NP-MRD: Showing NP-Card for {3-hydroxy-1h,3h,4h,5h,6h-cyclopenta[c]furan-4-yl}acetic acid (NP0230616)

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Record Information

Version

1.0

Created at

2022-09-06 11:07:14 UTC

Updated at

2022-09-06 11:07:14 UTC

NP-MRD ID

NP0230616

Secondary Accession Numbers

None

Natural Product Identification

Common Name

{3-hydroxy-1h,3h,4h,5h,6h-cyclopenta[c]furan-4-yl}acetic 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 is an extremely weak basic (essentially neutral) compound (based on its pKa). Outside of the human body, Genipic acid has been detected, but not quantified in, beverages and fruits. {3-hydroxy-1h,3h,4h,5h,6h-cyclopenta[c]furan-4-yl}acetic acid is found in Genipa americana. This could make genipic acid a potential biomarker for the consumption of these foods.

Structure

MOL 3D MOL SDF 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>
NP0230616

> <DATABASE_NAME>
NP-MRD

> <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

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 Mass

184.1892 Da

Monoisotopic Mass

184.07356 Da

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

Not Available

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

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
Genipa americana	LOTUS Database	35616633

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

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	-0.08	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

External Links

HMDB ID

HMDB0036072

DrugBank ID

Not Available

Phenol Explorer Compound ID

Not Available

FoodDB ID

FDB014903

KNApSAcK ID

C00010562

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

78384968

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

LOTUS database [Link]

Showing NP-Card for {3-hydroxy-1h,3h,4h,5h,6h-cyclopenta[c]furan-4-yl}acetic acid (NP0230616)

MOL for NP0230616 ({3-hydroxy-1h,3h,4h,5h,6h-cyclopenta[c]furan-4-yl}acetic acid)

3D MOL for NP0230616 ({3-hydroxy-1h,3h,4h,5h,6h-cyclopenta[c]furan-4-yl}acetic acid)

3D SDF for NP0230616 ({3-hydroxy-1h,3h,4h,5h,6h-cyclopenta[c]furan-4-yl}acetic acid)

3D-SDF for NP0230616 ({3-hydroxy-1h,3h,4h,5h,6h-cyclopenta[c]furan-4-yl}acetic acid)

PDB for NP0230616 ({3-hydroxy-1h,3h,4h,5h,6h-cyclopenta[c]furan-4-yl}acetic acid)

3D PDB for NP0230616 ({3-hydroxy-1h,3h,4h,5h,6h-cyclopenta[c]furan-4-yl}acetic acid)

SMILES for NP0230616 ({3-hydroxy-1h,3h,4h,5h,6h-cyclopenta[c]furan-4-yl}acetic acid)

INCHI for NP0230616 ({3-hydroxy-1h,3h,4h,5h,6h-cyclopenta[c]furan-4-yl}acetic acid)

Structure for NP0230616 ({3-hydroxy-1h,3h,4h,5h,6h-cyclopenta[c]furan-4-yl}acetic acid)

3D Structure for NP0230616 ({3-hydroxy-1h,3h,4h,5h,6h-cyclopenta[c]furan-4-yl}acetic acid)