl]oxy}-4,5-dihydroxycyclohexane-1-carboxylic acid

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 04-SEP-22   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   04-SEP-22         0                                  
HETATM    1  O   UNK     0       0.202 -11.021   0.000  0.00  0.00           O+0
HETATM    2  C   UNK     0       0.202  -9.481   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0      -1.131  -8.711   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0      -2.465  -9.481   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0      -2.465 -11.021   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0      -3.799 -11.791   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0      -3.799 -13.331   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0      -2.465 -14.101   0.000  0.00  0.00           C+0
HETATM    9  O   UNK     0      -2.465 -15.641   0.000  0.00  0.00           O+0
HETATM   10  C   UNK     0      -1.131 -13.331   0.000  0.00  0.00           C+0
HETATM   11  O   UNK     0       0.202 -14.101   0.000  0.00  0.00           O+0
HETATM   12  C   UNK     0      -1.131 -11.791   0.000  0.00  0.00           C+0
HETATM   13  O   UNK     0       1.536  -8.711   0.000  0.00  0.00           O+0
HETATM   14  C   UNK     0       2.870  -9.481   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0       4.203  -8.711   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0       5.537  -9.481   0.000  0.00  0.00           C+0
HETATM   17  O   UNK     0       6.064  -8.034   0.000  0.00  0.00           O+0
HETATM   18  C   UNK     0       5.074  -6.854   0.000  0.00  0.00           C+0
HETATM   19  O   UNK     0       3.557  -7.122   0.000  0.00  0.00           O+0
HETATM   20  C   UNK     0       5.601  -5.407   0.000  0.00  0.00           C+0
HETATM   21  C   UNK     0       4.611  -4.227   0.000  0.00  0.00           C+0
HETATM   22  C   UNK     0       5.137  -2.780   0.000  0.00  0.00           C+0
HETATM   23  C   UNK     0       4.147  -1.601   0.000  0.00  0.00           C+0
HETATM   24  C   UNK     0       4.674  -0.153   0.000  0.00  0.00           C+0
HETATM   25  C   UNK     0       6.191   0.114   0.000  0.00  0.00           C+0
HETATM   26  O   UNK     0       6.718   1.561   0.000  0.00  0.00           O+0
HETATM   27  C   UNK     0       7.181  -1.066   0.000  0.00  0.00           C+0
HETATM   28  O   UNK     0       8.697  -0.798   0.000  0.00  0.00           O+0
HETATM   29  C   UNK     0       6.654  -2.513   0.000  0.00  0.00           C+0
HETATM   30  C   UNK     0       7.054  -9.749   0.000  0.00  0.00           C+0
HETATM   31  O   UNK     0       7.580 -11.196   0.000  0.00  0.00           O+0
HETATM   32  O   UNK     0       8.044  -8.569   0.000  0.00  0.00           O+0
HETATM   33  C   UNK     0       5.537 -11.021   0.000  0.00  0.00           C+0
HETATM   34  C   UNK     0       4.203 -11.791   0.000  0.00  0.00           C+0
HETATM   35  O   UNK     0       4.203 -13.331   0.000  0.00  0.00           O+0
HETATM   36  C   UNK     0       2.870 -11.021   0.000  0.00  0.00           C+0
HETATM   37  O   UNK     0       1.536 -11.791   0.000  0.00  0.00           O+0
CONECT    1    2                                                            
CONECT    2    1    3   13                                                  
CONECT    3    2    4                                                       
CONECT    4    3    5                                                       
CONECT    5    4    6   12                                                  
CONECT    6    5    7                                                       
CONECT    7    6    8                                                       
CONECT    8    7    9   10                                                  
CONECT    9    8                                                            
CONECT   10    8   11   12                                                  
CONECT   11   10                                                            
CONECT   12   10    5                                                       
CONECT   13    2   14                                                       
CONECT   14   13   15   36                                                  
CONECT   15   14   16                                                       
CONECT   16   15   17   30   33                                             
CONECT   17   16   18                                                       
CONECT   18   17   19   20                                                  
CONECT   19   18                                                            
CONECT   20   18   21                                                       
CONECT   21   20   22                                                       
CONECT   22   21   23   29                                                  
CONECT   23   22   24                                                       
CONECT   24   23   25                                                       
CONECT   25   24   26   27                                                  
CONECT   26   25                                                            
CONECT   27   25   28   29                                                  
CONECT   28   27                                                            
CONECT   29   27   22                                                       
CONECT   30   16   31   32                                                  
CONECT   31   30                                                            
CONECT   32   30                                                            
CONECT   33   16   34                                                       
CONECT   34   33   35   36                                                  
CONECT   35   34                                                            
CONECT   36   34   14   37                                                  
CONECT   37   36                                                            
MASTER        0    0    0    0    0    0    0    0   37    0   78    0
END

View in JSmol

Synonyms

Value	Source
1,5-Dicaffeoylquinic acid	MeSH
Cinarin	MeSH
Cynarin, (1alpha,3alpha,4alpha,5beta)-isomer	MeSH
Cynarix	MeSH
Listrocol	MeSH
Cinarine	MeSH
Cynarine	MeSH
Nivellipid	MeSH
1-Carboxy-4,5-dihydroxy-1,3-cyclohexylenebis-(3,4-dihydroxycinnamate)	MeSH
Cynarex	MeSH
Cinarina	MeSH
Listricol	MeSH
Phemocil	MeSH

Chemical Formula

C₂₅H₂₄O₁₂

Average Mass

516.4550 Da

Monoisotopic Mass

516.12678 Da

IUPAC Name

(1S,3S,4R,5S)-1-{[(2E)-3-(3,4-dihydroxyphenyl)prop-2-enoyl]oxy}-3-{[(2Z)-3-(3,4-dihydroxyphenyl)prop-2-enoyl]oxy}-4,5-dihydroxycyclohexane-1-carboxylic acid

Traditional Name

(1S,3S,4R,5S)-1-{[(2E)-3-(3,4-dihydroxyphenyl)prop-2-enoyl]oxy}-3-{[(2Z)-3-(3,4-dihydroxyphenyl)prop-2-enoyl]oxy}-4,5-dihydroxycyclohexane-1-carboxylic acid

CAS Registry Number

Not Available

SMILES

O[C@H]1C[C@@](C[C@H](OC(=O)\C=C/C2=CC=C(O)C(O)=C2)[C@@H]1O)(OC(=O)\C=C\C1=CC=C(O)C(O)=C1)C(O)=O

InChI Identifier

InChI=1S/C25H24O12/c26-15-5-1-13(9-17(15)28)3-7-21(31)36-20-12-25(24(34)35,11-19(30)23(20)33)37-22(32)8-4-14-2-6-16(27)18(29)10-14/h1-10,19-20,23,26-30,33H,11-12H2,(H,34,35)/b7-3-,8-4+/t19-,20-,23+,25-/m0/s1

InChI Key

YDDUMTOHNYZQPO-CZWHYVATSA-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

Not Available

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as quinic acids and derivatives. Quinic acids and derivatives are compounds containing a quinic acid moiety (or a derivative thereof), which is a cyclitol made up of a cyclohexane ring that bears four hydroxyl groups at positions 1,3.4, And 5, as well as a carboxylic acid at position 1.

Kingdom

Organic compounds

Super Class

Organic oxygen compounds

Class

Organooxygen compounds

Sub Class

Alcohols and polyols

Direct Parent

Quinic acids and derivatives

Alternative Parents

Substituents

Quinic acid
Cinnamic acid or derivatives
Coumaric acid or derivatives
Cinnamic acid ester
Hydroxycinnamic acid or derivatives
Tricarboxylic acid or derivatives
Catechol
Styrene
1-hydroxy-4-unsubstituted benzenoid
1-hydroxy-2-unsubstituted benzenoid
Cyclohexanol
Phenol
Fatty acid ester
Monocyclic benzene moiety
Fatty acyl
Benzenoid
Alpha,beta-unsaturated carboxylic ester
Enoate ester
1,2-diol
Carboxylic acid ester
Secondary alcohol
Carboxylic acid
Carboxylic acid derivative
Hydrocarbon derivative
Carbonyl group
Organic oxide
Aromatic homomonocyclic compound

Molecular Framework

Aromatic homomonocyclic 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	2.16	ChemAxon
pKa (Strongest Acidic)	3.18	ChemAxon
pKa (Strongest Basic)	-3.2	ChemAxon
Physiological Charge	-1	ChemAxon
Hydrogen Acceptor Count	10	ChemAxon
Hydrogen Donor Count	7	ChemAxon
Polar Surface Area	211.28 Å²	ChemAxon
Rotatable Bond Count	9	ChemAxon
Refractivity	126.76 m³·mol⁻¹	ChemAxon
Polarizability	48.7 Å³	ChemAxon
Number of Rings	3	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

21468689

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Cynarine

METLIN ID

Not Available

PubChem Compound

24720973

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

Liao HJ, Tzen JTC: The Potential Role of Phenolic Acids from Salvia miltiorrhiza and Cynara scolymus and Their Derivatives as JAK Inhibitors: An In Silico Study. Int J Mol Sci. 2022 Apr 5;23(7). pii: ijms23074033. doi: 10.3390/ijms23074033. [PubMed:35409393 ]
Chen Y, Su JY, Yang CY: Ultrasound-Assisted Aqueous Extraction of Chlorogenic Acid and Cynarin with the Impact of Inulin from Burdock (Arctium lappa L.) Roots. Antioxidants (Basel). 2022 Jun 22;11(7):1219. doi: 10.3390/antiox11071219. [PubMed:35883710 ]
Kim DB, Unenkhuu B, Kim GJ, Kim SW, Kim HS: Cynarin attenuates LPS-induced endothelial inflammation via upregulation of the negative regulator MKP-3. Anim Cells Syst (Seoul). 2022 May 20;26(3):119-128. doi: 10.1080/19768354.2022.2077438. eCollection 2022. [PubMed:35784390 ]
Wu C, Chen S, Liu Y, Kong B, Yan W, Jiang T, Tian H, Liu Z, Shi Q, Wang Y, Liang Q, Xi X, Xu H: Cynarin suppresses gouty arthritis induced by monosodium urate crystals. Bioengineered. 2022 May;13(5):11782-11793. doi: 10.1080/21655979.2022.2072055. [PubMed:35546047 ]
Corona A, Fanunza E, Salata C, Morwitzer MJ, Distinto S, Zinzula L, Sanna C, Frau A, Daino GL, Quartu M, Taglialatela-Scafati O, Rigano D, Reid S, Mirazimi A, Tramontano E: Cynarin blocks Ebola virus replication by counteracting VP35 inhibition of interferon-beta production. Antiviral Res. 2022 Feb;198:105251. doi: 10.1016/j.antiviral.2022.105251. Epub 2022 Jan 20. [PubMed:35066016 ]
LOTUS database [Link]

Showing NP-Card for (1s,3s,4r,5s)-1-{[(2e)-3-(3,4-dihydroxyphenyl)prop-2-enoyl]oxy}-3-{[(2z)-3-(3,4-dihydroxyphenyl)prop-2-enoyl]oxy}-4,5-dihydroxycyclohexane-1-carboxylic acid (NP0186771)

MOL for NP0186771 ((1s,3s,4r,5s)-1-{[(2e)-3-(3,4-dihydroxyphenyl)prop-2-enoyl]oxy}-3-{[(2z)-3-(3,4-dihydroxyphenyl)prop-2-enoyl]oxy}-4,5-dihydroxycyclohexane-1-carboxylic acid)

3D MOL for NP0186771 ((1s,3s,4r,5s)-1-{[(2e)-3-(3,4-dihydroxyphenyl)prop-2-enoyl]oxy}-3-{[(2z)-3-(3,4-dihydroxyphenyl)prop-2-enoyl]oxy}-4,5-dihydroxycyclohexane-1-carboxylic acid)

3D SDF for NP0186771 ((1s,3s,4r,5s)-1-{[(2e)-3-(3,4-dihydroxyphenyl)prop-2-enoyl]oxy}-3-{[(2z)-3-(3,4-dihydroxyphenyl)prop-2-enoyl]oxy}-4,5-dihydroxycyclohexane-1-carboxylic acid)

3D-SDF for NP0186771 ((1s,3s,4r,5s)-1-{[(2e)-3-(3,4-dihydroxyphenyl)prop-2-enoyl]oxy}-3-{[(2z)-3-(3,4-dihydroxyphenyl)prop-2-enoyl]oxy}-4,5-dihydroxycyclohexane-1-carboxylic acid)

PDB for NP0186771 ((1s,3s,4r,5s)-1-{[(2e)-3-(3,4-dihydroxyphenyl)prop-2-enoyl]oxy}-3-{[(2z)-3-(3,4-dihydroxyphenyl)prop-2-enoyl]oxy}-4,5-dihydroxycyclohexane-1-carboxylic acid)

3D PDB for NP0186771 ((1s,3s,4r,5s)-1-{[(2e)-3-(3,4-dihydroxyphenyl)prop-2-enoyl]oxy}-3-{[(2z)-3-(3,4-dihydroxyphenyl)prop-2-enoyl]oxy}-4,5-dihydroxycyclohexane-1-carboxylic acid)

SMILES for NP0186771 ((1s,3s,4r,5s)-1-{[(2e)-3-(3,4-dihydroxyphenyl)prop-2-enoyl]oxy}-3-{[(2z)-3-(3,4-dihydroxyphenyl)prop-2-enoyl]oxy}-4,5-dihydroxycyclohexane-1-carboxylic acid)

INCHI for NP0186771 ((1s,3s,4r,5s)-1-{[(2e)-3-(3,4-dihydroxyphenyl)prop-2-enoyl]oxy}-3-{[(2z)-3-(3,4-dihydroxyphenyl)prop-2-enoyl]oxy}-4,5-dihydroxycyclohexane-1-carboxylic acid)

Structure for NP0186771 ((1s,3s,4r,5s)-1-{[(2e)-3-(3,4-dihydroxyphenyl)prop-2-enoyl]oxy}-3-{[(2z)-3-(3,4-dihydroxyphenyl)prop-2-enoyl]oxy}-4,5-dihydroxycyclohexane-1-carboxylic acid)

3D Structure for NP0186771 ((1s,3s,4r,5s)-1-{[(2e)-3-(3,4-dihydroxyphenyl)prop-2-enoyl]oxy}-3-{[(2z)-3-(3,4-dihydroxyphenyl)prop-2-enoyl]oxy}-4,5-dihydroxycyclohexane-1-carboxylic acid)