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Showing NP-Card for (S)-Homostachydrine (NP0047643)

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Record Information
Version2.0
Created at2022-03-17 20:43:34 UTC
Updated at2022-03-17 20:43:34 UTC
NP-MRD IDNP0047643
Secondary Accession NumbersNone
Natural Product Identification
Common Name(S)-Homostachydrine
Description(S)-Homostachydrine, also known as pipecolic acid betaine, belongs to the class of organic compounds known as l-alpha-amino acids. These are alpha amino acids which have the L-configuration of the alpha-carbon atom (S)-Homostachydrine is a moderately acidic compound (based on its pKa). Outside of the human body, (S)-Homostachydrine has been detected, but not quantified in, a few different foods, such as alfalfa, herbs and spices, and pulses. (S)-Homostachydrine is found in Achillea millefolium . (S)-Homostachydrine was first documented in 2012 (PMID: 22208890). This could make (S)-homostachydrine a potential biomarker for the consumption of these foods (PMID: 27006213).
Structure
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MOLSDFPDBSMILESInChI

MOL for NP0047643 ((S)-Homostachydrine)


  Mrv1652312111717312D          

 11 11  0  0  0  0            999 V2000
   -0.2678    1.2267    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   -0.9823   -0.0108    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2678   -0.4232    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.4466   -0.0108    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.4466    0.8142    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2678    2.0517    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9823    2.4642    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.4466    2.4642    0.0000 O   0  5  0  0  0  0  0  0  0  0  0  0
   -0.9823    0.8142    0.0000 N   0  3  0  0  0  0  0  0  0  0  0  0
   -1.7792    0.6007    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1959    1.6111    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
  1  5  1  0  0  0  0
  2  3  1  0  0  0  0
  3  4  1  0  0  0  0
  4  5  1  0  0  0  0
  1  6  1  6  0  0  0
  6  7  2  0  0  0  0
  6  8  1  0  0  0  0
  9 10  1  0  0  0  0
  9 11  1  0  0  0  0
  1  9  1  0  0  0  0
  9  2  1  0  0  0  0
M  CHG  2   8  -1   9   1
M  END
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3D MOL for NP0047643 ((S)-Homostachydrine)

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3D SDF for NP0047643 ((S)-Homostachydrine)

  Mrv1652312111717312D          

 11 11  0  0  0  0            999 V2000
   -0.2678    1.2267    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   -0.9823   -0.0108    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2678   -0.4232    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.4466   -0.0108    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.4466    0.8142    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2678    2.0517    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9823    2.4642    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.4466    2.4642    0.0000 O   0  5  0  0  0  0  0  0  0  0  0  0
   -0.9823    0.8142    0.0000 N   0  3  0  0  0  0  0  0  0  0  0  0
   -1.7792    0.6007    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1959    1.6111    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
  1  5  1  0  0  0  0
  2  3  1  0  0  0  0
  3  4  1  0  0  0  0
  4  5  1  0  0  0  0
  1  6  1  6  0  0  0
  6  7  2  0  0  0  0
  6  8  1  0  0  0  0
  9 10  1  0  0  0  0
  9 11  1  0  0  0  0
  1  9  1  0  0  0  0
  9  2  1  0  0  0  0
M  CHG  2   8  -1   9   1
M  END
> <DATABASE_ID>
NP0047643

> <DATABASE_NAME>
NP-MRD

> <SMILES>
C[N+]1(C)CCCC[C@H]1C([O-])=O

> <INCHI_IDENTIFIER>
InChI=1S/C8H15NO2/c1-9(2)6-4-3-5-7(9)8(10)11/h7H,3-6H2,1-2H3/t7-/m0/s1

> <INCHI_KEY>
XULZWQRXYTVUTE-ZETCQYMHSA-N

> <FORMULA>
C8H15NO2

> <MOLECULAR_WEIGHT>
157.2102

> <EXACT_MASS>
157.110278729

> <JCHEM_ACCEPTOR_COUNT>
2

> <JCHEM_ATOM_COUNT>
26

> <JCHEM_AVERAGE_POLARIZABILITY>
16.915878699414627

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
0

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(2S)-1,1-dimethylpiperidin-1-ium-2-carboxylate

> <ALOGPS_LOGP>
-1.95

> <JCHEM_LOGP>
-3.4318614231384124

> <ALOGPS_LOGS>
-3.19

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
1

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA_STRONGEST_ACIDIC>
2.3852048466810145

> <JCHEM_POLAR_SURFACE_AREA>
40.129999999999995

> <JCHEM_REFRACTIVITY>
64.7107

> <JCHEM_ROTATABLE_BOND_COUNT>
1

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
1.37e-01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
homostachydrine

> <JCHEM_VEBER_RULE>
0

$$$$

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3D-SDF for NP0047643 ((S)-Homostachydrine)
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PDB for NP0047643 ((S)-Homostachydrine)
HEADER    PROTEIN                                 11-DEC-17   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   11-DEC-17         0                                  
HETATM    1  C   UNK     0      -0.500   2.290   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0      -1.834  -0.020   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0      -0.500  -0.790   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       0.834  -0.020   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       0.834   1.520   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0      -0.500   3.830   0.000  0.00  0.00           C+0
HETATM    7  O   UNK     0      -1.834   4.600   0.000  0.00  0.00           O+0
HETATM    8  O   UNK     0       0.834   4.600   0.000  0.00  0.00           O-1
HETATM    9  N   UNK     0      -1.834   1.520   0.000  0.00  0.00           N+1
HETATM   10  C   UNK     0      -3.321   1.121   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0      -2.232   3.007   0.000  0.00  0.00           C+0
CONECT    1    5    6    9                                                  
CONECT    2    3    9                                                       
CONECT    3    2    4                                                       
CONECT    4    3    5                                                       
CONECT    5    1    4                                                       
CONECT    6    1    7    8                                                  
CONECT    7    6                                                            
CONECT    8    6                                                            
CONECT    9   10   11    1    2                                             
CONECT   10    9                                                            
CONECT   11    9                                                            
MASTER        0    0    0    0    0    0    0    0   11    0   22    0
END

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3D PDB for NP0047643 ((S)-Homostachydrine)
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SMILES for NP0047643 ((S)-Homostachydrine)
C[N+]1(C)CCCC[C@H]1C([O-])=O
Download
INCHI for NP0047643 ((S)-Homostachydrine)
InChI=1S/C8H15NO2/c1-9(2)6-4-3-5-7(9)8(10)11/h7H,3-6H2,1-2H3/t7-/m0/s1
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View in JSmol
Synonyms
ValueSource
HomostachydrineHMDB
Pipecolic acid betaineHMDB
S-HomostachydrineHMDB
(2S)-1,1-Dimethylpiperidin-1-ium-2-carboxylic acidGenerator
Chemical FormulaC8H15NO2
Average Mass157.2102 Da
Monoisotopic Mass157.11028 Da
IUPAC Name(2S)-1,1-dimethylpiperidin-1-ium-2-carboxylate
Traditional Namehomostachydrine
CAS Registry Number472-22-0
SMILES
C[N+]1(C)CCCC[C@H]1C([O-])=O
InChI Identifier
InChI=1S/C8H15NO2/c1-9(2)6-4-3-5-7(9)8(10)11/h7H,3-6H2,1-2H3/t7-/m0/s1
InChI KeyXULZWQRXYTVUTE-ZETCQYMHSA-N
Experimental Spectra
Not Available
Predicted Spectra
Not Available
Chemical Shift Submissions
Not Available
Species
Species of Origin
Species NameSourceReference
Achillea millefoliumPlant
Medicago sativaFooDB
Chemical Taxonomy
Description Belongs to the class of organic compounds known as l-alpha-amino acids. These are alpha amino acids which have the L-configuration of the alpha-carbon atom.
KingdomOrganic compounds  
Super ClassOrganic acids and derivatives  
ClassCarboxylic acids and derivatives  
Sub ClassAmino acids, peptides, and analogues  
Direct ParentL-alpha-amino acids  
Alternative Parents
Substituents
  • L-alpha-amino acid
    • 

  • Piperidinecarboxylic acid
    • 

  • Piperidine
    • 

  • Quaternary ammonium salt
    • 

  • Tetraalkylammonium salt
    • 

  • Carboxylic acid salt
    • 

  • Carboxylic acid
    • 

  • Monocarboxylic acid or derivatives
    • 

  • Organoheterocyclic compound
    • 

  • Azacycle
    • 

  • Organic oxide
    • 

  • Organopnictogen compound
    • 

  • Organic oxygen compound
    • 

  • Organooxygen compound
    • 

  • Organonitrogen compound
    • 

  • Amine
    • 

  • Organic salt
    • 

  • Carbonyl group
    • 

  • Organic nitrogen compound
    • 

  • Hydrocarbon derivative
    • 

  • 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-2ALOGPS
logP-3.4ChemAxon
logS-3.2ALOGPS
pKa (Strongest Acidic)2.39ChemAxon
Physiological Charge0ChemAxon
Hydrogen Acceptor Count2ChemAxon
Hydrogen Donor Count0ChemAxon
Polar Surface Area40.13 ŲChemAxon
Rotatable Bond Count1ChemAxon
Refractivity64.71 m³·mol⁻¹ChemAxon
Polarizability16.92 ųChemAxon
Number of Rings1ChemAxon
BioavailabilityYesChemAxon
Rule of FiveYesChemAxon
Ghose FilterNoChemAxon
Veber's RuleNoChemAxon
MDDR-like RuleNoChemAxon
HMDB IDHMDB0033433  
DrugBank IDNot Available
Phenol Explorer Compound IDNot Available
FoodDB IDFDB011471  
KNApSAcK IDC00001367  
Chemspider ID390180  
KEGG Compound IDC08283  
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkNot Available
METLIN IDNot Available
PubChem Compound441447  
PDB IDNot Available
ChEBI IDNot Available
Good Scents IDNot Available
References
General References
  1. Servillo L, Giovane A, Balestrieri ML, Ferrari G, Cautela D, Castaldo D: Occurrence of pipecolic acid and pipecolic acid betaine (homostachydrine) in Citrus genus plants. J Agric Food Chem. 2012 Jan 11;60(1):315-21. doi: 10.1021/jf204286r. Epub 2011 Dec 29. [PubMed:22208890  ] 
  2. Servillo L, Giovane A, Casale R, Cautela D, D'Onofrio N, Balestrieri ML, Castaldo D: Homostachydrine (pipecolic acid betaine) as authentication marker of roasted blends of Coffea arabica and Coffea canephora (Robusta) beans. Food Chem. 2016 Aug 15;205:52-7. doi: 10.1016/j.foodchem.2016.02.154. Epub 2016 Mar 3. [PubMed:27006213  ]