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Showing metabocard for (2S,6S)-6-(carboxymethyl)piperidine-w-carboxylic acid (HMDB0340289)

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Record Information
Version5.0
StatusExpected but not Quantified
Creation Date2022-04-13 15:56:05 UTC
Update Date2022-04-13 15:56:05 UTC
HMDB IDHMDB0340289
Secondary Accession NumbersNone
Metabolite Identification
Common Name(2S,6S)-6-(carboxymethyl)piperidine-w-carboxylic acid
DescriptionBased on a literature review very few articles have been published on (2S,6S)-6-(carboxymethyl)piperidine-w-carboxylic acid.
Structure
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MOLSDFPDBSMILESInChI

MOL for HMDB0340289 ((2S,6S)-6-(carboxymethyl)piperidine-w-carboxylic acid)


  Mrv1652304132217542D          

 15 15  0  0  0  0            999 V2000
    1.4289   -0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289    0.8250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145   -0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145    2.0625    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145    1.2375    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    0.0000   -0.0000    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    1.4289    2.4750    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7145   -0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    0.8250    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289    3.3000    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.1434    2.0625    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7145   -1.2375    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4289    0.0000    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289    1.6500    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7145    0.4125    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
  2  1  1  0  0  0  0
  3  1  1  0  0  0  0
  5  2  1  0  0  0  0
  5  4  1  6  0  0  0
  6  3  1  0  0  0  0
  7  4  1  0  0  0  0
  6  8  1  1  0  0  0
  9  5  1  0  0  0  0
  9  6  1  0  0  0  0
 10  7  2  0  0  0  0
 11  7  1  0  0  0  0
 12  8  2  0  0  0  0
 13  8  1  0  0  0  0
  5 14  1  1  0  0  0
  6 15  1  6  0  0  0
M  END
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3D MOL for HMDB0340289 ((2S,6S)-6-(carboxymethyl)piperidine-w-carboxylic acid)

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3D SDF for HMDB0340289 ((2S,6S)-6-(carboxymethyl)piperidine-w-carboxylic acid)

  Mrv1652304132217542D          

 15 15  0  0  0  0            999 V2000
    1.4289   -0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289    0.8250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145   -0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145    2.0625    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145    1.2375    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    0.0000   -0.0000    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    1.4289    2.4750    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7145   -0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    0.8250    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289    3.3000    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.1434    2.0625    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7145   -1.2375    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4289    0.0000    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289    1.6500    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7145    0.4125    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
  2  1  1  0  0  0  0
  3  1  1  0  0  0  0
  5  2  1  0  0  0  0
  5  4  1  6  0  0  0
  6  3  1  0  0  0  0
  7  4  1  0  0  0  0
  6  8  1  1  0  0  0
  9  5  1  0  0  0  0
  9  6  1  0  0  0  0
 10  7  2  0  0  0  0
 11  7  1  0  0  0  0
 12  8  2  0  0  0  0
 13  8  1  0  0  0  0
  5 14  1  1  0  0  0
  6 15  1  6  0  0  0
M  END
> <DATABASE_ID>
HMDB0340289

> <DATABASE_NAME>
hmdb

> <SMILES>
[H][C@@]1(CC(O)=O)CCC[C@]([H])(N1)C(O)=O

> <INCHI_IDENTIFIER>
InChI=1S/C8H13NO4/c10-7(11)4-5-2-1-3-6(9-5)8(12)13/h5-6,9H,1-4H2,(H,10,11)(H,12,13)/t5-,6-/m0/s1

> <INCHI_KEY>
PKAQHNPJZMWVHG-WDSKDSINSA-N

> <FORMULA>
C8H13NO4

> <MOLECULAR_WEIGHT>
187.195

> <EXACT_MASS>
187.084457903

> <JCHEM_ACCEPTOR_COUNT>
5

> <JCHEM_ATOM_COUNT>
26

> <JCHEM_AVERAGE_POLARIZABILITY>
18.21398243663735

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
3

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(2S,6S)-6-(carboxymethyl)piperidine-2-carboxylic acid

> <JCHEM_LOGP>
-2.422480695330005

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
1

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-1

> <JCHEM_PKA>
3.821961728345339

> <JCHEM_PKA_STRONGEST_ACIDIC>
1.6216167811038211

> <JCHEM_PKA_STRONGEST_BASIC>
10.40667987190199

> <JCHEM_POLAR_SURFACE_AREA>
86.63000000000001

> <JCHEM_REFRACTIVITY>
43.1195

> <JCHEM_ROTATABLE_BOND_COUNT>
3

> <JCHEM_RULE_OF_FIVE>
1

> <JCHEM_TRADITIONAL_IUPAC>
(2S,6S)-6-(carboxymethyl)piperidine-2-carboxylic acid

> <JCHEM_VEBER_RULE>
0

$$$$

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3D-SDF for HMDB0340289 ((2S,6S)-6-(carboxymethyl)piperidine-w-carboxylic acid)
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PDB for HMDB0340289 ((2S,6S)-6-(carboxymethyl)piperidine-w-carboxylic acid)
HEADER    PROTEIN                                 13-APR-22   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   13-APR-22         0                                  
HETATM    1  C   UNK     0       2.667  -0.000   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       2.667   1.540   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       1.334  -0.770   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       1.334   3.850   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       1.334   2.310   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       0.000  -0.000   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       2.667   4.620   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0      -1.334  -0.770   0.000  0.00  0.00           C+0
HETATM    9  N   UNK     0       0.000   1.540   0.000  0.00  0.00           N+0
HETATM   10  O   UNK     0       2.667   6.160   0.000  0.00  0.00           O+0
HETATM   11  O   UNK     0       4.001   3.850   0.000  0.00  0.00           O+0
HETATM   12  O   UNK     0      -1.334  -2.310   0.000  0.00  0.00           O+0
HETATM   13  O   UNK     0      -2.667   0.000   0.000  0.00  0.00           O+0
HETATM   14  H   UNK     0       2.667   3.080   0.000  0.00  0.00           H+0
HETATM   15  H   UNK     0      -1.334   0.770   0.000  0.00  0.00           H+0
CONECT    1    2    3                                                       
CONECT    2    1    5                                                       
CONECT    3    1    6                                                       
CONECT    4    5    7                                                       
CONECT    5    2    4    9   14                                             
CONECT    6    3    8    9   15                                             
CONECT    7    4   10   11                                                  
CONECT    8    6   12   13                                                  
CONECT    9    5    6                                                       
CONECT   10    7                                                            
CONECT   11    7                                                            
CONECT   12    8                                                            
CONECT   13    8                                                            
CONECT   14    5                                                            
CONECT   15    6                                                            
MASTER        0    0    0    0    0    0    0    0   15    0   30    0
END

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3D PDB for HMDB0340289 ((2S,6S)-6-(carboxymethyl)piperidine-w-carboxylic acid)
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SMILES for HMDB0340289 ((2S,6S)-6-(carboxymethyl)piperidine-w-carboxylic acid)
[H][C@@]1(CC(O)=O)CCC[C@]([H])(N1)C(O)=O
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INCHI for HMDB0340289 ((2S,6S)-6-(carboxymethyl)piperidine-w-carboxylic acid)
InChI=1S/C8H13NO4/c10-7(11)4-5-2-1-3-6(9-5)8(12)13/h5-6,9H,1-4H2,(H,10,11)(H,12,13)/t5-,6-/m0/s1
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View in JSmolView Stereo Labels
Synonyms
ValueSource
(2S,6S)-6-(Carboxymethyl)piperidine-W-carboxylateGenerator
Chemical FormulaC8H13NO4
Average Molecular Weight187.195
Monoisotopic Molecular Weight187.084457903
IUPAC Name(2S,6S)-6-(carboxymethyl)piperidine-2-carboxylic acid
Traditional Name(2S,6S)-6-(carboxymethyl)piperidine-2-carboxylic acid
CAS Registry NumberNot Available
SMILES
[H][C@@]1(CC(O)=O)CCC[C@]([H])(N1)C(O)=O
InChI Identifier
InChI=1S/C8H13NO4/c10-7(11)4-5-2-1-3-6(9-5)8(12)13/h5-6,9H,1-4H2,(H,10,11)(H,12,13)/t5-,6-/m0/s1
InChI KeyPKAQHNPJZMWVHG-WDSKDSINSA-N
Chemical Taxonomy
ClassificationNot classified
Ontology
Physiological effectNot Available
DispositionNot Available
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-2.4ChemAxon
pKa (Strongest Acidic)1.62ChemAxon
pKa (Strongest Basic)10.41ChemAxon
Physiological Charge-1ChemAxon
Hydrogen Acceptor Count5ChemAxon
Hydrogen Donor Count3ChemAxon
Polar Surface Area86.63 ŲChemAxon
Rotatable Bond Count3ChemAxon
Refractivity43.12 m³·mol⁻¹ChemAxon
Polarizability18.21 ųChemAxon
Number of Rings1ChemAxon
BioavailabilityYesChemAxon
Rule of FiveYesChemAxon
Ghose FilterNoChemAxon
Veber's RuleNoChemAxon
MDDR-like RuleNoChemAxon
Predicted Chromatographic Properties
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. 1.25 minutes32390414  
Predicted by Siyang on May 30, 20229.4053 minutes33406817  
Predicted by Siyang using ReTip algorithm on June 8, 20226.02 minutes32390414  
Fem_Long = Waters ACQUITY UPLC HSS T3 C18 with Water:MeOH and 0.1% Formic Acid487.7 seconds40023050  
Fem_Lipids = Ascentis Express C18 with (60:40 water:ACN):(90:10 IPA:ACN) and 10mM NH4COOH + 0.1% Formic Acid265.5 seconds40023050  
Life_Old = Waters ACQUITY UPLC BEH C18 with Water:(20:80 acetone:ACN) and 0.1% Formic Acid57.6 seconds40023050  
Life_New = RP Waters ACQUITY UPLC HSS T3 C18 with Water:(30:70 MeOH:ACN) and 0.1% Formic Acid165.0 seconds40023050  
RIKEN = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid51.3 seconds40023050  
Eawag_XBridgeC18 = XBridge C18 3.5u 2.1x50 mm with Water:MeOH and 0.1% Formic Acid269.1 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 Acid237.1 seconds40023050  
HILIC_BDD_2 = Merck SeQuant ZIC-HILIC with ACN(0.1% formic acid):water(16 mM ammonium formate)787.7 seconds40023050  
UniToyama_Atlantis = RP Waters Atlantis T3 (2.1 x 150 mm, 5 um) with ACN:Water and 0.1% Formic Acid580.0 seconds40023050  
BDD_C18 = Hypersil Gold 1.9µm C18 with Water:ACN and 0.1% Formic Acid56.2 seconds40023050  
UFZ_Phenomenex = Kinetex Core-Shell C18 2.6 um, 3.0 x 100 mm, Phenomenex with Water:MeOH and 0.1% Formic Acid705.6 seconds40023050  
SNU_RIKEN_POS = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid170.2 seconds40023050  
RPMMFDA = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid195.3 seconds40023050  
MTBLS87 = Merck SeQuant ZIC-pHILIC column with ACN:Water and :ammonium carbonate814.2 seconds40023050  
KI_GIAR_zic_HILIC_pH2_7 = Merck SeQuant ZIC-HILIC with ACN:Water and 0.1% FA438.1 seconds40023050  
Meister zic-pHILIC pH9.3 = Merck SeQuant ZIC-pHILIC column with ACN:Water 5mM NH4Ac pH9.3 and 5mM ammonium acetate in water415.7 seconds40023050  
Predicted Kovats Retention Indices
Not Available
Spectra
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 IDNot Available
KNApSAcK IDNot Available
Chemspider ID24769855  
KEGG Compound IDNot Available
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkNot Available
METLIN IDNot Available
PubChem Compound130944669  
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