NP-MRD: Showing NP-Card for methyl 1-hydroxy-7-(hydroxymethyl)-1h,4ah,5h,7ah-cyclopenta[c]pyran-4-carboxylate (NP0191666)

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Record Information

Version

2.0

Created at

2022-09-04 08:42:07 UTC

Updated at

2022-09-04 08:42:07 UTC

NP-MRD ID

NP0191666

Secondary Accession Numbers

None

Natural Product Identification

Common Name

methyl 1-hydroxy-7-(hydroxymethyl)-1h,4ah,5h,7ah-cyclopenta[c]pyran-4-carboxylate

Description

Genipin belongs to the class of organic compounds known as iridoids and derivatives. These are monoterpenes containing a skeleton structurally characterized by the presence of a cylopentane fused to a pyran ( forming a 4,7-dimethylcyclopenta[c]pyran), or a derivative where the pentane moiety is open. Furthermore, genipin can be used as a regulating agent for drug delivery, as the raw material for gardenia blue pigment preparation, and as the intermediate for alkaloid syntheses. Genipin is an excellent natural cross-linker for proteins, collagen, gelatin, and chitosan cross-linking. Genipin is an extremely weak basic (essentially neutral) compound (based on its pKa). Genipin is a chemical compound found in gardenia fruit extract. It is an aglycone derived from an iridoid glycoside called geniposide present in fruit of Gardenia jasminoides. Outside of the human body, Genipin has been detected, but not quantified in, beverages and fruits. This could make genipin a potential biomarker for the consumption of these foods. In vitro experiments have shown that genipin blocks the action of the enzyme uncoupling protein 2. It has a low acute toxicity, with LD50 i.V. methyl 1-hydroxy-7-(hydroxymethyl)-1h,4ah,5h,7ah-cyclopenta[c]pyran-4-carboxylate is found in Eucommia ulmoides, Gardenia jasminoides, Garrya elliptica, Genipa americana and Rothmannia globosa. methyl 1-hydroxy-7-(hydroxymethyl)-1h,4ah,5h,7ah-cyclopenta[c]pyran-4-carboxylate was first documented in 2005 (PMID: 16143311). 382 Mg/kg in mice, therefore, much less toxic than glutaraldehyde and many other commonly used synthetic cross-linking reagents (PMID: 20686229) (PMID: 20561935) (PMID: 16169698).

Structure

MOL 3D MOL SDF PDB SMILES InChI

     RDKit          3D

 30 31  0  0  0  0  0  0  0  0999 V2000
    4.8487   -0.5641    0.1086 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.5470   -0.1340    0.3916 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.4785   -0.1721   -0.4584 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.6424   -0.6287   -1.6071 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.1251    0.2948   -0.1098 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.8724    0.7934    1.0939 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4023    1.2302    1.4113 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0798    1.8660    0.3237 C   0  0  2  0  0  0  0  0  0  0  0  0
   -2.2760    2.4373    0.7364 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2722    0.7799   -0.6959 C   0  0  2  0  0  0  0  0  0  0  0  0
   -1.9691   -0.3559   -0.0074 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.1228   -0.2486    0.9160 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5277   -1.4974    1.3800 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4009   -1.5204   -0.3413 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2698   -1.2813   -1.2838 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0403    0.1997   -1.1074 C   0  0  2  0  0  0  0  0  0  0  0  0
    4.9482   -1.6487    0.0826 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.2534   -0.1352   -0.8435 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.5137   -0.1506    0.9117 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.7232    0.8208    1.7663 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4965    2.6746   -0.1452 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7646    2.6887   -0.0931 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8712    1.1439   -1.5625 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8943    0.3610    1.8139 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.9830    0.2431    0.4191 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.3483   -1.8049    0.9051 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6735   -2.5186   -0.0119 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6018   -1.5236   -2.3094 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.5888   -1.9260   -1.0252 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.3722    0.5767   -2.1040 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  1  0
  3  4  2  0
  3  5  1  0
  5  6  2  0
  6  7  1  0
  7  8  1  0
  8  9  1  0
  8 10  1  0
 10 16  1  0
 16 15  1  0
 15 14  1  0
 14 11  2  0
 11 12  1  0
 12 13  1  0
 16  5  1  0
 11 10  1  0
  1 17  1  0
  1 18  1  0
  1 19  1  0
  6 20  1  0
  8 21  1  6
  9 22  1  0
 10 23  1  6
 16 30  1  6
 15 28  1  0
 15 29  1  0
 14 27  1  0
 12 24  1  0
 12 25  1  0
 13 26  1  0
M  END


  Mrv0541 05061308442D          

 16 17  0  0  0  0            999 V2000
    3.9934    3.3000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.2949    0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.7798    1.0799    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.5249   -1.0396    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.9934    0.8250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.7798   -0.2549    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.5645    0.8250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.2789    1.2375    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.5645    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.2789    2.0625    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.2789   -0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.0769   -1.6527    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.5645    2.4750    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.2789   -1.2375    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.9934    2.4750    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.9934    0.0000    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  3  2  1  0  0  0  0
  6  2  2  0  0  0  0
  6  4  1  0  0  0  0
  7  3  1  0  0  0  0
  8  5  2  0  0  0  0
  8  7  1  0  0  0  0
  9  6  1  0  0  0  0
  9  7  1  0  0  0  0
 10  8  1  0  0  0  0
 11  9  1  0  0  0  0
 12  4  1  0  0  0  0
 13 10  2  0  0  0  0
 14 11  1  0  0  0  0
 15  1  1  0  0  0  0
 15 10  1  0  0  0  0
 16  5  1  0  0  0  0
 16 11  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0191666

> <DATABASE_NAME>
NP-MRD

> <SMILES>
COC(=O)C1=COC(O)C2C1CC=C2CO

> <INCHI_IDENTIFIER>
InChI=1S/C11H14O5/c1-15-10(13)8-5-16-11(14)9-6(4-12)2-3-7(8)9/h2,5,7,9,11-12,14H,3-4H2,1H3

> <INCHI_KEY>
AZKVWQKMDGGDSV-UHFFFAOYSA-N

> <FORMULA>
C11H14O5

> <MOLECULAR_WEIGHT>
226.2259

> <EXACT_MASS>
226.084123558

> <JCHEM_ACCEPTOR_COUNT>
4

> <JCHEM_AVERAGE_POLARIZABILITY>
22.433060913491364

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
2

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
methyl 1-hydroxy-7-(hydroxymethyl)-1H,4aH,5H,7aH-cyclopenta[c]pyran-4-carboxylate

> <ALOGPS_LOGP>
0.07

> <JCHEM_LOGP>
-0.44389565966666605

> <ALOGPS_LOGS>
-1.50

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
2

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
15.150537367169974

> <JCHEM_PKA_STRONGEST_ACIDIC>
12.036945977145045

> <JCHEM_PKA_STRONGEST_BASIC>
-2.7354177854672015

> <JCHEM_POLAR_SURFACE_AREA>
75.99000000000001

> <JCHEM_REFRACTIVITY>
56.093300000000006

> <JCHEM_ROTATABLE_BOND_COUNT>
3

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
7.18e+00 g/l

> <JCHEM_TRADITIONAL_IUPAC>
methyl 1-hydroxy-7-(hydroxymethyl)-1H,4aH,5H,7aH-cyclopenta[c]pyran-4-carboxylate

> <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       7.454   6.160   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       2.417   0.770   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       3.322   2.016   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       2.846  -1.941   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       7.454   1.540   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       3.322  -0.476   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       4.787   1.540   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0       6.121   2.310   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0       4.787   0.000   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0       6.121   3.850   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0       6.121  -0.770   0.000  0.00  0.00           C+0
HETATM   12  O   UNK     0       3.877  -3.085   0.000  0.00  0.00           O+0
HETATM   13  O   UNK     0       4.787   4.620   0.000  0.00  0.00           O+0
HETATM   14  O   UNK     0       6.121  -2.310   0.000  0.00  0.00           O+0
HETATM   15  O   UNK     0       7.454   4.620   0.000  0.00  0.00           O+0
HETATM   16  O   UNK     0       7.454   0.000   0.000  0.00  0.00           O+0
CONECT    1   15                                                            
CONECT    2    3    6                                                       
CONECT    3    2    7                                                       
CONECT    4    6   12                                                       
CONECT    5    8   16                                                       
CONECT    6    2    4    9                                                  
CONECT    7    3    8    9                                                  
CONECT    8    5    7   10                                                  
CONECT    9    6    7   11                                                  
CONECT   10    8   13   15                                                  
CONECT   11    9   14   16                                                  
CONECT   12    4                                                            
CONECT   13   10                                                            
CONECT   14   11                                                            
CONECT   15    1   10                                                       
CONECT   16    5   11                                                       
MASTER        0    0    0    0    0    0    0    0   16    0   34    0
END

View in JSmol

Synonyms

Value	Source
Methyl 1-hydroxy-7-(hydroxymethyl)-1H,4ah,5H,7ah-cyclopenta[c]pyran-4-carboxylic acid	Generator

Chemical Formula

C₁₁H₁₄O₅

Average Mass

226.2259 Da

Monoisotopic Mass

226.08412 Da

IUPAC Name

methyl 1-hydroxy-7-(hydroxymethyl)-1H,4aH,5H,7aH-cyclopenta[c]pyran-4-carboxylate

Traditional Name

methyl 1-hydroxy-7-(hydroxymethyl)-1H,4aH,5H,7aH-cyclopenta[c]pyran-4-carboxylate

CAS Registry Number

Not Available

SMILES

COC(=O)C1=COC(O)C2C1CC=C2CO

InChI Identifier

InChI=1S/C11H14O5/c1-15-10(13)8-5-16-11(14)9-6(4-12)2-3-7(8)9/h2,5,7,9,11-12,14H,3-4H2,1H3

InChI Key

AZKVWQKMDGGDSV-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
Eucommia ulmoides	LOTUS Database	35616633
Gardenia jasminoides	LOTUS Database	35616633
Garrya elliptica	LOTUS Database	35616633
Genipa americana	LOTUS Database	35616633
Rothmannia globosa	LOTUS Database	35616633

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as iridoids and derivatives. These are monoterpenes containing a skeleton structurally characterized by the presence of a cylopentane fused to a pyran ( forming a 4,7-dimethylcyclopenta[c]pyran), or a derivative where the pentane moiety is open.

Kingdom

Organic compounds

Super Class

Lipids and lipid-like molecules

Class

Prenol lipids

Sub Class

Monoterpenoids

Direct Parent

Iridoids and derivatives

Alternative Parents

Substituents

Iridoid-skeleton
Bicyclic monoterpenoid
Methyl ester
Vinylogous ester
Alpha,beta-unsaturated carboxylic ester
Enoate ester
Carboxylic acid ester
Hemiacetal
Carboxylic acid derivative
Oxacycle
Monocarboxylic acid or derivatives
Organoheterocyclic compound
Hydrocarbon derivative
Organic oxide
Alcohol
Organic oxygen compound
Organooxygen compound
Primary alcohol
Carbonyl group
Aliphatic heteropolycyclic compound

Molecular Framework

Aliphatic 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	0.07	ALOGPS
logP	-0.44	ChemAxon
logS	-1.5	ALOGPS
pKa (Strongest Acidic)	12.04	ChemAxon
pKa (Strongest Basic)	-2.7	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	4	ChemAxon
Hydrogen Donor Count	2	ChemAxon
Polar Surface Area	75.99 Å²	ChemAxon
Rotatable Bond Count	3	ChemAxon
Refractivity	56.09 m³·mol⁻¹	ChemAxon
Polarizability	22.43 Å³	ChemAxon
Number of Rings	2	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

HMDB0035830

DrugBank ID

Not Available

Phenol Explorer Compound ID

Not Available

FoodDB ID

KNApSAcK ID

Chemspider ID

KEGG Compound ID

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Genipin

METLIN ID

Not Available

PubChem Compound

23340

PDB ID

Not Available

ChEBI ID

94318

Good Scents ID

Not Available

References

General References

Cao H, Feng Q, Xu W, Li X, Kang Z, Ren Y, Du L: Genipin induced apoptosis associated with activation of the c-Jun NH2-terminal kinase and p53 protein in HeLa cells. Biol Pharm Bull. 2010;33(8):1343-8. doi: 10.1248/bpb.33.1343. [PubMed:20686229 ]
Tian JS, Cui YL, Hu LM, Gao S, Chi W, Dong TJ, Liu LP: Antidepressant-like effect of genipin in mice. Neurosci Lett. 2010 Aug 2;479(3):236-9. doi: 10.1016/j.neulet.2010.05.069. Epub 2010 Jun 1. [PubMed:20561935 ]
Kim BC, Kim HG, Lee SA, Lim S, Park EH, Kim SJ, Lim CJ: Genipin-induced apoptosis in hepatoma cells is mediated by reactive oxygen species/c-Jun NH2-terminal kinase-dependent activation of mitochondrial pathway. Biochem Pharmacol. 2005 Nov 1;70(9):1398-407. doi: 10.1016/j.bcp.2005.07.025. [PubMed:16143311 ]
Koo HJ, Lim KH, Jung HJ, Park EH: Anti-inflammatory evaluation of gardenia extract, geniposide and genipin. J Ethnopharmacol. 2006 Feb 20;103(3):496-500. doi: 10.1016/j.jep.2005.08.011. Epub 2005 Sep 19. [PubMed:16169698 ]
LOTUS database [Link]

Showing NP-Card for methyl 1-hydroxy-7-(hydroxymethyl)-1h,4ah,5h,7ah-cyclopenta[c]pyran-4-carboxylate (NP0191666)

MOL for NP0191666 (methyl 1-hydroxy-7-(hydroxymethyl)-1h,4ah,5h,7ah-cyclopenta[c]pyran-4-carboxylate)

3D MOL for NP0191666 (methyl 1-hydroxy-7-(hydroxymethyl)-1h,4ah,5h,7ah-cyclopenta[c]pyran-4-carboxylate)

3D SDF for NP0191666 (methyl 1-hydroxy-7-(hydroxymethyl)-1h,4ah,5h,7ah-cyclopenta[c]pyran-4-carboxylate)

3D-SDF for NP0191666 (methyl 1-hydroxy-7-(hydroxymethyl)-1h,4ah,5h,7ah-cyclopenta[c]pyran-4-carboxylate)

PDB for NP0191666 (methyl 1-hydroxy-7-(hydroxymethyl)-1h,4ah,5h,7ah-cyclopenta[c]pyran-4-carboxylate)

3D PDB for NP0191666 (methyl 1-hydroxy-7-(hydroxymethyl)-1h,4ah,5h,7ah-cyclopenta[c]pyran-4-carboxylate)

SMILES for NP0191666 (methyl 1-hydroxy-7-(hydroxymethyl)-1h,4ah,5h,7ah-cyclopenta[c]pyran-4-carboxylate)

INCHI for NP0191666 (methyl 1-hydroxy-7-(hydroxymethyl)-1h,4ah,5h,7ah-cyclopenta[c]pyran-4-carboxylate)

Structure for NP0191666 (methyl 1-hydroxy-7-(hydroxymethyl)-1h,4ah,5h,7ah-cyclopenta[c]pyran-4-carboxylate)

3D Structure for NP0191666 (methyl 1-hydroxy-7-(hydroxymethyl)-1h,4ah,5h,7ah-cyclopenta[c]pyran-4-carboxylate)