NP-MRD: Showing NP-Card for 1,3-Benzodioxole-5-pentanoic acid (NP0084877)

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Record Information

Version

2.0

Created at

2022-04-29 05:29:56 UTC

Updated at

2022-04-29 05:29:56 UTC

NP-MRD ID

NP0084877

Secondary Accession Numbers

None

Natural Product Identification

Common Name

1,3-Benzodioxole-5-pentanoic acid

Description

5-(3,4-Methylenedioxyphenyl)pentanoic acid, also known as 1,3-benzodioxole-5-pentanoic acid, 9CI or piperhydronic acid, belongs to the class of organic compounds known as benzodioxoles. These are organic compounds containing a benzene ring fused to either isomers of dioxole. Dioxole is a five-membered unsaturated ring of two oxygen atoms and three carbon atoms. 5-(3,4-Methylenedioxyphenyl)pentanoic acid is an extremely weak basic (essentially neutral) compound (based on its pKa). Outside of the human body, 5-(3,4-Methylenedioxyphenyl)pentanoic acid has been detected, but not quantified in, herbs and spices. 1,3-Benzodioxole-5-pentanoic acid is found in Peperomia heyneana and Piper longum . This could make 5-(3,4-methylenedioxyphenyl)pentanoic acid a potential biomarker for the consumption of these foods.

Structure

MOL 3D MOL SDF PDB SMILES InChI

     RDKit          3D

 30 31  0  0  0  0  0  0  0  0999 V2000
    2.9924    2.3928   -0.6961 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.4043    1.3187   -0.1428 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.6199    1.3023    1.2208 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.6286    0.1597   -0.9795 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.9170   -1.0751   -0.6019 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4417   -1.0663   -0.5821 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7989   -0.1612    0.3849 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7028   -0.2782    0.2905 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3971   -1.1700    1.0451 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7900   -1.2430    0.9500 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.4967   -0.4176    0.0935 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7986    0.4742   -0.6615 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4039    0.5428   -0.5625 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.7377    1.1709   -1.4260 O   0  0  0  0  0  0  0  0  0  0  0  0
   -4.9467    1.1145   -0.6583 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.8599   -0.2524   -0.2200 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.0569    2.1134    1.6838 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.7347   -0.0497   -0.9991 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.3815    0.3769   -2.0569 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.2083   -1.8637   -1.3755 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.3634   -1.4885    0.3487 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.0977   -0.7707   -1.6075 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.0085   -2.1001   -0.4100 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.0813    0.8800    0.3028 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.1243   -0.4778    1.4223 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8783   -1.8186    1.7147 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.3433   -1.9610    1.5566 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8792    1.2566   -1.1751 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.8420    1.3303   -1.2354 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.7833    1.7608    0.2265 H   0  0  0  0  0  0  0  0  0  0  0  0
  3  2  1  0
  2  1  2  0
  2  4  1  0
  4  5  1  0
  5  6  1  0
  6  7  1  0
  7  8  1  0
  8 13  2  0
 13 12  1  0
 12 11  2  0
 11 16  1  0
 16 15  1  0
 15 14  1  0
 11 10  1  0
 10  9  2  0
  9  8  1  0
 14 12  1  0
  3 17  1  0
  4 18  1  0
  4 19  1  0
  5 20  1  0
  5 21  1  0
  6 22  1  0
  6 23  1  0
  7 24  1  0
  7 25  1  0
 13 28  1  0
 15 29  1  0
 15 30  1  0
 10 27  1  0
  9 26  1  0
M  END


  Mrv0541 05061307322D          

 16 17  0  0  0  0            999 V2000
   -1.4289    0.8250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1434    1.2375    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7145    1.2375    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8579    0.8250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145   -0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145    1.2375    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.6985    0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    0.8250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289    0.8250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5724    1.2375    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.2868    0.8250    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5724    2.0625    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.2136   -0.2549    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.2136    1.0799    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  2  1  1  0  0  0  0
  3  1  1  0  0  0  0
  4  2  1  0  0  0  0
  6  5  2  0  0  0  0
  9  3  1  0  0  0  0
  9  5  1  0  0  0  0
  9  7  2  0  0  0  0
 10  6  1  0  0  0  0
 11  7  1  0  0  0  0
 11 10  2  0  0  0  0
 12  4  1  0  0  0  0
 13 12  2  0  0  0  0
 14 12  1  0  0  0  0
 15  8  1  0  0  0  0
 15 10  1  0  0  0  0
 16  8  1  0  0  0  0
 16 11  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0084877

> <DATABASE_NAME>
NP-MRD

> <SMILES>
OC(=O)CCCCC1=CC2=C(OCO2)C=C1

> <INCHI_IDENTIFIER>
InChI=1S/C12H14O4/c13-12(14)4-2-1-3-9-5-6-10-11(7-9)16-8-15-10/h5-7H,1-4,8H2,(H,13,14)

> <INCHI_KEY>
VSLFLWQBWGEPBW-UHFFFAOYSA-N

> <FORMULA>
C12H14O4

> <MOLECULAR_WEIGHT>
222.2372

> <EXACT_MASS>
222.089208936

> <JCHEM_ACCEPTOR_COUNT>
4

> <JCHEM_AVERAGE_POLARIZABILITY>
23.480301811682185

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
1

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
1

> <JCHEM_IUPAC>
5-(2H-1,3-benzodioxol-5-yl)pentanoic acid

> <ALOGPS_LOGP>
2.48

> <JCHEM_LOGP>
2.567933568

> <ALOGPS_LOGS>
-2.67

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
2

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-1

> <JCHEM_PKA_STRONGEST_ACIDIC>
3.8745805214556013

> <JCHEM_PKA_STRONGEST_BASIC>
-4.736786885005781

> <JCHEM_POLAR_SURFACE_AREA>
55.760000000000005

> <JCHEM_REFRACTIVITY>
56.93550000000001

> <JCHEM_ROTATABLE_BOND_COUNT>
5

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
4.76e-01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
5-(2H-1,3-benzodioxol-5-yl)pentanoic 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      -2.667   1.540   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0      -4.001   2.310   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0      -1.334   2.310   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0      -5.335   1.540   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       1.334  -0.770   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       1.334   2.310   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0       5.037   0.770   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0       0.000   1.540   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0       2.667   0.000   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0       2.667   1.540   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0      -6.668   2.310   0.000  0.00  0.00           C+0
HETATM   13  O   UNK     0      -8.002   1.540   0.000  0.00  0.00           O+0
HETATM   14  O   UNK     0      -6.668   3.850   0.000  0.00  0.00           O+0
HETATM   15  O   UNK     0       4.132  -0.476   0.000  0.00  0.00           O+0
HETATM   16  O   UNK     0       4.132   2.016   0.000  0.00  0.00           O+0
CONECT    1    2    3                                                       
CONECT    2    1    4                                                       
CONECT    3    1    9                                                       
CONECT    4    2   12                                                       
CONECT    5    6    9                                                       
CONECT    6    5   10                                                       
CONECT    7    9   11                                                       
CONECT    8   15   16                                                       
CONECT    9    3    5    7                                                  
CONECT   10    6   11   15                                                  
CONECT   11    7   10   16                                                  
CONECT   12    4   13   14                                                  
CONECT   13   12                                                            
CONECT   14   12                                                            
CONECT   15    8   10                                                       
CONECT   16    8   11                                                       
MASTER        0    0    0    0    0    0    0    0   16    0   34    0
END

View in JSmol

Synonyms

Value	Source
5-(3,4-Methylenedioxyphenyl)pentanoate	Generator
1,3-Benzodioxole-5-pentanoic acid, 9ci	HMDB
Piperhydronic acid	HMDB
Tetrahydropiperinic acid	HMDB
5-(2H-1,3-Benzodioxol-5-yl)pentanoate	Generator

Chemical Formula

C₁₂H₁₄O₄

Average Mass

222.2372 Da

Monoisotopic Mass

222.08921 Da

IUPAC Name

5-(2H-1,3-benzodioxol-5-yl)pentanoic acid

Traditional Name

5-(2H-1,3-benzodioxol-5-yl)pentanoic acid

CAS Registry Number

Not Available

SMILES

OC(=O)CCCCC1=CC2=C(OCO2)C=C1

InChI Identifier

InChI=1S/C12H14O4/c13-12(14)4-2-1-3-9-5-6-10-11(7-9)16-8-15-10/h5-7H,1-4,8H2,(H,13,14)

InChI Key

VSLFLWQBWGEPBW-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, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 100 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 252 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 1000 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 50 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 200 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 75 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 300 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 101 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 400 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 126 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 500 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 151 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 600 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 176 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 700 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 201 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 800 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 226 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 900 MHz, D₂O, 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
Peperomia heyneana	LOTUS Database	35616633
Piper longum	Plant	KNApSAcK

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as benzodioxoles. These are organic compounds containing a benzene ring fused to either isomers of dioxole. Dioxole is a five-membered unsaturated ring of two oxygen atoms and three carbon atoms.

Kingdom

Organic compounds

Super Class

Organoheterocyclic compounds

Class

Benzodioxoles

Sub Class

Not Available

Direct Parent

Benzodioxoles

Alternative Parents

Substituents

Benzodioxole
Medium-chain fatty acid
Heterocyclic fatty acid
Benzenoid
Fatty acyl
Fatty acid
Acetal
Carboxylic acid derivative
Carboxylic acid
Monocarboxylic acid or derivatives
Oxacycle
Organic oxygen compound
Organic oxide
Carbonyl group
Organooxygen compound
Hydrocarbon derivative
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	2.48	ALOGPS
logP	2.57	ChemAxon
logS	-2.7	ALOGPS
pKa (Strongest Acidic)	3.87	ChemAxon
pKa (Strongest Basic)	-4.7	ChemAxon
Physiological Charge	-1	ChemAxon
Hydrogen Acceptor Count	4	ChemAxon
Hydrogen Donor Count	1	ChemAxon
Polar Surface Area	55.76 Å²	ChemAxon
Rotatable Bond Count	5	ChemAxon
Refractivity	56.94 m³·mol⁻¹	ChemAxon
Polarizability	23.48 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

HMDB0034056

DrugBank ID

Not Available

Phenol Explorer Compound ID

Not Available

FoodDB ID

FDB012302

KNApSAcK ID

Not Available

Chemspider ID

4479488

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

5321853

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

Not Available

Showing NP-Card for 1,3-Benzodioxole-5-pentanoic acid (NP0084877)

MOL for NP0084877 (1,3-Benzodioxole-5-pentanoic acid)

3D MOL for NP0084877 (1,3-Benzodioxole-5-pentanoic acid)

3D SDF for NP0084877 (1,3-Benzodioxole-5-pentanoic acid)

3D-SDF for NP0084877 (1,3-Benzodioxole-5-pentanoic acid)

PDB for NP0084877 (1,3-Benzodioxole-5-pentanoic acid)

3D PDB for NP0084877 (1,3-Benzodioxole-5-pentanoic acid)

SMILES for NP0084877 (1,3-Benzodioxole-5-pentanoic acid)

INCHI for NP0084877 (1,3-Benzodioxole-5-pentanoic acid)

Structure for NP0084877 (1,3-Benzodioxole-5-pentanoic acid)

3D Structure for NP0084877 (1,3-Benzodioxole-5-pentanoic acid)