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Record Information

Version

5.0

Status

Expected but not Quantified

Creation Date

2012-09-11 21:08:32 UTC

Update Date

2022-03-07 02:54:46 UTC

HMDB ID

HMDB0036072

Secondary Accession Numbers

HMDB36072

Metabolite Identification

Common Name

Genipic acid

Description

Genipic acid, also known as genipate, belongs to the class of organic compounds known as dihydrofurans. Dihydrofurans are compounds containing a dihydrofuran moiety, which is a furan derivative with only one double bond. Genipic acid has been detected, but not quantified in, beverages and fruits. This could make genipic acid a potential biomarker for the consumption of these foods. Based on a literature review very few articles have been published on Genipic acid.

Structure

MOL 3D MOL SDF 3D SDF PDB 3D PDB SMILES InChI

  Mrv0541 05061308522D          

 13 14  0  0  0  0            999 V2000
    0.7846   -0.2549    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.2695    0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.0146   -1.7070    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8388    0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.2695   -0.9224    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.0542    0.1576    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.2076   -1.8785    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.0542   -0.6674    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8388   -0.9224    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0473   -2.6631    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3444   -1.2654    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.0937   -1.7070    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.3237   -0.2549    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  2  1  1  0  0  0  0
  5  1  1  0  0  0  0
  5  3  1  0  0  0  0
  6  2  1  0  0  0  0
  6  4  1  0  0  0  0
  7  3  1  0  0  0  0
  8  5  1  0  0  0  0
  8  6  2  0  0  0  0
  9  8  1  0  0  0  0
 10  7  2  0  0  0  0
 11  7  1  0  0  0  0
 12  9  1  0  0  0  0
 13  4  1  0  0  0  0
 13  9  1  0  0  0  0
M  END
> <DATABASE_ID>
HMDB0036072

> <DATABASE_NAME>
hmdb

> <SMILES>
OC1OCC2=C1C(CC(O)=O)CC2

> <INCHI_IDENTIFIER>
InChI=1S/C9H12O4/c10-7(11)3-5-1-2-6-4-13-9(12)8(5)6/h5,9,12H,1-4H2,(H,10,11)

> <INCHI_KEY>
KWBASGHXHPTPGU-UHFFFAOYSA-N

> <FORMULA>
C9H12O4

> <MOLECULAR_WEIGHT>
184.1892

> <EXACT_MASS>
184.073558872

> <JCHEM_ACCEPTOR_COUNT>
4

> <JCHEM_AVERAGE_POLARIZABILITY>
18.307557741295398

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
2

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
1

> <JCHEM_IUPAC>
2-{3-hydroxy-1H,3H,4H,5H,6H-cyclopenta[c]furan-4-yl}acetic acid

> <ALOGPS_LOGP>
-0.08

> <JCHEM_LOGP>
-0.00507247466666641

> <ALOGPS_LOGS>
-1.12

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
2

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-1

> <JCHEM_PKA>
11.816273564979662

> <JCHEM_PKA_STRONGEST_ACIDIC>
4.259449336024242

> <JCHEM_PKA_STRONGEST_BASIC>
-4.191886802133079

> <JCHEM_POLAR_SURFACE_AREA>
66.76

> <JCHEM_REFRACTIVITY>
44.56980000000001

> <JCHEM_ROTATABLE_BOND_COUNT>
2

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
1.39e+01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
{3-hydroxy-1H,3H,4H,5H,6H-cyclopenta[c]furan-4-yl}acetic 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       1.465  -0.476   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       2.370   0.770   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       1.894  -3.186   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       5.299   0.770   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       2.370  -1.722   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       3.835   0.294   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       0.388  -3.507   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0       3.835  -1.246   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0       5.299  -1.722   0.000  0.00  0.00           C+0
HETATM   10  O   UNK     0      -0.088  -4.971   0.000  0.00  0.00           O+0
HETATM   11  O   UNK     0      -0.643  -2.362   0.000  0.00  0.00           O+0
HETATM   12  O   UNK     0       5.775  -3.186   0.000  0.00  0.00           O+0
HETATM   13  O   UNK     0       6.204  -0.476   0.000  0.00  0.00           O+0
CONECT    1    2    5                                                       
CONECT    2    1    6                                                       
CONECT    3    5    7                                                       
CONECT    4    6   13                                                       
CONECT    5    1    3    8                                                  
CONECT    6    2    4    8                                                  
CONECT    7    3   10   11                                                  
CONECT    8    5    6    9                                                  
CONECT    9    8   12   13                                                  
CONECT   10    7                                                            
CONECT   11    7                                                            
CONECT   12    9                                                            
CONECT   13    4    9                                                       
MASTER        0    0    0    0    0    0    0    0   13    0   28    0
END

View in JSmol View NMR Assignments View Stereo Labels

Synonyms

Value	Source
Genipate	Generator
2-Hydroxy-3-oxabicyclo[3.3.0]oct-1(5)-eneacetic acid	HMDB
2-{3-hydroxy-1H,3H,4H,5H,6H-cyclopenta[c]furan-4-yl}acetate	Generator

Chemical Formula

C₉H₁₂O₄

Average Molecular Weight

184.1892

Monoisotopic Molecular Weight

184.073558872

IUPAC Name

2-{3-hydroxy-1H,3H,4H,5H,6H-cyclopenta[c]furan-4-yl}acetic acid

Traditional Name

{3-hydroxy-1H,3H,4H,5H,6H-cyclopenta[c]furan-4-yl}acetic acid

CAS Registry Number

6902-76-7

SMILES

OC1OCC2=C1C(CC(O)=O)CC2

InChI Identifier

InChI=1S/C9H12O4/c10-7(11)3-5-1-2-6-4-13-9(12)8(5)6/h5,9,12H,1-4H2,(H,10,11)

InChI Key

KWBASGHXHPTPGU-UHFFFAOYSA-N

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as dihydrofurans. Dihydrofurans are compounds containing a dihydrofuran moiety, which is a furan derivative with only one double bond.

Kingdom

Organic compounds

Super Class

Organoheterocyclic compounds

Class

Dihydrofurans

Sub Class

Not Available

Direct Parent

Dihydrofurans

Alternative Parents

Substituents

Dihydrofuran
Hemiacetal
Oxacycle
Monocarboxylic acid or derivatives
Carboxylic acid
Carboxylic acid derivative
Organic oxygen compound
Organic oxide
Hydrocarbon derivative
Organooxygen compound
Carbonyl group
Aliphatic heteropolycyclic compound

Molecular Framework

Aliphatic heteropolycyclic compounds

External Descriptors

Not Available

Ontology

Physiological effect

Not Available

Disposition

Biological location

Cellular substructure

Route of exposure

Enteral

Ingestion (HMDB: HMDB0036072)

Source

Endogenous

Endogenous (HMDB: HMDB0036072)

Plant

Plant (HMDB: HMDB0036072)

Exogenous

Food

Food (HMDB: HMDB0036072)

Fruit

Fruits (FooDB: FOOD00871)

Beverage

Beverages (FooDB: FOOD00870)

Exogenous (HMDB: HMDB0036072)

Process

Naturally occurring process

Biological process

Cellular process

Cell signaling (HMDB: HMDB0036072)

Role

Biological role

Energy source (HMDB: HMDB0036072)

Industrial application

Manufacturing industry

Material processing agent

Fluid processing agent

Surfactant

Surfactant (HMDB: HMDB0036072)

Physical Properties

State

Not Available

Experimental Molecular Properties

Property	Value	Reference
Melting Point	Not Available	Not Available
Boiling Point	Not Available	Not Available
Water Solubility	433300 mg/L @ 25 °C (est)	The Good Scents Company Information System
LogP	Not Available	Not Available

Experimental Chromatographic Properties

Not Available

Predicted Molecular Properties

Property	Value	Source
Water Solubility	13.9 g/L	ALOGPS
logP	-0.08	ALOGPS
logP	-0.0051	ChemAxon
logS	-1.1	ALOGPS
pKa (Strongest Acidic)	4.26	ChemAxon
pKa (Strongest Basic)	-4.2	ChemAxon
Physiological Charge	-1	ChemAxon
Hydrogen Acceptor Count	4	ChemAxon
Hydrogen Donor Count	2	ChemAxon
Polar Surface Area	66.76 Å²	ChemAxon
Rotatable Bond Count	2	ChemAxon
Refractivity	44.57 m³·mol⁻¹	ChemAxon
Polarizability	18.31 Å³	ChemAxon
Number of Rings	2	ChemAxon
Bioavailability	Yes	ChemAxon
Rule of Five	Yes	ChemAxon
Ghose Filter	Yes	ChemAxon
Veber's Rule	No	ChemAxon
MDDR-like Rule	No	ChemAxon

Predicted Chromatographic Properties

Predicted Collision Cross Sections

Predictor	Adduct Type	CCS Value (Å²)	Reference
DarkChem	[M+H]+	142.242	31661259
DarkChem	[M-H]-	135.013	31661259
DeepCCS	[M+H]+	139.393	30932474
DeepCCS	[M-H]-	135.565	30932474
DeepCCS	[M-2H]-	173.145	30932474
DeepCCS	[M+Na]+	148.684	30932474
AllCCS	[M+H]+	140.1	32859911
AllCCS	[M+H-H2O]+	135.9	32859911
AllCCS	[M+NH4]+	144.0	32859911
AllCCS	[M+Na]+	145.1	32859911
AllCCS	[M-H]-	139.4	32859911
AllCCS	[M+Na-2H]-	139.9	32859911
AllCCS	[M+HCOO]-	140.6	32859911

Predicted Kovats Retention Indices

Underivatized

Metabolite	SMILES	Kovats RI Value	Column Type	Reference
Genipic acid	OC1OCC2=C1C(CC(O)=O)CC2	3088.9	Standard polar	33892256
Genipic acid	OC1OCC2=C1C(CC(O)=O)CC2	1570.3	Standard non polar	33892256
Genipic acid	OC1OCC2=C1C(CC(O)=O)CC2	1655.3	Semi standard non polar	33892256

Derivatized

Derivative Name / Structure	SMILES	Kovats RI Value	Column Type	Reference
Genipic acid,1TMS,isomer #1	C[Si](C)(C)OC1OCC2=C1C(CC(=O)O)CC2	1776.1	Semi standard non polar	33892256
Genipic acid,1TMS,isomer #2	C[Si](C)(C)OC(=O)CC1CCC2=C1C(O)OC2	1678.0	Semi standard non polar	33892256
Genipic acid,2TMS,isomer #1	C[Si](C)(C)OC(=O)CC1CCC2=C1C(O[Si](C)(C)C)OC2	1757.7	Semi standard non polar	33892256
Genipic acid,1TBDMS,isomer #1	CC(C)(C)[Si](C)(C)OC1OCC2=C1C(CC(=O)O)CC2	2030.3	Semi standard non polar	33892256
Genipic acid,1TBDMS,isomer #2	CC(C)(C)[Si](C)(C)OC(=O)CC1CCC2=C1C(O)OC2	1913.3	Semi standard non polar	33892256
Genipic acid,2TBDMS,isomer #1	CC(C)(C)[Si](C)(C)OC(=O)CC1CCC2=C1C(O[Si](C)(C)C(C)(C)C)OC2	2220.1	Semi standard non polar	33892256

Spectra

GC-MS Spectra

Spectrum Type	Description	Splash Key	Deposition Date	Source	View
Predicted GC-MS	Predicted GC-MS Spectrum - Genipic acid GC-MS (Non-derivatized) - 70eV, Positive	splash10-0fmi-5900000000-e49349367f6bd11a43ae	2017-09-01	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - Genipic acid GC-MS (2 TMS) - 70eV, Positive	splash10-01pa-9671000000-0e6d0d9ed2246677e0cc	2017-10-06	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - Genipic acid GC-MS (Non-derivatized) - 70eV, Positive	Not Available	2021-10-12	Wishart Lab	View Spectrum

MS/MS Spectra

Spectrum Type	Description	Splash Key	Deposition Date	Source	View
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Genipic acid 10V, Positive-QTOF	splash10-00kr-0900000000-a46426675efaa9174d72	2016-08-03	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Genipic acid 20V, Positive-QTOF	splash10-000i-2900000000-d5e921d96da37ad1de07	2016-08-03	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Genipic acid 40V, Positive-QTOF	splash10-0fbc-9100000000-56315dcb296928c27734	2016-08-03	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Genipic acid 10V, Negative-QTOF	splash10-001r-0900000000-6eba814011dfa6b5abf3	2016-08-04	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Genipic acid 20V, Negative-QTOF	splash10-0019-1900000000-248316188fe0d0cfee11	2016-08-04	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Genipic acid 40V, Negative-QTOF	splash10-0abi-9800000000-7f2829967a52869a6a15	2016-08-04	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Genipic acid 10V, Positive-QTOF	splash10-000i-0900000000-f715902c0b9e2547ecaf	2021-09-23	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Genipic acid 20V, Positive-QTOF	splash10-00y1-1900000000-a97d236f579ea8085e43	2021-09-23	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Genipic acid 40V, Positive-QTOF	splash10-056u-9100000000-77cbeb8f5dedf56cb81a	2021-09-23	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Genipic acid 10V, Negative-QTOF	splash10-001i-0900000000-f5ef380cac44712ae8b7	2021-09-24	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Genipic acid 20V, Negative-QTOF	splash10-052o-9700000000-a96a9e610e85316accf4	2021-09-24	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Genipic acid 40V, Negative-QTOF	splash10-0006-9700000000-e21cff7cf08c1612a29a	2021-09-24	Wishart Lab	View Spectrum

NMR Spectra

Spectrum Type	Description	Deposition Date	Source	View
Predicted 1D NMR	¹H NMR Spectrum (1D, 100 MHz, D₂O, predicted)	2021-09-25	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 100 MHz, D₂O, predicted)	2021-09-25	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 1000 MHz, D₂O, predicted)	2021-09-25	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 1000 MHz, D₂O, predicted)	2021-09-25	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 200 MHz, D₂O, predicted)	2021-09-25	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 200 MHz, D₂O, predicted)	2021-09-25	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 300 MHz, D₂O, predicted)	2021-09-25	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 300 MHz, D₂O, predicted)	2021-09-25	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 400 MHz, D₂O, predicted)	2021-09-25	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 400 MHz, D₂O, predicted)	2021-09-25	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 500 MHz, D₂O, predicted)	2021-09-25	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 500 MHz, D₂O, predicted)	2021-09-25	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 600 MHz, D₂O, predicted)	2021-09-25	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 600 MHz, D₂O, predicted)	2021-09-25	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 700 MHz, D₂O, predicted)	2021-09-25	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 700 MHz, D₂O, predicted)	2021-09-25	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 800 MHz, D₂O, predicted)	2021-09-25	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 800 MHz, D₂O, predicted)	2021-09-25	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 900 MHz, D₂O, predicted)	2021-09-25	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 900 MHz, D₂O, predicted)	2021-09-25	Wishart Lab	View Spectrum

Biological Properties

Cellular Locations

Cytoplasm
Extracellular
Membrane

Biospecimen Locations

Not Available

Tissue Locations

Not Available

Pathways

Not Available

Name	SMPDB/PathBank	KEGG

Normal Concentrations

Not Available

Abnormal Concentrations

Not Available

Associated Disorders and Diseases

Disease References

None

Associated OMIM IDs

None

External Links

DrugBank ID

Not Available

Phenol Explorer Compound ID

Not Available

FooDB ID

FDB014903

KNApSAcK ID

C00010562

Chemspider ID

35014089

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

78384968

PDB ID

Not Available

ChEBI ID

156151

Food Biomarker Ontology

Not Available

VMH ID

Not Available

MarkerDB ID

Not Available

Good Scents ID

rw1853521

References

Synthesis Reference

Not Available

Material Safety Data Sheet (MSDS)

Not Available

General References

(). Yannai, Shmuel. (2004) Dictionary of food compounds with CD-ROM: Additives, flavors, and ingredients. Boca Raton: Chapman & Hall/CRC.. .

Showing metabocard for Genipic acid (HMDB0036072)

MOL for HMDB0036072 (Genipic acid)

3D MOL for HMDB0036072 (Genipic acid)

3D SDF for HMDB0036072 (Genipic acid)

3D-SDF for HMDB0036072 (Genipic acid)

PDB for HMDB0036072 (Genipic acid)

3D PDB for HMDB0036072 (Genipic acid)

SMILES for HMDB0036072 (Genipic acid)

INCHI for HMDB0036072 (Genipic acid)

Structure for HMDB0036072 (Genipic acid)

3D Structure for HMDB0036072 (Genipic acid)

Predicted Collision Cross Sections

Predicted Kovats Retention Indices

Underivatized

Derivatized

GC-MS Spectra

MS/MS Spectra

NMR Spectra