Np mrd loader

Showing NP-Card for (+)-pipecolic acid (NP0212494)

Jump To Section:
IdentificationSpectraBioTaxonomyChemoTaxonomyPhysical propertiesLinksReferencesXML
Record Information
Version2.0
Created at2022-09-05 11:10:53 UTC
Updated at2022-09-05 11:10:53 UTC
NP-MRD IDNP0212494
Secondary Accession NumbersNone
Natural Product Identification
Common Name(+)-pipecolic acid
DescriptionD-Pipecolic acid, also known as 6-carboxypiperidine or (R)-pipecolate, belongs to the class of organic compounds known as d-alpha-amino acids. These are alpha amino acids which have the D-configuration of the alpha-carbon atom. D-Pipecolic acid is a very strong basic compound (based on its pKa). The D-enantiomer of pipecolic acid. Outside of the human body, D-Pipecolic acid has been detected, but not quantified in, milk (cow). (+)-pipecolic acid is found in Acacia excelsa, Lunaria annua and Petalonia fascia. (+)-pipecolic acid was first documented in 1993 (PMID: 8398594). This could make D-pipecolic acid a potential biomarker for the consumption of these foods (PMID: 11719476).
Structure
Thumb
MOL3D MOLSDFPDBSMILESInChI

MOL for NP0212494 ((+)-pipecolic acid)


  Mrv0541 02231220312D          

  9  9  0  0  1  0            999 V2000
   16.0779   -4.5653    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   16.7924   -5.8029    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   18.2214   -4.9778    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   17.5069   -3.7403    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   17.5069   -4.5653    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   18.2214   -3.3278    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   18.9359   -3.7403    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   18.9359   -4.5653    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   16.7924   -4.9778    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
  1  9  1  0  0  0  0
  2  9  2  0  0  0  0
  3  5  1  0  0  0  0
  3  8  1  0  0  0  0
  4  5  1  0  0  0  0
  4  6  1  0  0  0  0
  5  9  1  1  0  0  0
  6  7  1  0  0  0  0
  7  8  1  0  0  0  0
M  END
Download

3D MOL for NP0212494 ((+)-pipecolic acid)

     RDKit          3D

 20 20  0  0  0  0  0  0  0  0999 V2000
    2.6756   -1.2330   -0.0981 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.1210   -0.1251   -0.0024 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.6587    0.8927    0.8196 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.8699    0.1914   -0.7346 C   0  0  1  0  0  0  0  0  0  0  0  0
    0.0789   -1.1742   -0.5372 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7419   -1.0048    0.7249 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9295   -0.1103    0.3289 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2988    1.1796   -0.1546 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.1184    1.1860    0.0299 N   0  0  0  0  0  0  0  0  0  0  0  0
    3.5249    0.7797    1.3016 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.9766    0.3390   -1.7870 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6196   -1.3001   -1.3631 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.7627   -2.0091   -0.4821 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1835   -1.9883    1.0481 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1246   -0.5705    1.5086 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6658    0.0146    1.1040 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3782   -0.5939   -0.5548 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5911    1.4245   -1.1910 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6829    1.9997    0.5181 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.4290    2.1021   -0.4789 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  4  1  0
  3 10  1  0
  4 11  1  6
  5 12  1  0
  5 13  1  0
  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 NP0212494 ((+)-pipecolic acid)


  Mrv0541 02231220312D          

  9  9  0  0  1  0            999 V2000
   16.0779   -4.5653    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   16.7924   -5.8029    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   18.2214   -4.9778    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   17.5069   -3.7403    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   17.5069   -4.5653    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   18.2214   -3.3278    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   18.9359   -3.7403    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   18.9359   -4.5653    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   16.7924   -4.9778    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
  1  9  1  0  0  0  0
  2  9  2  0  0  0  0
  3  5  1  0  0  0  0
  3  8  1  0  0  0  0
  4  5  1  0  0  0  0
  4  6  1  0  0  0  0
  5  9  1  1  0  0  0
  6  7  1  0  0  0  0
  7  8  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0212494

> <DATABASE_NAME>
NP-MRD

> <SMILES>
OC(=O)[C@H]1CCCCN1

> <INCHI_IDENTIFIER>
InChI=1S/C6H11NO2/c8-6(9)5-3-1-2-4-7-5/h5,7H,1-4H2,(H,8,9)/t5-/m1/s1

> <INCHI_KEY>
HXEACLLIILLPRG-RXMQYKEDSA-N

> <FORMULA>
C6H11NO2

> <MOLECULAR_WEIGHT>
129.157

> <EXACT_MASS>
129.078978601

> <JCHEM_ACCEPTOR_COUNT>
3

> <JCHEM_AVERAGE_POLARIZABILITY>
13.474461965926004

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
2

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(2R)-piperidine-2-carboxylic acid

> <ALOGPS_LOGP>
-2.17

> <JCHEM_LOGP>
-2.1239620485400845

> <ALOGPS_LOGS>
0.09

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
1

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA_STRONGEST_ACIDIC>
2.063103444066461

> <JCHEM_PKA_STRONGEST_BASIC>
10.388033490366288

> <JCHEM_POLAR_SURFACE_AREA>
49.33

> <JCHEM_REFRACTIVITY>
32.6653

> <JCHEM_ROTATABLE_BOND_COUNT>
1

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
1.58e+02 g/l

> <JCHEM_TRADITIONAL_IUPAC>
(+)-pipecolic acid

> <JCHEM_VEBER_RULE>
0

$$$$
Download

3D-SDF for NP0212494 ((+)-pipecolic acid)

Download
PDB for NP0212494 ((+)-pipecolic acid)
HEADER    PROTEIN                                 23-FEB-12   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   23-FEB-12         0                                  
HETATM    1  O   UNK     0      30.012  -8.522   0.000  0.00  0.00           O+0
HETATM    2  O   UNK     0      31.346 -10.832   0.000  0.00  0.00           O+0
HETATM    3  N   UNK     0      34.013  -9.292   0.000  0.00  0.00           N+0
HETATM    4  C   UNK     0      32.680  -6.982   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0      32.680  -8.522   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0      34.013  -6.212   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0      35.347  -6.982   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0      35.347  -8.522   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0      31.346  -9.292   0.000  0.00  0.00           C+0
CONECT    1    9                                                            
CONECT    2    9                                                            
CONECT    3    5    8                                                       
CONECT    4    5    6                                                       
CONECT    5    3    4    9                                                  
CONECT    6    4    7                                                       
CONECT    7    6    8                                                       
CONECT    8    3    7                                                       
CONECT    9    1    2    5                                                  
MASTER        0    0    0    0    0    0    0    0    9    0   18    0
END

Download
3D PDB for NP0212494 ((+)-pipecolic acid)
Download
SMILES for NP0212494 ((+)-pipecolic acid)
OC(=O)[C@H]1CCCCN1
Download
INCHI for NP0212494 ((+)-pipecolic acid)
InChI=1S/C6H11NO2/c8-6(9)5-3-1-2-4-7-5/h5,7H,1-4H2,(H,8,9)/t5-/m1/s1
Download
View in JSmol
Synonyms
ValueSource
(R)-Pipecolic acidChEBI
(R)-Piperidine-2-carboxylic acidChEBI
6-CARBOXYPIPERIDINEChEBI
(R)-PipecolateGenerator
(R)-Piperidine-2-carboxylateGenerator
D-PipecolateGenerator
(+)-Pipecolic acidHMDB
(+)-Pipecolinic acidHMDB
(2R)-2-Piperidinecarboxylic acidHMDB
(2R)-Piperidine-2-carboxylic acidHMDB
(R)-()-2-Piperidinecarboxylic acidHMDB
(R)-(+)-Pipecolic acidHMDB
(R)-2-Piperidinecarboxylic acidHMDB
(R)-Pipecolinic acidHMDB
D-(+)- Pipecolic acidHMDB
D-(+)-Pipecolic acidHMDB
D-HomoprolineHMDB
D-Pipecolinic acidHMDB
D-Piperidine-2-carboxylic acidHMDB
Chemical FormulaC6H11NO2
Average Mass129.1570 Da
Monoisotopic Mass129.07898 Da
IUPAC Name(2R)-piperidine-2-carboxylic acid
Traditional Name(+)-pipecolic acid
CAS Registry NumberNot Available
SMILES
OC(=O)[C@H]1CCCCN1
InChI Identifier
InChI=1S/C6H11NO2/c8-6(9)5-3-1-2-4-7-5/h5,7H,1-4H2,(H,8,9)/t5-/m1/s1
InChI KeyHXEACLLIILLPRG-RXMQYKEDSA-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
Acacia excelsaLOTUS Database
Lunaria annuaLOTUS Database
Petalonia fasciaLOTUS Database
Chemical Taxonomy
Description Belongs to the class of organic compounds known as d-alpha-amino acids. These are alpha amino acids which have the D-configuration of the alpha-carbon atom.
KingdomOrganic compounds  
Super ClassOrganic acids and derivatives  
ClassCarboxylic acids and derivatives  
Sub ClassAmino acids, peptides, and analogues  
Direct ParentD-alpha-amino acids  
Alternative Parents
Substituents
  • D-alpha-amino acid
    • 

  • Piperidinecarboxylic acid
    • 

  • Piperidine
    • 

  • Amino acid
    • 

  • Carboxylic acid
    • 

  • Secondary aliphatic amine
    • 

  • Monocarboxylic acid or derivatives
    • 

  • Secondary amine
    • 

  • Organoheterocyclic compound
    • 

  • Azacycle
    • 

  • Organic oxygen compound
    • 

  • Organic nitrogen compound
    • 

  • Organooxygen compound
    • 

  • Organonitrogen compound
    • 

  • Amine
    • 

  • Carbonyl group
    • 

  • Organopnictogen compound
    • 

  • Hydrocarbon derivative
    • 

  • Organic oxide
    • 

  • Aliphatic heteromonocyclic compound
Molecular FrameworkAliphatic heteromonocyclic compounds
External Descriptors
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-2.2ALOGPS
logP-2.1ChemAxon
logS0.09ALOGPS
pKa (Strongest Acidic)2.06ChemAxon
pKa (Strongest Basic)10.39ChemAxon
Physiological Charge0ChemAxon
Hydrogen Acceptor Count3ChemAxon
Hydrogen Donor Count2ChemAxon
Polar Surface Area49.33 ŲChemAxon
Rotatable Bond Count1ChemAxon
Refractivity32.67 m³·mol⁻¹ChemAxon
Polarizability13.47 ųChemAxon
Number of Rings1ChemAxon
BioavailabilityYesChemAxon
Rule of FiveYesChemAxon
Ghose FilterNoChemAxon
Veber's RuleNoChemAxon
MDDR-like RuleNoChemAxon
HMDB IDHMDB0005960  
DrugBank IDNot Available
Phenol Explorer Compound IDNot Available
FoodDB IDFDB023791  
KNApSAcK IDNot Available
Chemspider ID643442  
KEGG Compound IDNot Available
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkPipecolic acid  
METLIN IDNot Available
PubChem Compound736316  
PDB IDNot Available
ChEBI ID41582  
Good Scents IDNot Available
References
General References
  1. Rashed MS, Al-Ahaidib LY, Aboul-Enein HY, Al-Amoudi M, Jacob M: Determination of L-pipecolic acid in plasma using chiral liquid chromatography-electrospray tandem mass spectrometry. Clin Chem. 2001 Dec;47(12):2124-30. [PubMed:11719476  ] 
  2. Armstrong DW, Gasper M, Lee SH, Zukowski J, Ercal N: D-amino acid levels in human physiological fluids. Chirality. 1993;5(5):375-8. doi: 10.1002/chir.530050519. [PubMed:8398594  ] 
  3. LOTUS database [Link]