Hmdb loader

Showing metabocard for Baikiain (HMDB0302856)

Jump To Section:
IdentificationTaxonomyOntologyPhysical propertiesSpectraBiological propertiesConcentrationsLinksReferencesXML
Record Information
Version5.0
StatusExpected but not Quantified
Creation Date2021-09-23 21:11:58 UTC
Update Date2021-09-23 21:11:59 UTC
HMDB IDHMDB0302856
Secondary Accession NumbersNone
Metabolite Identification
Common NameBaikiain
DescriptionBaikiain, also known as 4,5-dehydropipecolic acid, (+-)-isomer, is a member of the class of compounds known as alpha amino acids. Alpha amino acids are amino acids in which the amino group is attached to the carbon atom immediately adjacent to the carboxylate group (alpha carbon). Baikiain is soluble (in water) and a moderately acidic compound (based on its pKa). Baikiain can be found in date, which makes baikiain a potential biomarker for the consumption of this food product.
Structure
Thumb
MOL3D MOLSDF3D SDFPDB3D PDBSMILESInChI

MOL for HMDB0302856 (Baikiain)


  Mrv0541 02241223382D          

  9  9  0  0  0  0            999 V2000
   -0.7009    1.4434    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.0409    1.0309    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7009    1.4434    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.0409    0.2059    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7009   -0.2059    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7009   -1.0309    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0409   -1.4434    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7009   -1.0309    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7009   -0.2059    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  2  0  0  0  0
  2  3  1  0  0  0  0
  2  4  1  0  0  0  0
  4  5  1  0  0  0  0
  4  9  1  0  0  0  0
  5  6  1  0  0  0  0
  6  7  2  0  0  0  0
  7  8  1  0  0  0  0
  8  9  1  0  0  0  0
M  END
Download

3D MOL for HMDB0302856 (Baikiain)

HMDB0302856
     RDKit          3D
Baikiain
 18 18  0  0  0  0  0  0  0  0999 V2000
    2.5586   -1.0265    1.3601 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.9644   -0.6292    0.4417 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.5280   -0.3163   -0.8142 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.4980   -0.3416    0.4229 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.2101    1.0801    0.5864 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0135    1.5052   -0.1106 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9267    0.6375   -0.5520 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6567   -0.8305   -0.3242 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2204   -0.9812   -0.6221 N   0  0  0  0  0  0  0  0  0  0  0  0
    3.5305   -0.2837   -0.8864 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.1017   -0.8602    1.3963 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.3077    1.3701    1.6310 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.0736    1.6064    0.0568 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1983    2.5652   -0.2570 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7217    0.9246   -1.1578 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7926   -1.0910    0.7393 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3078   -1.4640   -0.9454 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.0651   -1.8650   -0.9648 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  2  0
  7  8  1  0
  8  9  1  0
  9  4  1  0
  3 10  1  0
  4 11  1  0
  5 12  1  0
  5 13  1  0
  6 14  1  0
  7 15  1  0
  8 16  1  0
  8 17  1  0
  9 18  1  0
M  END
Download

3D SDF for HMDB0302856 (Baikiain)


  Mrv0541 02241223382D          

  9  9  0  0  0  0            999 V2000
   -0.7009    1.4434    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.0409    1.0309    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7009    1.4434    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.0409    0.2059    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7009   -0.2059    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7009   -1.0309    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0409   -1.4434    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7009   -1.0309    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7009   -0.2059    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  2  0  0  0  0
  2  3  1  0  0  0  0
  2  4  1  0  0  0  0
  4  5  1  0  0  0  0
  4  9  1  0  0  0  0
  5  6  1  0  0  0  0
  6  7  2  0  0  0  0
  7  8  1  0  0  0  0
  8  9  1  0  0  0  0
M  END
> <DATABASE_ID>
HMDB0302856

> <DATABASE_NAME>
hmdb

> <SMILES>
OC(=O)C1CC=CCN1

> <INCHI_IDENTIFIER>
InChI=1S/C6H9NO2/c8-6(9)5-3-1-2-4-7-5/h1-2,5,7H,3-4H2,(H,8,9)

> <INCHI_KEY>
YCQPUTODZKESPK-UHFFFAOYSA-N

> <FORMULA>
C6H9NO2

> <MOLECULAR_WEIGHT>
127.1412

> <EXACT_MASS>
127.063328537

> <JCHEM_ACCEPTOR_COUNT>
3

> <JCHEM_AVERAGE_POLARIZABILITY>
12.662565461156639

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
2

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
1,2,3,6-tetrahydropyridine-2-carboxylic acid

> <ALOGPS_LOGP>
-1.96

> <JCHEM_LOGP>
-2.329787222343675

> <ALOGPS_LOGS>
0.06

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
1

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA_STRONGEST_ACIDIC>
1.961701708660721

> <JCHEM_PKA_STRONGEST_BASIC>
9.921352913367354

> <JCHEM_POLAR_SURFACE_AREA>
49.33

> <JCHEM_REFRACTIVITY>
33.627900000000004

> <JCHEM_ROTATABLE_BOND_COUNT>
1

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
1.46e+02 g/l

> <JCHEM_TRADITIONAL_IUPAC>
1,2,3,6-tetrahydropyridine-2-carboxylic acid

> <JCHEM_VEBER_RULE>
0

$$$$
Download

3D-SDF for HMDB0302856 (Baikiain)

HMDB0302856
     RDKit          3D
Baikiain
 18 18  0  0  0  0  0  0  0  0999 V2000
    2.5586   -1.0265    1.3601 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.9644   -0.6292    0.4417 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.5280   -0.3163   -0.8142 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.4980   -0.3416    0.4229 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.2101    1.0801    0.5864 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0135    1.5052   -0.1106 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9267    0.6375   -0.5520 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6567   -0.8305   -0.3242 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2204   -0.9812   -0.6221 N   0  0  0  0  0  0  0  0  0  0  0  0
    3.5305   -0.2837   -0.8864 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.1017   -0.8602    1.3963 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.3077    1.3701    1.6310 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.0736    1.6064    0.0568 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1983    2.5652   -0.2570 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7217    0.9246   -1.1578 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7926   -1.0910    0.7393 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3078   -1.4640   -0.9454 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.0651   -1.8650   -0.9648 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  2  0
  7  8  1  0
  8  9  1  0
  9  4  1  0
  3 10  1  0
  4 11  1  0
  5 12  1  0
  5 13  1  0
  6 14  1  0
  7 15  1  0
  8 16  1  0
  8 17  1  0
  9 18  1  0
M  END
Download

PDB for HMDB0302856 (Baikiain)

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  O   UNK     0      -1.308   2.694   0.000  0.00  0.00           O+0
HETATM    2  C   UNK     0       0.076   1.924   0.000  0.00  0.00           C+0
HETATM    3  O   UNK     0       1.308   2.694   0.000  0.00  0.00           O+0
HETATM    4  C   UNK     0       0.076   0.384   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       1.308  -0.384   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       1.308  -1.924   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       0.076  -2.694   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0      -1.308  -1.924   0.000  0.00  0.00           C+0
HETATM    9  N   UNK     0      -1.308  -0.384   0.000  0.00  0.00           N+0
CONECT    1    2                                                            
CONECT    2    1    3    4                                                  
CONECT    3    2                                                            
CONECT    4    2    5    9                                                  
CONECT    5    4    6                                                       
CONECT    6    5    7                                                       
CONECT    7    6    8                                                       
CONECT    8    7    9                                                       
CONECT    9    4    8                                                       
MASTER        0    0    0    0    0    0    0    0    9    0   18    0
END
Download

3D PDB for HMDB0302856 (Baikiain)

COMPND    HMDB0302856
HETATM    1  O1  UNL     1       2.559  -1.026   1.360  1.00  0.00           O  
HETATM    2  C1  UNL     1       1.964  -0.629   0.442  1.00  0.00           C  
HETATM    3  O2  UNL     1       2.528  -0.316  -0.814  1.00  0.00           O  
HETATM    4  C2  UNL     1       0.498  -0.342   0.423  1.00  0.00           C  
HETATM    5  C3  UNL     1       0.210   1.080   0.586  1.00  0.00           C  
HETATM    6  C4  UNL     1      -1.014   1.505  -0.111  1.00  0.00           C  
HETATM    7  C5  UNL     1      -1.927   0.638  -0.552  1.00  0.00           C  
HETATM    8  C6  UNL     1      -1.657  -0.831  -0.324  1.00  0.00           C  
HETATM    9  N1  UNL     1      -0.220  -0.981  -0.622  1.00  0.00           N  
HETATM   10  H1  UNL     1       3.530  -0.284  -0.886  1.00  0.00           H  
HETATM   11  H2  UNL     1       0.102  -0.860   1.396  1.00  0.00           H  
HETATM   12  H3  UNL     1       0.308   1.370   1.631  1.00  0.00           H  
HETATM   13  H4  UNL     1       1.074   1.606   0.057  1.00  0.00           H  
HETATM   14  H5  UNL     1      -1.198   2.565  -0.257  1.00  0.00           H  
HETATM   15  H6  UNL     1      -2.722   0.925  -1.158  1.00  0.00           H  
HETATM   16  H7  UNL     1      -1.793  -1.091   0.739  1.00  0.00           H  
HETATM   17  H8  UNL     1      -2.308  -1.464  -0.945  1.00  0.00           H  
HETATM   18  H9  UNL     1       0.065  -1.865  -0.965  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    7   14
CONECT    7    8   15
CONECT    8    9   16   17
CONECT    9   18
END
Download

SMILES for HMDB0302856 (Baikiain)

OC(=O)C1CC=CCN1
Download

INCHI for HMDB0302856 (Baikiain)

InChI=1S/C6H9NO2/c8-6(9)5-3-1-2-4-7-5/h1-2,5,7H,3-4H2,(H,8,9)
Download
View in JSmolView Stereo Labels
Synonyms
ValueSource
4,5-Dehydropipecolic acidMeSH
4,5-Dehydropipecolic acid, (+-)-isomerMeSH
4,5-Dehydropipecolic acid, (S)-isomerMeSH
Chemical FormulaC6H9NO2
Average Molecular Weight127.1412
Monoisotopic Molecular Weight127.063328537
IUPAC Name1,2,3,6-tetrahydropyridine-2-carboxylic acid
Traditional Name1,2,3,6-tetrahydropyridine-2-carboxylic acid
CAS Registry NumberNot Available
SMILES
OC(=O)C1CC=CCN1
InChI Identifier
InChI=1S/C6H9NO2/c8-6(9)5-3-1-2-4-7-5/h1-2,5,7H,3-4H2,(H,8,9)
InChI KeyYCQPUTODZKESPK-UHFFFAOYSA-N
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
  • Hydropyridine
  • Amino acid
  • Carboxylic acid
  • Secondary aliphatic amine
  • Monocarboxylic acid or derivatives
  • Azacycle
  • Organoheterocyclic compound
  • Secondary amine
  • Organic nitrogen compound
  • Organooxygen compound
  • Organonitrogen compound
  • Hydrocarbon derivative
  • Organic oxide
  • Organopnictogen compound
  • Organic oxygen compound
  • Carbonyl group
  • Amine
  • Aliphatic heteromonocyclic compound
Molecular FrameworkAliphatic heteromonocyclic compounds
External DescriptorsNot Available
Ontology
Physiological effectNot Available
Disposition
Source
ProcessNot Available
RoleNot Available
Physical Properties
StateNot Available
Experimental Molecular Properties
PropertyValueReference
Melting PointNot AvailableNot Available
Boiling PointNot AvailableNot Available
Water SolubilityNot AvailableNot Available
LogPNot AvailableNot Available
Experimental Chromatographic PropertiesNot Available
Predicted Molecular Properties
PropertyValueSource
logP-2ALOGPS
logP-2.3ChemAxon
logS0.06ALOGPS
pKa (Strongest Acidic)1.96ChemAxon
pKa (Strongest Basic)9.92ChemAxon
Physiological Charge0ChemAxon
Hydrogen Acceptor Count3ChemAxon
Hydrogen Donor Count2ChemAxon
Polar Surface Area49.33 ŲChemAxon
Rotatable Bond Count1ChemAxon
Refractivity33.63 m³·mol⁻¹ChemAxon
Polarizability12.66 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
AllCCS[M+H]+127.6232859911
AllCCS[M+H-H2O]+122.82332859911
AllCCS[M+Na]+133.39132859911
AllCCS[M+NH4]+132.09832859911
AllCCS[M-H]-124.90532859911
AllCCS[M+Na-2H]-126.97232859911
AllCCS[M+HCOO]-129.29132859911
DeepCCS[M+H]+120.65730932474
DeepCCS[M-H]-117.28530932474
DeepCCS[M-2H]-154.1930932474
DeepCCS[M+Na]+129.27630932474

Predicted Kovats Retention Indices

Derivatized

Derivative Name / StructureSMILESKovats RI ValueColumn TypeReference
Baikiain,2TMS,isomer #1C[Si](C)(C)OC(=O)C1CC=CCN1[Si](C)(C)C1358.7Semi standard non polar33892256
Baikiain,2TMS,isomer #1C[Si](C)(C)OC(=O)C1CC=CCN1[Si](C)(C)C1399.5Standard non polar33892256
Baikiain,2TMS,isomer #1C[Si](C)(C)OC(=O)C1CC=CCN1[Si](C)(C)C1665.6Standard polar33892256
Baikiain,2TBDMS,isomer #1CC(C)(C)[Si](C)(C)OC(=O)C1CC=CCN1[Si](C)(C)C(C)(C)C1817.4Semi standard non polar33892256
Baikiain,2TBDMS,isomer #1CC(C)(C)[Si](C)(C)OC(=O)C1CC=CCN1[Si](C)(C)C(C)(C)C1802.0Standard non polar33892256
Baikiain,2TBDMS,isomer #1CC(C)(C)[Si](C)(C)OC(=O)C1CC=CCN1[Si](C)(C)C(C)(C)C1938.6Standard polar33892256
Spectra

MS/MS Spectra

Spectrum TypeDescriptionSplash KeyDeposition DateSourceView
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Baikiain 10V, Positive-QTOFsplash10-004i-3900000000-fde35d314b896ab26ccb2016-06-03Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Baikiain 20V, Positive-QTOFsplash10-001i-9300000000-6ca0559b51ac26c808c62016-06-03Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Baikiain 40V, Positive-QTOFsplash10-0udi-9000000000-dba870023a8a4f0b6d0f2016-06-03Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Baikiain 10V, Negative-QTOFsplash10-004i-3900000000-8facd3eaca289ff2f9522016-08-03Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Baikiain 20V, Negative-QTOFsplash10-003r-9700000000-0cfef25068de2e3367c82016-08-03Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Baikiain 40V, Negative-QTOFsplash10-001i-9100000000-e72a52a50e8c3f6b436b2016-08-03Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Baikiain 10V, Positive-QTOFsplash10-001i-9200000000-cbf1b8e349aa6ca996622021-10-21Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Baikiain 20V, Positive-QTOFsplash10-001i-9000000000-29fae23b5d3c449f94d62021-10-21Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Baikiain 40V, Positive-QTOFsplash10-0f89-9000000000-ec4ce96dafceeebdf3cd2021-10-21Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Baikiain 10V, Negative-QTOFsplash10-004i-0900000000-f5ad3a146c0d7eb97e472021-10-21Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Baikiain 20V, Negative-QTOFsplash10-00c0-7900000000-96e71ce815ef6429ac142021-10-21Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Baikiain 40V, Negative-QTOFsplash10-000x-9000000000-404d719baaaf7bb0afa42021-10-21Wishart LabView Spectrum
Biological Properties
Cellular LocationsNot Available
Biospecimen LocationsNot Available
Tissue LocationsNot Available
Pathways
Normal Concentrations
Not Available
Abnormal Concentrations
Not Available
Associated Disorders and Diseases
Disease ReferencesNone
Associated OMIM IDsNone
DrugBank IDNot Available
Phenol Explorer Compound IDNot Available
FooDB IDFDB006553
KNApSAcK IDC00001344
Chemspider ID484710
KEGG Compound IDNot Available
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkNot Available
METLIN IDNot Available
PubChem Compound557590
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 ReferencesNot Available