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Showing NP-Card for (+/-)-homoproline (NP0309612)

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Record Information
Version1.0
Created at2022-09-11 04:19:53 UTC
Updated at2022-09-11 04:19:54 UTC
NP-MRD IDNP0309612
Secondary Accession NumbersNone
Natural Product Identification
Common Name(+/-)-homoproline
Description2-Pyrrolidineacetic acid, also known as (+/-)-homoproline or beta-homoproline, belongs to the class of organic compounds known as pyrrolidines. Pyrrolidines are compounds containing a pyrrolidine ring, which is a five-membered saturated aliphatic heterocycle with one nitrogen atom and four carbon atoms. 2-Pyrrolidineacetic acid is a very strong basic compound (based on its pKa). Outside of the human body, 2-Pyrrolidineacetic acid has been detected, but not quantified in, tea. (+/-)-homoproline is found in Arnica montana and Melampodium divaricatum. This could make 2-pyrrolidineacetic acid a potential biomarker for the consumption of these foods.
Structure
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MOL3D MOLSDFPDBSMILESInChI

MOL for NP0309612 ((+/-)-homoproline)


  Mrv0541 02241214342D          

  9  9  0  0  0  0            999 V2000
    1.6923    0.2475    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.7837    0.3298    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.3713   -0.4128    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4537   -0.4128    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8667   -1.0730    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6923   -0.8253    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6923   -0.0003    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8667    0.2475    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.4537    1.0730    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  2  3  1  0  0  0  0
  2  9  2  0  0  0  0
  3  4  1  0  0  0  0
  4  5  1  0  0  0  0
  4  8  1  0  0  0  0
  5  6  1  0  0  0  0
  6  7  1  0  0  0  0
  7  8  1  0  0  0  0
M  END
Download

3D MOL for NP0309612 ((+/-)-homoproline)

     RDKit          3D

 20 20  0  0  0  0  0  0  0  0999 V2000
    3.1100    0.0645   -1.8389 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.3049   -0.0740   -0.8849 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.5738   -0.9582    0.1466 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.0711    0.7429   -0.9148 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.1726    0.4769    0.2615 C   0  0  2  0  0  0  0  0  0  0  0  0
   -0.2842   -0.9409    0.3440 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6400   -0.8693   -0.3511 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1436    0.4719    0.1208 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9890    1.3160    0.2815 N   0  0  0  0  0  0  0  0  0  0  0  0
    3.5271   -1.0964    0.4488 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.4133    1.8155   -0.8144 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.5833    0.5615   -1.8852 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.7573    0.7036    1.1947 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5181   -1.2110    1.4080 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.3749   -1.6772   -0.1060 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3119   -1.6635    0.0281 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5260   -0.8706   -1.4501 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8639    0.8615   -0.6248 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6863    0.3386    1.0833 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9253    2.0083   -0.4971 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  9  1  0
  9  5  1  0
  3 10  1  0
  4 11  1  0
  4 12  1  0
  5 13  1  1
  6 14  1  0
  6 15  1  0
  7 16  1  0
  7 17  1  0
  8 18  1  0
  8 19  1  0
  9 20  1  0
M  END
Download

3D SDF for NP0309612 ((+/-)-homoproline)


  Mrv0541 02241214342D          

  9  9  0  0  0  0            999 V2000
    1.6923    0.2475    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.7837    0.3298    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.3713   -0.4128    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4537   -0.4128    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8667   -1.0730    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6923   -0.8253    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6923   -0.0003    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8667    0.2475    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.4537    1.0730    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  2  3  1  0  0  0  0
  2  9  2  0  0  0  0
  3  4  1  0  0  0  0
  4  5  1  0  0  0  0
  4  8  1  0  0  0  0
  5  6  1  0  0  0  0
  6  7  1  0  0  0  0
  7  8  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0309612

> <DATABASE_NAME>
NP-MRD

> <SMILES>
OC(=O)CC1CCCN1

> <INCHI_IDENTIFIER>
InChI=1S/C6H11NO2/c8-6(9)4-5-2-1-3-7-5/h5,7H,1-4H2,(H,8,9)

> <INCHI_KEY>
ADSALMJPJUKESW-UHFFFAOYSA-N

> <FORMULA>
C6H11NO2

> <MOLECULAR_WEIGHT>
129.157

> <EXACT_MASS>
129.078978601

> <JCHEM_ACCEPTOR_COUNT>
3

> <JCHEM_AVERAGE_POLARIZABILITY>
13.482172529012129

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
2

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
2-(pyrrolidin-2-yl)acetic acid

> <ALOGPS_LOGP>
-2.41

> <JCHEM_LOGP>
-2.4840327352110783

> <ALOGPS_LOGS>
-0.03

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
1

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA_STRONGEST_ACIDIC>
3.8372938491245954

> <JCHEM_PKA_STRONGEST_BASIC>
11.255614818464315

> <JCHEM_POLAR_SURFACE_AREA>
49.33

> <JCHEM_REFRACTIVITY>
32.6886

> <JCHEM_ROTATABLE_BOND_COUNT>
2

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
1.20e+02 g/l

> <JCHEM_TRADITIONAL_IUPAC>
pyrrolidin-2-ylacetic acid

> <JCHEM_VEBER_RULE>
0

$$$$
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3D-SDF for NP0309612 ((+/-)-homoproline)

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PDB for NP0309612 ((+/-)-homoproline)
HEADER    PROTEIN                                 24-FEB-12   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   24-FEB-12         0                                  
HETATM    1  O   UNK     0       3.159   0.462   0.000  0.00  0.00           O+0
HETATM    2  C   UNK     0       1.463   0.616   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       0.693  -0.771   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0      -0.847  -0.771   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0      -1.618  -2.003   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0      -3.159  -1.541   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0      -3.159  -0.001   0.000  0.00  0.00           C+0
HETATM    8  N   UNK     0      -1.618   0.462   0.000  0.00  0.00           N+0
HETATM    9  O   UNK     0       0.847   2.003   0.000  0.00  0.00           O+0
CONECT    1    2                                                            
CONECT    2    1    3    9                                                  
CONECT    3    2    4                                                       
CONECT    4    3    5    8                                                  
CONECT    5    4    6                                                       
CONECT    6    5    7                                                       
CONECT    7    6    8                                                       
CONECT    8    4    7                                                       
CONECT    9    2                                                            
MASTER        0    0    0    0    0    0    0    0    9    0   18    0
END

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3D PDB for NP0309612 ((+/-)-homoproline)
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SMILES for NP0309612 ((+/-)-homoproline)
OC(=O)CC1CCCN1
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INCHI for NP0309612 ((+/-)-homoproline)
InChI=1S/C6H11NO2/c8-6(9)4-5-2-1-3-7-5/h5,7H,1-4H2,(H,8,9)
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View in JSmol
Synonyms
ValueSource
2-PyrrolidineacetateGenerator
(+/-)-homoprolineHMDB
b-Homoproline?HMDB
beta-HomoprolineHMDB
HomoprolineHMDB
Pyrrolidine-2-acetic acidHMDB
Homo-beta-prolineHMDB
2-(Pyrrolidin-2-yl)acetateGenerator
Chemical FormulaC6H11NO2
Average Mass129.1570 Da
Monoisotopic Mass129.07898 Da
IUPAC Name2-(pyrrolidin-2-yl)acetic acid
Traditional Namepyrrolidin-2-ylacetic acid
CAS Registry NumberNot Available
SMILES
OC(=O)CC1CCCN1
InChI Identifier
InChI=1S/C6H11NO2/c8-6(9)4-5-2-1-3-7-5/h5,7H,1-4H2,(H,8,9)
InChI KeyADSALMJPJUKESW-UHFFFAOYSA-N
Experimental Spectra
Not Available
Predicted Spectra
Spectrum TypeDescriptionDepositor IDDepositor OrganizationDepositorDeposition DateView
1D NMR13C NMR Spectrum (1D, 25 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 100 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 252 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 1000 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 50 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 200 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 75 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 300 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 101 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 400 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 126 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 500 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 151 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 600 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 176 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 700 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 201 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 800 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 226 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 900 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
Chemical Shift Submissions
Not Available
Species
Species of Origin
Species NameSourceReference
Arnica montanaLOTUS Database
Melampodium divaricatumLOTUS Database
Chemical Taxonomy
Description Belongs to the class of organic compounds known as pyrrolidines. Pyrrolidines are compounds containing a pyrrolidine ring, which is a five-membered saturated aliphatic heterocycle with one nitrogen atom and four carbon atoms.
KingdomOrganic compounds  
Super ClassOrganoheterocyclic compounds  
ClassPyrrolidines  
Sub ClassNot Available
Direct ParentPyrrolidines  
Alternative Parents
Substituents
  • Pyrrolidine
    • 

  • Amino acid or derivatives
    • 

  • Amino acid
    • 

  • Carboxylic acid derivative
    • 

  • Carboxylic acid
    • 

  • Secondary aliphatic amine
    • 

  • Monocarboxylic acid or derivatives
    • 

  • Azacycle
    • 

  • Secondary amine
    • 

  • Amine
    • 

  • Organooxygen compound
    • 

  • Organonitrogen compound
    • 

  • Hydrocarbon derivative
    • 

  • Organic oxide
    • 

  • Organopnictogen compound
    • 

  • Organic oxygen compound
    • 

  • Carbonyl group
    • 

  • Organic nitrogen compound
    • 

  • Aliphatic heteromonocyclic compound
Molecular FrameworkAliphatic heteromonocyclic compounds
External DescriptorsNot Available
Physical Properties
StateNot Available
Experimental Properties
PropertyValueReference
Melting PointNot AvailableNot Available
Boiling PointNot AvailableNot Available
Water SolubilityNot AvailableNot Available
LogPNot AvailableNot Available
Predicted Properties
PropertyValueSource
logP-2.4ALOGPS
logP-2.5ChemAxon
logS-0.03ALOGPS
pKa (Strongest Acidic)3.84ChemAxon
pKa (Strongest Basic)11.26ChemAxon
Physiological Charge0ChemAxon
Hydrogen Acceptor Count3ChemAxon
Hydrogen Donor Count2ChemAxon
Polar Surface Area49.33 ŲChemAxon
Rotatable Bond Count2ChemAxon
Refractivity32.69 m³·mol⁻¹ChemAxon
Polarizability13.48 ųChemAxon
Number of Rings1ChemAxon
BioavailabilityYesChemAxon
Rule of FiveYesChemAxon
Ghose FilterNoChemAxon
Veber's RuleNoChemAxon
MDDR-like RuleNoChemAxon
HMDB IDHMDB0029444  
DrugBank IDNot Available
Phenol Explorer Compound IDNot Available
FoodDB IDFDB000554  
KNApSAcK IDNot Available
Chemspider ID110335  
KEGG Compound IDNot Available
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkNot Available
METLIN IDNot Available
PubChem Compound123784  
PDB IDNot Available
ChEBI IDNot Available
Good Scents IDNot Available
References
General References
  1. LOTUS database [Link]