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Showing NP-Card for 5-hydroxypipecolic acid (NP0241061)

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Record Information
Version2.0
Created at2022-09-07 01:02:24 UTC
Updated at2022-09-07 01:02:24 UTC
NP-MRD IDNP0241061
Secondary Accession NumbersNone
Natural Product Identification
Common Name5-hydroxypipecolic acid
DescriptionL-trans-5-Hydroxy-2-piperidinecarboxylic acid belongs to the class of organic compounds known as alpha amino acids. These are amino acids in which the amino group is attached to the carbon atom immediately adjacent to the carboxylate group (alpha carbon). L-trans-5-Hydroxy-2-piperidinecarboxylic acid is a very strong basic compound (based on its pKa). Outside of the human body, L-trans-5-Hydroxy-2-piperidinecarboxylic acid has been detected, but not quantified in, fruits. This could make L-trans-5-hydroxy-2-piperidinecarboxylic acid a potential biomarker for the consumption of these foods. 5-hydroxypipecolic acid is found in Byrsonima crassifolia, Calliandra angustifolia, Leucaena leucocephala, Morus alba and Salix smithiana. 5-hydroxypipecolic acid was first documented in 1956 (PMID: 13324096). A piperidinemonocarboxylic acid that is pipecolic acid with a hydroxy substituent at position 5 (PMID: 11065274) (PMID: 3661981).
Structure
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MOL3D MOLSDFPDBSMILESInChI

MOL for NP0241061 (5-hydroxypipecolic acid)


  Mrv0541 02241210422D          

 10 10  0  0  0  0            999 V2000
   -0.7015   -0.6185    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7015    0.2065    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.0409    0.6185    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7015    0.2065    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7015   -0.6185    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0409   -1.0314    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0409   -1.8572    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7015    1.8572    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.0409    1.4443    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7015    1.8572    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  1  6  1  0  0  0  0
  2  3  1  0  0  0  0
  3  4  1  0  0  0  0
  3  9  1  0  0  0  0
  4  5  1  0  0  0  0
  5  6  1  0  0  0  0
  6  7  1  0  0  0  0
  8  9  2  0  0  0  0
  9 10  1  0  0  0  0
M  END
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3D MOL for NP0241061 (5-hydroxypipecolic acid)

     RDKit          3D

 21 21  0  0  0  0  0  0  0  0999 V2000
    2.8427    0.9735   -0.5330 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.3697   -0.0859   -0.0505 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.1561   -1.2061   -0.0403 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.9831   -0.0496    0.4780 C   0  0  2  0  0  0  0  0  0  0  0  0
    0.1671   -1.0223   -0.3278 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2914   -0.9408   -0.1127 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8281    0.3069    0.4562 C   0  0  2  0  0  0  0  0  0  0  0  0
   -2.5723    1.0363   -0.5003 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8559    1.2372    1.0716 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.3983    1.2450    0.3403 N   0  0  0  0  0  0  0  0  0  0  0  0
    4.1447   -1.0985    0.1449 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.0252   -0.4070    1.5250 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.4593   -0.8724   -1.3990 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.5691   -2.0478   -0.0768 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7938   -1.1118   -1.1117 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6023   -1.8416    0.4943 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5908    0.0400    1.2464 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6335    0.5674   -1.3491 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2536    2.2751    1.0799 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6974    0.9633    2.1419 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.0037    2.0389    0.5514 H   0  0  0  0  0  0  0  0  0  0  0  0
  8  7  1  0
  7  6  1  0
  6  5  1  0
  5  4  1  0
  4 10  1  0
 10  9  1  0
  4  2  1  0
  2  3  1  0
  2  1  2  0
  9  7  1  0
  8 18  1  0
  7 17  1  1
  6 15  1  0
  6 16  1  0
  5 13  1  0
  5 14  1  0
  4 12  1  1
 10 21  1  0
  9 19  1  0
  9 20  1  0
  3 11  1  0
M  END
Download

3D SDF for NP0241061 (5-hydroxypipecolic acid)


  Mrv0541 02241210422D          

 10 10  0  0  0  0            999 V2000
   -0.7015   -0.6185    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7015    0.2065    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.0409    0.6185    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7015    0.2065    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7015   -0.6185    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0409   -1.0314    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0409   -1.8572    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7015    1.8572    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.0409    1.4443    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7015    1.8572    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  1  6  1  0  0  0  0
  2  3  1  0  0  0  0
  3  4  1  0  0  0  0
  3  9  1  0  0  0  0
  4  5  1  0  0  0  0
  5  6  1  0  0  0  0
  6  7  1  0  0  0  0
  8  9  2  0  0  0  0
  9 10  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0241061

> <DATABASE_NAME>
NP-MRD

> <SMILES>
OC1CCC(NC1)C(O)=O

> <INCHI_IDENTIFIER>
InChI=1S/C6H11NO3/c8-4-1-2-5(6(9)10)7-3-4/h4-5,7-8H,1-3H2,(H,9,10)

> <INCHI_KEY>
RKEYKDXXZCICFZ-UHFFFAOYSA-N

> <FORMULA>
C6H11NO3

> <MOLECULAR_WEIGHT>
145.1564

> <EXACT_MASS>
145.073893223

> <JCHEM_ACCEPTOR_COUNT>
4

> <JCHEM_AVERAGE_POLARIZABILITY>
14.380955833404975

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
3

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
5-hydroxypiperidine-2-carboxylic acid

> <ALOGPS_LOGP>
-2.97

> <JCHEM_LOGP>
-3.1987333114645162

> <ALOGPS_LOGS>
0.25

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
1

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
14.89594218630327

> <JCHEM_PKA_STRONGEST_ACIDIC>
1.7813913645023671

> <JCHEM_PKA_STRONGEST_BASIC>
9.787525750840254

> <JCHEM_POLAR_SURFACE_AREA>
69.56

> <JCHEM_REFRACTIVITY>
34.0268

> <JCHEM_ROTATABLE_BOND_COUNT>
1

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
2.58e+02 g/l

> <JCHEM_TRADITIONAL_IUPAC>
5-hydroxypiperidine-2-carboxylic acid

> <JCHEM_VEBER_RULE>
0

$$$$
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3D-SDF for NP0241061 (5-hydroxypipecolic acid)

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PDB for NP0241061 (5-hydroxypipecolic acid)
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  C   UNK     0      -1.309  -1.155   0.000  0.00  0.00           C+0
HETATM    2  N   UNK     0      -1.309   0.385   0.000  0.00  0.00           N+0
HETATM    3  C   UNK     0       0.076   1.155   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       1.309   0.385   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       1.309  -1.155   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       0.076  -1.925   0.000  0.00  0.00           C+0
HETATM    7  O   UNK     0       0.076  -3.467   0.000  0.00  0.00           O+0
HETATM    8  O   UNK     0      -1.309   3.467   0.000  0.00  0.00           O+0
HETATM    9  C   UNK     0       0.076   2.696   0.000  0.00  0.00           C+0
HETATM   10  O   UNK     0       1.309   3.467   0.000  0.00  0.00           O+0
CONECT    1    2    6                                                       
CONECT    2    1    3                                                       
CONECT    3    2    4    9                                                  
CONECT    4    3    5                                                       
CONECT    5    4    6                                                       
CONECT    6    1    5    7                                                  
CONECT    7    6                                                            
CONECT    8    9                                                            
CONECT    9    3    8   10                                                  
CONECT   10    9                                                            
MASTER        0    0    0    0    0    0    0    0   10    0   20    0
END

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3D PDB for NP0241061 (5-hydroxypipecolic acid)
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SMILES for NP0241061 (5-hydroxypipecolic acid)
OC1CCC(NC1)C(O)=O
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INCHI for NP0241061 (5-hydroxypipecolic acid)
InChI=1S/C6H11NO3/c8-4-1-2-5(6(9)10)7-3-4/h4-5,7-8H,1-3H2,(H,9,10)
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View in JSmol
Synonyms
ValueSource
L-trans-5-Hydroxy-2-piperidinecarboxylateGenerator
L-trans-5-Hydroxypipecolic acidHMDB
5-Hydroxypipecolic acid, cis-isomerHMDB
5-Hydroxypipecolic acid, ion (1-)-cis-isomerHMDB
5-Hydroxypipecolic acid, trans-isomerHMDB
5-HydroxypipecolateGenerator
5-Hydroxypipecolic acidMeSH
Chemical FormulaC6H11NO3
Average Mass145.1564 Da
Monoisotopic Mass145.07389 Da
IUPAC Name5-hydroxypiperidine-2-carboxylic acid
Traditional Name5-hydroxypiperidine-2-carboxylic acid
CAS Registry NumberNot Available
SMILES
OC1CCC(NC1)C(O)=O
InChI Identifier
InChI=1S/C6H11NO3/c8-4-1-2-5(6(9)10)7-3-4/h4-5,7-8H,1-3H2,(H,9,10)
InChI KeyRKEYKDXXZCICFZ-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
Byrsonima crassifoliaLOTUS Database
Calliandra angustifoliaLOTUS Database
Leucaena glaucaLOTUS Database
Morus albaLOTUS Database
Salix smithianaLOTUS Database
Chemical Taxonomy
Description Belongs to the class of organic compounds known as alpha amino acids. These are amino acids in which the amino group is attached to the carbon atom immediately adjacent to the carboxylate group (alpha carbon).
KingdomOrganic compounds  
Super ClassOrganic acids and derivatives  
ClassCarboxylic acids and derivatives  
Sub ClassAmino acids, peptides, and analogues  
Direct ParentAlpha amino acids  
Alternative Parents
Substituents
  • Alpha-amino acid
    • 

  • Piperidinecarboxylic acid
    • 

  • Piperidine
    • 

  • 1,2-aminoalcohol
    • 

  • Amino acid
    • 

  • Secondary alcohol
    • 

  • Carboxylic acid
    • 

  • Secondary aliphatic amine
    • 

  • Monocarboxylic acid or derivatives
    • 

  • Secondary amine
    • 

  • Organoheterocyclic compound
    • 

  • Azacycle
    • 

  • Organooxygen compound
    • 

  • Organonitrogen compound
    • 

  • Alcohol
    • 

  • Organic nitrogen compound
    • 

  • Organopnictogen compound
    • 

  • Organic oxide
    • 

  • Hydrocarbon derivative
    • 

  • Organic oxygen compound
    • 

  • Amine
    • 

  • Carbonyl group
    • 

  • 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-3ALOGPS
logP-3.2ChemAxon
logS0.25ALOGPS
pKa (Strongest Acidic)1.78ChemAxon
pKa (Strongest Basic)9.79ChemAxon
Physiological Charge0ChemAxon
Hydrogen Acceptor Count4ChemAxon
Hydrogen Donor Count3ChemAxon
Polar Surface Area69.56 ŲChemAxon
Rotatable Bond Count1ChemAxon
Refractivity34.03 m³·mol⁻¹ChemAxon
Polarizability14.38 ųChemAxon
Number of Rings1ChemAxon
BioavailabilityYesChemAxon
Rule of FiveYesChemAxon
Ghose FilterNoChemAxon
Veber's RuleNoChemAxon
MDDR-like RuleNoChemAxon
HMDB IDHMDB0029426  
DrugBank IDNot Available
Phenol Explorer Compound IDNot Available
FoodDB IDFDB000527  
KNApSAcK IDNot Available
Chemspider ID133730  
KEGG Compound IDNot Available
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkNot Available
METLIN IDNot Available
PubChem Compound151730  
PDB IDNot Available
ChEBI ID74048  
Good Scents IDNot Available
References
General References
  1. El Khalabi R, El Hallaoui A, Ouazzani F, Elachqar A, Atmani A, Roumestant ML, Viallefont P, Martinez J: Synthesis of phosphonic analogues of 4-hydroxyproline and 5-hydroxypipecolic acid. Prep Biochem Biotechnol. 2000 Nov;30(4):295-304. doi: 10.1080/10826060008544968. [PubMed:11065274  ] 
  2. COHEN LA, IRREVERRE F, PIEZ KA, WITKOP B, WOLFF HL: Synthesis of 5-hydroxypipecolic acid and separation of its diastereoisomers. Science. 1956 May 11;123(3202):842-3. doi: 10.1126/science.123.3202.842. [PubMed:13324096  ] 
  3. Miyata T, Okano Y, Nagata-Tanoue J, Ijima-Miyamura S, Iwamura H, Takahama K, Hitoshi T: Identification and quantification of 5-hydroxypipecolic acid and hydroxyproline in mammalian brain and blood by selected ion monitoring. Anal Biochem. 1987 Jun;163(2):303-8. doi: 10.1016/0003-2697(87)90228-4. [PubMed:3661981  ] 
  4. LOTUS database [Link]