Hmdb loader

Showing metabocard for (S)-Homostachydrine (HMDB0033433)

Jump To Section:
IdentificationTaxonomyOntologyPhysical propertiesSpectraBiological propertiesConcentrationsLinksReferencesXML
Record Information
Version5.0
StatusDetected but not Quantified
Creation Date2012-09-11 18:10:03 UTC
Update Date2023-02-21 17:23:18 UTC
HMDB IDHMDB0033433
Secondary Accession Numbers
  • HMDB33433
Metabolite Identification
Common Name(S)-Homostachydrine
Description(S)-Homostachydrine (also known as pipecolic acid betaine or homostachydrine) can be found in green coffee beans of Robusta and Arabica species (PMID: 27006213 ). (S)-Homostachydrine content is unaffected by coffee bean roasting treatment because of its remarkable heat stability. This makes it a good candidate marker for determining the content of Robusta and Arabica species in roasted coffee blends. (S)-Homostachydrine is also a potential marker of coffee consumption as it can be found in both human serum and human urine. It is also found in alfalfa seeds and leaves. More specifically, (S)-homostachydrine can be isolated from the seeds of Medicago sativa (alfalfa) as well as from Achillea millefolium (yarrow). (S)-Homostachydrine is also found in the fruits, seeds, and leaves of orange, lemon, and bergamot (PMID: 22208890 ).
Structure
Data?1677000198
MOL3D MOLSDF3D SDFPDB3D PDBSMILESInChI

MOL for HMDB0033433 ((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
Download

3D MOL for HMDB0033433 ((S)-Homostachydrine)

HMDB0033433
     RDKit          3D
(S)-Homostachydrine
 26 26  0  0  0  0  0  0  0  0999 V2000
    1.7932   -0.1878   -1.1139 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.6429   -0.3235   -0.2065 N   0  0  0  0  0  4  0  0  0  0  0  0
    1.1113   -0.9622    0.9781 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3413   -1.1238   -0.8871 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6311   -1.2080   -0.1140 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1838    0.1869    0.0111 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1826    1.0317    0.7326 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.1230    0.9911   -0.0230 C   0  0  1  0  0  0  0  0  0  0  0  0
    1.1035    1.9475    0.5474 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.0869    2.3899   -0.0989 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.9386    2.3792    1.8490 O   0  0  0  0  0  1  0  0  0  0  0  0
    2.6377    0.1487   -0.4775 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.0576   -1.1576   -1.5775 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.6141    0.6162   -1.8556 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.3445   -1.2055    1.7138 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.5899   -1.9262    0.6742 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.9357   -0.3573    1.4215 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.0272   -2.1480   -1.1044 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5636   -0.6242   -1.8500 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4981   -1.6027    0.9091 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3299   -1.8698   -0.6376 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4267    0.6190   -0.9698 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.1144    0.1769    0.6274 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5385    2.0804    0.7173 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0790    0.7428    1.7880 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1168    1.3864   -1.0535 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  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 10  2  0
  9 11  1  0
  8  2  1  0
  1 12  1  0
  1 13  1  0
  1 14  1  0
  3 15  1  0
  3 16  1  0
  3 17  1  0
  4 18  1  0
  4 19  1  0
  5 20  1  0
  5 21  1  0
  6 22  1  0
  6 23  1  0
  7 24  1  0
  7 25  1  0
  8 26  1  6
M  CHG  2   2   1  11  -1
M  END
Download

3D SDF for HMDB0033433 ((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>
HMDB0033433

> <DATABASE_NAME>
hmdb

> <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

$$$$
Download

3D-SDF for HMDB0033433 ((S)-Homostachydrine)

HMDB0033433
     RDKit          3D
(S)-Homostachydrine
 26 26  0  0  0  0  0  0  0  0999 V2000
    1.7932   -0.1878   -1.1139 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.6429   -0.3235   -0.2065 N   0  0  0  0  0  4  0  0  0  0  0  0
    1.1113   -0.9622    0.9781 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3413   -1.1238   -0.8871 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6311   -1.2080   -0.1140 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1838    0.1869    0.0111 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1826    1.0317    0.7326 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.1230    0.9911   -0.0230 C   0  0  1  0  0  0  0  0  0  0  0  0
    1.1035    1.9475    0.5474 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.0869    2.3899   -0.0989 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.9386    2.3792    1.8490 O   0  0  0  0  0  1  0  0  0  0  0  0
    2.6377    0.1487   -0.4775 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.0576   -1.1576   -1.5775 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.6141    0.6162   -1.8556 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.3445   -1.2055    1.7138 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.5899   -1.9262    0.6742 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.9357   -0.3573    1.4215 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.0272   -2.1480   -1.1044 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5636   -0.6242   -1.8500 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4981   -1.6027    0.9091 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3299   -1.8698   -0.6376 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4267    0.6190   -0.9698 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.1144    0.1769    0.6274 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5385    2.0804    0.7173 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0790    0.7428    1.7880 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1168    1.3864   -1.0535 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  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 10  2  0
  9 11  1  0
  8  2  1  0
  1 12  1  0
  1 13  1  0
  1 14  1  0
  3 15  1  0
  3 16  1  0
  3 17  1  0
  4 18  1  0
  4 19  1  0
  5 20  1  0
  5 21  1  0
  6 22  1  0
  6 23  1  0
  7 24  1  0
  7 25  1  0
  8 26  1  6
M  CHG  2   2   1  11  -1
M  END
Download

PDB for HMDB0033433 ((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
Download

3D PDB for HMDB0033433 ((S)-Homostachydrine)

COMPND    HMDB0033433
HETATM    1  C1  UNL     1       1.793  -0.188  -1.114  1.00  0.00           C  
HETATM    2  N1  UNL     1       0.643  -0.324  -0.207  1.00  0.00           N1+
HETATM    3  C2  UNL     1       1.111  -0.962   0.978  1.00  0.00           C  
HETATM    4  C3  UNL     1      -0.341  -1.124  -0.887  1.00  0.00           C  
HETATM    5  C4  UNL     1      -1.631  -1.208  -0.114  1.00  0.00           C  
HETATM    6  C5  UNL     1      -2.184   0.187   0.011  1.00  0.00           C  
HETATM    7  C6  UNL     1      -1.183   1.032   0.733  1.00  0.00           C  
HETATM    8  C7  UNL     1       0.123   0.991  -0.023  1.00  0.00           C  
HETATM    9  C8  UNL     1       1.104   1.947   0.547  1.00  0.00           C  
HETATM   10  O1  UNL     1       2.087   2.390  -0.099  1.00  0.00           O  
HETATM   11  O2  UNL     1       0.939   2.379   1.849  1.00  0.00           O1-
HETATM   12  H1  UNL     1       2.638   0.149  -0.478  1.00  0.00           H  
HETATM   13  H2  UNL     1       2.058  -1.158  -1.577  1.00  0.00           H  
HETATM   14  H3  UNL     1       1.614   0.616  -1.856  1.00  0.00           H  
HETATM   15  H4  UNL     1       0.344  -1.205   1.714  1.00  0.00           H  
HETATM   16  H5  UNL     1       1.590  -1.926   0.674  1.00  0.00           H  
HETATM   17  H6  UNL     1       1.936  -0.357   1.421  1.00  0.00           H  
HETATM   18  H7  UNL     1       0.027  -2.148  -1.104  1.00  0.00           H  
HETATM   19  H8  UNL     1      -0.564  -0.624  -1.850  1.00  0.00           H  
HETATM   20  H9  UNL     1      -1.498  -1.603   0.909  1.00  0.00           H  
HETATM   21  H10 UNL     1      -2.330  -1.870  -0.638  1.00  0.00           H  
HETATM   22  H11 UNL     1      -2.427   0.619  -0.970  1.00  0.00           H  
HETATM   23  H12 UNL     1      -3.114   0.177   0.627  1.00  0.00           H  
HETATM   24  H13 UNL     1      -1.538   2.080   0.717  1.00  0.00           H  
HETATM   25  H14 UNL     1      -1.079   0.743   1.788  1.00  0.00           H  
HETATM   26  H15 UNL     1      -0.117   1.386  -1.054  1.00  0.00           H  
CONECT    1    2   12   13   14
CONECT    2    3    4    8
CONECT    3   15   16   17
CONECT    4    5   18   19
CONECT    5    6   20   21
CONECT    6    7   22   23
CONECT    7    8   24   25
CONECT    8    9   26
CONECT    9   10   10   11
END
Download

SMILES for HMDB0033433 ((S)-Homostachydrine)

C[N+]1(C)CCCC[C@H]1C([O-])=O
Download

INCHI for HMDB0033433 ((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
Download
View in JSmolView NMR AssignmentsView Stereo Labels
Synonyms
ValueSource
HomostachydrineHMDB
Pipecolic acid betaineHMDB
S-HomostachydrineHMDB
(2S)-1,1-Dimethylpiperidin-1-ium-2-carboxylic acidGenerator
Chemical FormulaC8H15NO2
Average Molecular Weight157.2102
Monoisotopic Molecular Weight157.110278729
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
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
Ontology
Physiological effectNot Available
Disposition
Biological locationRoute of exposureSource
ProcessNot Available
Role
Biological role
Physical Properties
StateSolid
Experimental Molecular Properties
PropertyValueReference
Melting Point300 °CNot Available
Boiling PointNot AvailableNot Available
Water SolubilityNot AvailableNot Available
LogPNot AvailableNot Available
Experimental Chromatographic PropertiesNot Available
Predicted Molecular Properties
PropertyValueSource
Water Solubility0.14 g/LALOGPS
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
Predicted Chromatographic Properties

Predicted Collision Cross Sections

PredictorAdduct TypeCCS Value (Å2)Reference
DeepCCS[M+H]+129.25130932474
DeepCCS[M-H]-125.81230932474
DeepCCS[M-2H]-162.84230932474
DeepCCS[M+Na]+138.11830932474
AllCCS[M+H]+131.332859911
AllCCS[M+H-H2O]+126.932859911
AllCCS[M+NH4]+135.332859911
AllCCS[M+Na]+136.532859911
AllCCS[M-H]-141.332859911
AllCCS[M+Na-2H]-142.532859911
AllCCS[M+HCOO]-144.032859911

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
Predicted by Siyang on May 30, 20229.1438 minutes33406817
Predicted by Siyang using ReTip algorithm on June 8, 20226.17 minutes32390414
AjsUoB = Accucore 150 Amide HILIC with 10mM Ammonium Formate, 0.1% Formic Acid340.5 seconds40023050
Fem_Long = Waters ACQUITY UPLC HSS T3 C18 with Water:MeOH and 0.1% Formic Acid549.6 seconds40023050
Fem_Lipids = Ascentis Express C18 with (60:40 water:ACN):(90:10 IPA:ACN) and 10mM NH4COOH + 0.1% Formic Acid257.8 seconds40023050
Life_Old = Waters ACQUITY UPLC BEH C18 with Water:(20:80 acetone:ACN) and 0.1% Formic Acid109.2 seconds40023050
Life_New = RP Waters ACQUITY UPLC HSS T3 C18 with Water:(30:70 MeOH:ACN) and 0.1% Formic Acid165.4 seconds40023050
RIKEN = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid67.1 seconds40023050
Eawag_XBridgeC18 = XBridge C18 3.5u 2.1x50 mm with Water:MeOH and 0.1% Formic Acid258.4 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 Acid273.1 seconds40023050
HILIC_BDD_2 = Merck SeQuant ZIC-HILIC with ACN(0.1% formic acid):water(16 mM ammonium formate)781.9 seconds40023050
UniToyama_Atlantis = RP Waters Atlantis T3 (2.1 x 150 mm, 5 um) with ACN:Water and 0.1% Formic Acid791.3 seconds40023050
BDD_C18 = Hypersil Gold 1.9µm C18 with Water:ACN and 0.1% Formic Acid104.9 seconds40023050
UFZ_Phenomenex = Kinetex Core-Shell C18 2.6 um, 3.0 x 100 mm, Phenomenex with Water:MeOH and 0.1% Formic Acid1028.7 seconds40023050
SNU_RIKEN_POS = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid165.5 seconds40023050
RPMMFDA = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid210.1 seconds40023050
MTBLS87 = Merck SeQuant ZIC-pHILIC column with ACN:Water and :ammonium carbonate742.5 seconds40023050
KI_GIAR_zic_HILIC_pH2_7 = Merck SeQuant ZIC-HILIC with ACN:Water and 0.1% FA449.3 seconds40023050
Meister zic-pHILIC pH9.3 = Merck SeQuant ZIC-pHILIC column with ACN:Water 5mM NH4Ac pH9.3 and 5mM ammonium acetate in water149.4 seconds40023050

Predicted Kovats Retention Indices

Underivatized

MetaboliteSMILESKovats RI ValueColumn TypeReference
(S)-HomostachydrineC[N+]1(C)CCCC[C@H]1C([O-])=O1855.9Standard polar33892256
(S)-HomostachydrineC[N+]1(C)CCCC[C@H]1C([O-])=O1077.7Standard non polar33892256
(S)-HomostachydrineC[N+]1(C)CCCC[C@H]1C([O-])=O1199.8Semi standard non polar33892256
Spectra
Biological Properties
Cellular Locations
  • Cytoplasm
  • Extracellular
Biospecimen Locations
  • Blood
  • Feces
  • Urine
Tissue LocationsNot Available
Pathways
Normal Concentrations
BiospecimenStatusValueAgeSexConditionReferenceDetails
BloodDetected but not QuantifiedNot QuantifiedAdult (>18 years old)BothNormal details
FecesDetected but not QuantifiedNot QuantifiedAdult (>18 years old)Both
Normal		 details
UrineDetected but not QuantifiedNot QuantifiedAdult (>18 years old)BothNormal details
Abnormal Concentrations
BiospecimenStatusValueAgeSexConditionReferenceDetails
FecesDetected but not QuantifiedNot QuantifiedAdult (>18 years old)BothColorectal Cancer details
FecesDetected but not QuantifiedNot QuantifiedAdult (>18 years old)Both
Colorectal cancer		 details
FecesDetected but not QuantifiedNot QuantifiedAdult (>18 years old)Both
Colorectal cancer		 details
Associated Disorders and Diseases
Disease References
Colorectal cancer
  1. Brown DG, Rao S, Weir TL, O'Malia J, Bazan M, Brown RJ, Ryan EP: Metabolomics and metabolic pathway networks from human colorectal cancers, adjacent mucosa, and stool. Cancer Metab. 2016 Jun 6;4:11. doi: 10.1186/s40170-016-0151-y. eCollection 2016. [PubMed:27275383 ]
  2. Sinha R, Ahn J, Sampson JN, Shi J, Yu G, Xiong X, Hayes RB, Goedert JJ: Fecal Microbiota, Fecal Metabolome, and Colorectal Cancer Interrelations. PLoS One. 2016 Mar 25;11(3):e0152126. doi: 10.1371/journal.pone.0152126. eCollection 2016. [PubMed:27015276 ]
  3. Goedert JJ, Sampson JN, Moore SC, Xiao Q, Xiong X, Hayes RB, Ahn J, Shi J, Sinha R: Fecal metabolomics: assay performance and association with colorectal cancer. Carcinogenesis. 2014 Sep;35(9):2089-96. doi: 10.1093/carcin/bgu131. Epub 2014 Jul 18. [PubMed:25037050 ]
Associated OMIM IDs
DrugBank IDNot Available
Phenol Explorer Compound IDNot Available
FooDB 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
Food Biomarker OntologyNot Available
VMH IDNot Available
MarkerDB IDNot Available
Good Scents IDNot Available
References
Synthesis ReferenceNot Available
Material Safety Data Sheet (MSDS)Not Available
General References
  1. 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 ]
  2. 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 ]
  3. (). Yannai, Shmuel. (2004) Dictionary of food compounds with CD-ROM: Additives, flavors, and ingredients. Boca Raton: Chapman & Hall/CRC.. .