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Showing metabocard for D-Pipecolic acid (HMDB0005960)

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Record Information
Version5.0
StatusDetected and Quantified
Creation Date2007-04-12 18:42:28 UTC
Update Date2021-10-13 04:47:45 UTC
HMDB IDHMDB0005960
Secondary Accession Numbers
  • HMDB0062767
  • HMDB05960
  • HMDB62767
Metabolite Identification
Common NameD-Pipecolic acid
DescriptionD-Pipecolic acid is a normal human metabolite found in human biofluids. Normal adults excrete pipecolic acid primarily as the D-enantiomer even though it is present in the blood stream mainly as the L-enantiomer. It is believed that D-pipecolic acid originates from the metabolism of intestinal bacteria and from dietary sources. High levels of D-pipecolic acid are not found in plasma, but they are increased in urine of patients with chronic liver disease (PMID: 6501504 , 6490790 , 11719476 , 8398594 ).
Structure
Data?1582752369
MOL3D MOLSDF3D SDFPDB3D PDBSMILESInChI

MOL for HMDB0005960 (D-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
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3D MOL for HMDB0005960 (D-Pipecolic acid)

HMDB0005960
     RDKit          3D
D-Pipecolic acid
 20 20  0  0  0  0  0  0  0  0999 V2000
    1.6881    1.7407    1.3809 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.8312    0.7214    0.6705 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8667   -0.1470    0.9548 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.9374    0.4012   -0.4666 C   0  0  1  0  0  0  0  0  0  0  0  0
    0.4896   -1.0192   -0.3643 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8203   -1.2370    0.2867 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8487   -0.1911    0.0174 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2584    1.2048    0.1255 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0927    1.3571   -0.6726 N   0  0  0  0  0  0  0  0  0  0  0  0
    3.2440   -0.8151    0.2802 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.6073    0.4557   -1.3785 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.2628   -1.5809    0.2363 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.5069   -1.5370   -1.3665 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7080   -1.4072    1.3936 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2431   -2.2150   -0.0898 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6461   -0.2616    0.7734 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3214   -0.3163   -0.9814 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0461    1.8898   -0.2958 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1354    1.4887    1.1761 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3140    1.4680   -1.6798 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  2  0
  2  3  1  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
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3D SDF for HMDB0005960 (D-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>
HMDB0005960

> <DATABASE_NAME>
hmdb

> <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

$$$$
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3D-SDF for HMDB0005960 (D-Pipecolic acid)

HMDB0005960
     RDKit          3D
D-Pipecolic acid
 20 20  0  0  0  0  0  0  0  0999 V2000
    1.6881    1.7407    1.3809 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.8312    0.7214    0.6705 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8667   -0.1470    0.9548 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.9374    0.4012   -0.4666 C   0  0  1  0  0  0  0  0  0  0  0  0
    0.4896   -1.0192   -0.3643 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8203   -1.2370    0.2867 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8487   -0.1911    0.0174 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2584    1.2048    0.1255 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0927    1.3571   -0.6726 N   0  0  0  0  0  0  0  0  0  0  0  0
    3.2440   -0.8151    0.2802 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.6073    0.4557   -1.3785 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.2628   -1.5809    0.2363 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.5069   -1.5370   -1.3665 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7080   -1.4072    1.3936 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2431   -2.2150   -0.0898 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6461   -0.2616    0.7734 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3214   -0.3163   -0.9814 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0461    1.8898   -0.2958 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1354    1.4887    1.1761 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3140    1.4680   -1.6798 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  2  0
  2  3  1  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
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PDB for HMDB0005960 (D-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
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3D PDB for HMDB0005960 (D-Pipecolic acid)

COMPND    HMDB0005960
HETATM    1  O1  UNL     1       1.688   1.741   1.381  1.00  0.00           O  
HETATM    2  C1  UNL     1       1.831   0.721   0.671  1.00  0.00           C  
HETATM    3  O2  UNL     1       2.867  -0.147   0.955  1.00  0.00           O  
HETATM    4  C2  UNL     1       0.937   0.401  -0.467  1.00  0.00           C  
HETATM    5  C3  UNL     1       0.490  -1.019  -0.364  1.00  0.00           C  
HETATM    6  C4  UNL     1      -0.820  -1.237   0.287  1.00  0.00           C  
HETATM    7  C5  UNL     1      -1.849  -0.191   0.017  1.00  0.00           C  
HETATM    8  C6  UNL     1      -1.258   1.205   0.126  1.00  0.00           C  
HETATM    9  N1  UNL     1      -0.093   1.357  -0.673  1.00  0.00           N  
HETATM   10  H1  UNL     1       3.244  -0.815   0.280  1.00  0.00           H  
HETATM   11  H2  UNL     1       1.607   0.456  -1.379  1.00  0.00           H  
HETATM   12  H3  UNL     1       1.263  -1.581   0.236  1.00  0.00           H  
HETATM   13  H4  UNL     1       0.507  -1.537  -1.366  1.00  0.00           H  
HETATM   14  H5  UNL     1      -0.708  -1.407   1.394  1.00  0.00           H  
HETATM   15  H6  UNL     1      -1.243  -2.215  -0.090  1.00  0.00           H  
HETATM   16  H7  UNL     1      -2.646  -0.262   0.773  1.00  0.00           H  
HETATM   17  H8  UNL     1      -2.321  -0.316  -0.981  1.00  0.00           H  
HETATM   18  H9  UNL     1      -2.046   1.890  -0.296  1.00  0.00           H  
HETATM   19  H10 UNL     1      -1.135   1.489   1.176  1.00  0.00           H  
HETATM   20  H11 UNL     1      -0.314   1.468  -1.680  1.00  0.00           H  
CONECT    1    2    2
CONECT    2    3    4
CONECT    3   10
CONECT    4    5    9   11
CONECT    5    6   12   13
CONECT    6    7   14   15
CONECT    7    8   16   17
CONECT    8    9   18   19
CONECT    9   20
END
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SMILES for HMDB0005960 (D-Pipecolic acid)

OC(=O)[C@H]1CCCCN1
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INCHI for HMDB0005960 (D-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
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View in JSmolView NMR AssignmentsView Stereo Labels
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 Molecular Weight129.157
Monoisotopic Molecular Weight129.078978601
IUPAC Name(2R)-piperidine-2-carboxylic acid
Traditional Name(+)-pipecolic acid
CAS Registry Number1723-00-8
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
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
Ontology
Physiological effect
Health effect
Disposition
Biological locationSource
ProcessNot Available
Role
Industrial application
Physical Properties
StateSolid
Experimental Molecular Properties
PropertyValueReference
Melting Point266 - 268 °CNot Available
Boiling Point265.80 °C. @ 760.00 mm Hg (est)The Good Scents Company Information System
Water Solubility74060 mg/L @ 25 °C (est)The Good Scents Company Information System
LogPNot AvailableNot Available
Experimental Chromatographic PropertiesNot Available
Predicted Molecular Properties
PropertyValueSource
Water Solubility158 g/LALOGPS
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
Predicted Chromatographic Properties

Predicted Collision Cross Sections

PredictorAdduct TypeCCS Value (Å2)Reference
DarkChem[M+H]+128.24531661259
DarkChem[M-H]-122.87731661259
DeepCCS[M+H]+125.5530932474
DeepCCS[M-H]-122.12230932474
DeepCCS[M-2H]-159.12630932474
DeepCCS[M+Na]+134.64130932474
AllCCS[M+H]+127.832859911
AllCCS[M+H-H2O]+123.032859911
AllCCS[M+NH4]+132.232859911
AllCCS[M+Na]+133.532859911
AllCCS[M-H]-125.332859911
AllCCS[M+Na-2H]-127.432859911
AllCCS[M+HCOO]-129.732859911

Predicted Retention Times

Underivatized

Chromatographic MethodRetention TimeReference
Measured using a Waters Acquity ultraperformance liquid chromatography (UPLC) ethylene-bridged hybrid (BEH) C18 column (100 mm × 2.1 mm; 1.7 μmparticle diameter). Predicted by Afia on May 17, 2022. Predicted by Afia on May 17, 2022.1.09 minutes32390414
Measured using a Waters Acquity ultraperformance liquid chromatography (UPLC) ethylene-bridged hybrid (BEH) C18 column (100 mm × 2.1 mm; 1.7 μmparticle diameter). Predicted by Afia on May 17, 2022. Predicted by Afia on May 17, 2022.-5.51 minutes32390414
Predicted by Siyang on May 30, 20228.8951 minutes33406817
Predicted by Siyang using ReTip algorithm on June 8, 20225.99 minutes32390414
AjsUoB = Accucore 150 Amide HILIC with 10mM Ammonium Formate, 0.1% Formic Acid351.7 seconds40023050
Fem_Long = Waters ACQUITY UPLC HSS T3 C18 with Water:MeOH and 0.1% Formic Acid514.8 seconds40023050
Fem_Lipids = Ascentis Express C18 with (60:40 water:ACN):(90:10 IPA:ACN) and 10mM NH4COOH + 0.1% Formic Acid290.8 seconds40023050
Life_Old = Waters ACQUITY UPLC BEH C18 with Water:(20:80 acetone:ACN) and 0.1% Formic Acid65.5 seconds40023050
Life_New = RP Waters ACQUITY UPLC HSS T3 C18 with Water:(30:70 MeOH:ACN) and 0.1% Formic Acid176.6 seconds40023050
RIKEN = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid59.6 seconds40023050
Eawag_XBridgeC18 = XBridge C18 3.5u 2.1x50 mm with Water:MeOH and 0.1% Formic Acid260.4 seconds40023050
BfG_NTS_RP1 =Agilent Zorbax Eclipse Plus C18 (2.1 mm x 150 mm, 3.5 um) with Water:ACN and 0.1% Formic Acid235.8 seconds40023050
HILIC_BDD_2 = Merck SeQuant ZIC-HILIC with ACN(0.1% formic acid):water(16 mM ammonium formate)756.3 seconds40023050
UniToyama_Atlantis = RP Waters Atlantis T3 (2.1 x 150 mm, 5 um) with ACN:Water and 0.1% Formic Acid582.2 seconds40023050
BDD_C18 = Hypersil Gold 1.9µm C18 with Water:ACN and 0.1% Formic Acid51.4 seconds40023050
UFZ_Phenomenex = Kinetex Core-Shell C18 2.6 um, 3.0 x 100 mm, Phenomenex with Water:MeOH and 0.1% Formic Acid677.7 seconds40023050
SNU_RIKEN_POS = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid170.4 seconds40023050
RPMMFDA = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid197.4 seconds40023050
MTBLS87 = Merck SeQuant ZIC-pHILIC column with ACN:Water and :ammonium carbonate858.9 seconds40023050
KI_GIAR_zic_HILIC_pH2_7 = Merck SeQuant ZIC-HILIC with ACN:Water and 0.1% FA433.1 seconds40023050
Meister zic-pHILIC pH9.3 = Merck SeQuant ZIC-pHILIC column with ACN:Water 5mM NH4Ac pH9.3 and 5mM ammonium acetate in water309.9 seconds40023050

Predicted Kovats Retention Indices

Underivatized

MetaboliteSMILESKovats RI ValueColumn TypeReference
D-Pipecolic acidOC(=O)[C@H]1CCCCN11900.4Standard polar33892256
D-Pipecolic acidOC(=O)[C@H]1CCCCN11157.5Standard non polar33892256
D-Pipecolic acidOC(=O)[C@H]1CCCCN11246.2Semi standard non polar33892256

Derivatized

Derivative Name / StructureSMILESKovats RI ValueColumn TypeReference
D-Pipecolic acid,1TMS,isomer #1C[Si](C)(C)OC(=O)[C@H]1CCCCN11261.2Semi standard non polar33892256
D-Pipecolic acid,1TMS,isomer #2C[Si](C)(C)N1CCCC[C@@H]1C(=O)O1355.4Semi standard non polar33892256
D-Pipecolic acid,2TMS,isomer #1C[Si](C)(C)OC(=O)[C@H]1CCCCN1[Si](C)(C)C1344.3Semi standard non polar33892256
D-Pipecolic acid,2TMS,isomer #1C[Si](C)(C)OC(=O)[C@H]1CCCCN1[Si](C)(C)C1406.9Standard non polar33892256
D-Pipecolic acid,2TMS,isomer #1C[Si](C)(C)OC(=O)[C@H]1CCCCN1[Si](C)(C)C1703.7Standard polar33892256
D-Pipecolic acid,1TBDMS,isomer #1CC(C)(C)[Si](C)(C)OC(=O)[C@H]1CCCCN11500.1Semi standard non polar33892256
D-Pipecolic acid,1TBDMS,isomer #2CC(C)(C)[Si](C)(C)N1CCCC[C@@H]1C(=O)O1575.4Semi standard non polar33892256
D-Pipecolic acid,2TBDMS,isomer #1CC(C)(C)[Si](C)(C)OC(=O)[C@H]1CCCCN1[Si](C)(C)C(C)(C)C1828.0Semi standard non polar33892256
D-Pipecolic acid,2TBDMS,isomer #1CC(C)(C)[Si](C)(C)OC(=O)[C@H]1CCCCN1[Si](C)(C)C(C)(C)C1828.8Standard non polar33892256
D-Pipecolic acid,2TBDMS,isomer #1CC(C)(C)[Si](C)(C)OC(=O)[C@H]1CCCCN1[Si](C)(C)C(C)(C)C1961.8Standard polar33892256
Spectra

GC-MS Spectra

Spectrum TypeDescriptionSplash KeyDeposition DateSourceView
Predicted GC-MSPredicted GC-MS Spectrum - D-Pipecolic acid GC-MS (Non-derivatized) - 70eV, Positivesplash10-001i-9100000000-335cf7f41fca5cbc84cf2017-09-01Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - D-Pipecolic acid GC-MS (1 TMS) - 70eV, Positivesplash10-001i-9100000000-4611bf819d3b9d4fd0622017-10-06Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - D-Pipecolic acid GC-MS (Non-derivatized) - 70eV, PositiveNot Available2021-10-12Wishart LabView Spectrum

MS/MS Spectra

Spectrum TypeDescriptionSplash KeyDeposition DateSourceView
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - D-Pipecolic acid 10V, Positive-QTOFsplash10-001i-3900000000-bf71d20a7c8e71d335e52017-09-01Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - D-Pipecolic acid 20V, Positive-QTOFsplash10-001i-9400000000-fa70645b026293d659de2017-09-01Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - D-Pipecolic acid 40V, Positive-QTOFsplash10-053u-9000000000-f849cc3c4b11bc7d4de72017-09-01Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - D-Pipecolic acid 10V, Negative-QTOFsplash10-004i-2900000000-bf800b5cd197887a11d52017-09-01Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - D-Pipecolic acid 20V, Negative-QTOFsplash10-003r-7900000000-8a0e9f51df40067408632017-09-01Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - D-Pipecolic acid 40V, Negative-QTOFsplash10-001i-9000000000-effc196b5c15971f985a2017-09-01Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - D-Pipecolic acid 10V, Positive-QTOFsplash10-001i-9300000000-cb8df30f7267d610fd8d2021-09-23Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - D-Pipecolic acid 20V, Positive-QTOFsplash10-001i-9000000000-72c8691eb15dce6e0abb2021-09-23Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - D-Pipecolic acid 40V, Positive-QTOFsplash10-053r-9000000000-c7623c5058ad6c879ec32021-09-23Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - D-Pipecolic acid 10V, Negative-QTOFsplash10-004i-0900000000-b487cd2a72f17977a8cd2021-09-24Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - D-Pipecolic acid 20V, Negative-QTOFsplash10-01t9-1900000000-83b59287dc6d3e7263262021-09-24Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - D-Pipecolic acid 40V, Negative-QTOFsplash10-0036-9200000000-3ca813e7348e686ed9222021-09-24Wishart LabView Spectrum

NMR Spectra

Spectrum TypeDescriptionDeposition DateSourceView
Predicted 1D NMR13C NMR Spectrum (1D, 100 MHz, D2O, predicted)2021-09-24Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 100 MHz, D2O, predicted)2021-09-24Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 1000 MHz, D2O, predicted)2021-09-24Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 1000 MHz, D2O, predicted)2021-09-24Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 200 MHz, D2O, predicted)2021-09-24Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 200 MHz, D2O, predicted)2021-09-24Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 300 MHz, D2O, predicted)2021-09-24Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 300 MHz, D2O, predicted)2021-09-24Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 400 MHz, D2O, predicted)2021-09-24Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 400 MHz, D2O, predicted)2021-09-24Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 500 MHz, D2O, predicted)2021-09-24Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 500 MHz, D2O, predicted)2021-09-24Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 600 MHz, D2O, predicted)2021-09-24Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 600 MHz, D2O, predicted)2021-09-24Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 700 MHz, D2O, predicted)2021-09-24Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 700 MHz, D2O, predicted)2021-09-24Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 800 MHz, D2O, predicted)2021-09-24Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 800 MHz, D2O, predicted)2021-09-24Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 900 MHz, D2O, predicted)2021-09-24Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 900 MHz, D2O, predicted)2021-09-24Wishart LabView Spectrum
Biological Properties
Cellular LocationsNot Available
Biospecimen Locations
  • Blood
Tissue LocationsNot Available
Pathways
Normal Concentrations
BiospecimenStatusValueAgeSexConditionReferenceDetails
BloodDetected and Quantified0.11 +/- 0.10 uMAdult (>18 years old)BothNormal details
Abnormal Concentrations
BiospecimenStatusValueAgeSexConditionReferenceDetails
BloodDetected and Quantified0.16 +/- 0.14 uMAdult (>18 years old)BothUremia details
BloodDetected and Quantified1.58 +/- 0.50 uMAdult (>18 years old)Both
Hepatic Encephalopathy		 details
Associated Disorders and Diseases
Disease References
Uremia
  1. Fujita T, Amuro Y, Hada T, Higashino K: Plasma levels of pipecolic acid, both L- and D-enantiomers, in patients with chronic liver diseases, especially hepatic encephalopathy. Clin Chim Acta. 1999 Sep;287(1-2):99-109. [PubMed:10509899 ]
Hepatic encephalopathy
  1. Fujita T, Amuro Y, Hada T, Higashino K: Plasma levels of pipecolic acid, both L- and D-enantiomers, in patients with chronic liver diseases, especially hepatic encephalopathy. Clin Chim Acta. 1999 Sep;287(1-2):99-109. [PubMed:10509899 ]
Associated OMIM IDsNone
DrugBank IDNot Available
Phenol Explorer Compound IDNot Available
FooDB 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
Food Biomarker OntologyNot Available
VMH IDNot Available
MarkerDB IDMDB00000476
Good Scents IDrw1234121
References
Synthesis ReferenceFadel, Antoine; Lahrache, Nabil. An efficient synthesis of enantiomerically pure (R)-pipecolic acid, (S)-proline, and their N-alkylated derivatives. Journal of Organic Chemistry (2007), 72(5), 1780-1784.
Material Safety Data Sheet (MSDS)Download (PDF)
General References
  1. Lam S: Stereoselective analysis of D and L dansyl amino acids as the mixed chelate copper(II) complexes by HPLC. J Chromatogr Sci. 1984 Sep;22(9):416-23. [PubMed:6490790 ]
  2. Lam S, Azumaya H, Karmen A: High-performance liquid chromatography of amino acids in urine and cerebrospinal fluid. J Chromatogr. 1984 Oct 19;302:21-9. [PubMed:6501504 ]
  3. 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 ]
  4. Armstrong DW, Gasper M, Lee SH, Zukowski J, Ercal N: D-amino acid levels in human physiological fluids. Chirality. 1993;5(5):375-8. [PubMed:8398594 ]