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Showing metabocard for 3-Dehydrocarnitine (HMDB0012154)

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Record Information
Version5.0
StatusDetected but not Quantified
Creation Date2009-04-06 16:20:07 UTC
Update Date2023-02-21 17:17:41 UTC
HMDB IDHMDB0012154
Secondary Accession Numbers
  • HMDB12154
Metabolite Identification
Common Name3-Dehydrocarnitine
Description3-Dehydrocarnitine is a member of the carnitine family that is an intermediate in carnitine degradation. It can be formed from either D-carnitine or L-carnitine and the enzyme responsible for this oxidation reaction is (S)-carnitine 3-dehydrogenase (EC 1.1.1.254) or carnitine 3-dehydrogenase (EC 1.1.1.108), respectively. Carnitine is a quaternary ammonium compound biosynthesized from the amino acids lysine and methionine. In living cells, it is required for the transport of fatty acids from the cytosol into the mitochondria during the breakdown of lipids (or fats) for the generation of metabolic energy.
Structure
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MOL3D MOLSDF3D SDFPDB3D PDBSMILESInChI

MOL for HMDB0012154 (3-Dehydrocarnitine)

  Mrv1652303211800342D          

 11 10  0  0  0  0            999 V2000
10000.7151 9999.3258    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
10001.4302 9999.7372    0.0000 N   0  3  0  0  0  0  0  0  0  0  0  0
10002.1433 9999.3258    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
10001.428210000.7140    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
10002.143310000.1514    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
 9999.9999 9999.7372    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
 9999.2848 9999.3258    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
 9998.5707 9999.7372    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
 9997.8565 9999.3258    0.0000 O   0  5  0  0  0  0  0  0  0  0  0  0
 9998.570710000.5616    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
 9999.999910000.5616    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
  2  4  1  0  0  0  0
  2  5  1  0  0  0  0
  6  7  1  0  0  0  0
  6 11  2  0  0  0  0
  7  8  1  0  0  0  0
  8  9  1  0  0  0  0
  8 10  2  0  0  0  0
M  CHG  2   2   1   9  -1
M  END
Download

3D MOL for HMDB0012154 (3-Dehydrocarnitine)

HMDB0012154
     RDKit          3D
3-Dehydrocarnitine
 24 23  0  0  0  0  0  0  0  0999 V2000
   -0.7585   -0.8634   -1.2914 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0447    0.0714   -0.2672 N   0  0  0  0  0  4  0  0  0  0  0  0
   -2.4503    0.4952   -0.4197 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0049   -0.6521    1.0117 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1881    1.1975   -0.1482 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.2400    0.9766   -0.0321 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.9425    1.9889    0.1252 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.9600   -0.3070   -0.0781 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.4082   -0.1682    0.1173 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.9043    0.9516    0.2975 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.1985   -1.2972    0.0966 O   0  0  0  0  0  1  0  0  0  0  0  0
   -0.2777   -1.8115   -0.9038 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7441   -1.2525   -1.6905 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2631   -0.4517   -2.1775 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.0768   -0.3500   -0.7843 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4660    1.2606   -1.2093 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8744    0.8391    0.5262 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3023   -0.1657    1.7326 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6834   -1.6950    0.8803 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9891   -0.6381    1.5294 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5251    1.8367    0.7254 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4553    1.8678   -1.0256 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.6107   -1.0737    0.6246 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.8399   -0.7592   -1.1001 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
  2  5  1  0
  5  6  1  0
  6  7  2  0
  6  8  1  0
  8  9  1  0
  9 10  2  0
  9 11  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
  4 20  1  0
  5 21  1  0
  5 22  1  0
  8 23  1  0
  8 24  1  0
M  CHG  2   2   1  11  -1
M  END
Download

3D SDF for HMDB0012154 (3-Dehydrocarnitine)

  Mrv1652303211800342D          

 11 10  0  0  0  0            999 V2000
10000.7151 9999.3258    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
10001.4302 9999.7372    0.0000 N   0  3  0  0  0  0  0  0  0  0  0  0
10002.1433 9999.3258    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
10001.428210000.7140    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
10002.143310000.1514    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
 9999.9999 9999.7372    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
 9999.2848 9999.3258    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
 9998.5707 9999.7372    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
 9997.8565 9999.3258    0.0000 O   0  5  0  0  0  0  0  0  0  0  0  0
 9998.570710000.5616    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
 9999.999910000.5616    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
  2  4  1  0  0  0  0
  2  5  1  0  0  0  0
  6  7  1  0  0  0  0
  6 11  2  0  0  0  0
  7  8  1  0  0  0  0
  8  9  1  0  0  0  0
  8 10  2  0  0  0  0
M  CHG  2   2   1   9  -1
M  END
> <DATABASE_ID>
HMDB0012154

> <DATABASE_NAME>
hmdb

> <SMILES>
C[N+](C)(C)CC(=O)CC([O-])=O

> <INCHI_IDENTIFIER>
InChI=1S/C7H13NO3/c1-8(2,3)5-6(9)4-7(10)11/h4-5H2,1-3H3

> <INCHI_KEY>
YNOWULSFLVIUDH-UHFFFAOYSA-N

> <FORMULA>
C7H13NO3

> <MOLECULAR_WEIGHT>
159.183

> <EXACT_MASS>
159.089543287

> <JCHEM_ACCEPTOR_COUNT>
3

> <JCHEM_ATOM_COUNT>
24

> <JCHEM_AVERAGE_POLARIZABILITY>
16.077865287846002

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
0

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
3-oxo-4-(trimethylazaniumyl)butanoate

> <ALOGPS_LOGP>
-2.21

> <JCHEM_LOGP>
-4.272329873805079

> <ALOGPS_LOGS>
-2.31

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
0

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
13.175051998558235

> <JCHEM_PKA_STRONGEST_ACIDIC>
3.9402081107442175

> <JCHEM_PKA_STRONGEST_BASIC>
-8.734853509924461

> <JCHEM_POLAR_SURFACE_AREA>
57.199999999999996

> <JCHEM_REFRACTIVITY>
62.7186

> <JCHEM_ROTATABLE_BOND_COUNT>
4

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
1.04e+00 g/l

> <JCHEM_TRADITIONAL_IUPAC>
3-dehydrocarnitine

> <JCHEM_VEBER_RULE>
0

$$$$
Download

3D-SDF for HMDB0012154 (3-Dehydrocarnitine)

HMDB0012154
     RDKit          3D
3-Dehydrocarnitine
 24 23  0  0  0  0  0  0  0  0999 V2000
   -0.7585   -0.8634   -1.2914 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0447    0.0714   -0.2672 N   0  0  0  0  0  4  0  0  0  0  0  0
   -2.4503    0.4952   -0.4197 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0049   -0.6521    1.0117 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1881    1.1975   -0.1482 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.2400    0.9766   -0.0321 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.9425    1.9889    0.1252 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.9600   -0.3070   -0.0781 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.4082   -0.1682    0.1173 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.9043    0.9516    0.2975 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.1985   -1.2972    0.0966 O   0  0  0  0  0  1  0  0  0  0  0  0
   -0.2777   -1.8115   -0.9038 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7441   -1.2525   -1.6905 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2631   -0.4517   -2.1775 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.0768   -0.3500   -0.7843 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4660    1.2606   -1.2093 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8744    0.8391    0.5262 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3023   -0.1657    1.7326 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6834   -1.6950    0.8803 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9891   -0.6381    1.5294 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5251    1.8367    0.7254 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4553    1.8678   -1.0256 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.6107   -1.0737    0.6246 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.8399   -0.7592   -1.1001 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
  2  5  1  0
  5  6  1  0
  6  7  2  0
  6  8  1  0
  8  9  1  0
  9 10  2  0
  9 11  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
  4 20  1  0
  5 21  1  0
  5 22  1  0
  8 23  1  0
  8 24  1  0
M  CHG  2   2   1  11  -1
M  END
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PDB for HMDB0012154 (3-Dehydrocarnitine)

HEADER    PROTEIN                                 21-MAR-18   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   21-MAR-18         0                                  
HETATM    1  C   UNK     0    8668.0028665.408   0.000  0.00  0.00           C+0
HETATM    2  N   UNK     0    8669.3368666.176   0.000  0.00  0.00           N+1
HETATM    3  C   UNK     0    8670.6678665.408   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0    8669.3338667.999   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0    8670.6678666.949   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0    8666.6668666.176   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0    8665.3328665.408   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0    8663.9998666.176   0.000  0.00  0.00           C+0
HETATM    9  O   UNK     0    8662.6658665.408   0.000  0.00  0.00           O-1
HETATM   10  O   UNK     0    8663.9998667.715   0.000  0.00  0.00           O+0
HETATM   11  O   UNK     0    8666.6668667.715   0.000  0.00  0.00           O+0
CONECT    1    2    6                                                       
CONECT    2    1    3    4    5                                             
CONECT    3    2                                                            
CONECT    4    2                                                            
CONECT    5    2                                                            
CONECT    6    1    7   11                                                  
CONECT    7    6    8                                                       
CONECT    8    7    9   10                                                  
CONECT    9    8                                                            
CONECT   10    8                                                            
CONECT   11    6                                                            
MASTER        0    0    0    0    0    0    0    0   11    0   20    0
END
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3D PDB for HMDB0012154 (3-Dehydrocarnitine)

COMPND    HMDB0012154
HETATM    1  C1  UNL     1      -0.759  -0.863  -1.291  1.00  0.00           C  
HETATM    2  N1  UNL     1      -1.045   0.071  -0.267  1.00  0.00           N1+
HETATM    3  C2  UNL     1      -2.450   0.495  -0.420  1.00  0.00           C  
HETATM    4  C3  UNL     1      -1.005  -0.652   1.012  1.00  0.00           C  
HETATM    5  C4  UNL     1      -0.188   1.197  -0.148  1.00  0.00           C  
HETATM    6  C5  UNL     1       1.240   0.977  -0.032  1.00  0.00           C  
HETATM    7  O1  UNL     1       1.943   1.989   0.125  1.00  0.00           O  
HETATM    8  C6  UNL     1       1.960  -0.307  -0.078  1.00  0.00           C  
HETATM    9  C7  UNL     1       3.408  -0.168   0.117  1.00  0.00           C  
HETATM   10  O2  UNL     1       3.904   0.952   0.298  1.00  0.00           O  
HETATM   11  O3  UNL     1       4.198  -1.297   0.097  1.00  0.00           O1-
HETATM   12  H1  UNL     1      -0.278  -1.812  -0.904  1.00  0.00           H  
HETATM   13  H2  UNL     1      -1.744  -1.253  -1.691  1.00  0.00           H  
HETATM   14  H3  UNL     1      -0.263  -0.452  -2.178  1.00  0.00           H  
HETATM   15  H4  UNL     1      -3.077  -0.350  -0.784  1.00  0.00           H  
HETATM   16  H5  UNL     1      -2.466   1.261  -1.209  1.00  0.00           H  
HETATM   17  H6  UNL     1      -2.874   0.839   0.526  1.00  0.00           H  
HETATM   18  H7  UNL     1      -0.302  -0.166   1.733  1.00  0.00           H  
HETATM   19  H8  UNL     1      -0.683  -1.695   0.880  1.00  0.00           H  
HETATM   20  H9  UNL     1      -1.989  -0.638   1.529  1.00  0.00           H  
HETATM   21  H10 UNL     1      -0.525   1.837   0.725  1.00  0.00           H  
HETATM   22  H11 UNL     1      -0.455   1.868  -1.026  1.00  0.00           H  
HETATM   23  H12 UNL     1       1.611  -1.074   0.625  1.00  0.00           H  
HETATM   24  H13 UNL     1       1.840  -0.759  -1.100  1.00  0.00           H  
CONECT    1    2   12   13   14
CONECT    2    3    4    5
CONECT    3   15   16   17
CONECT    4   18   19   20
CONECT    5    6   21   22
CONECT    6    7    7    8
CONECT    8    9   23   24
CONECT    9   10   10   11
END
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SMILES for HMDB0012154 (3-Dehydrocarnitine)

C[N+](C)(C)CC(=O)CC([O-])=O
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INCHI for HMDB0012154 (3-Dehydrocarnitine)

InChI=1S/C7H13NO3/c1-8(2,3)5-6(9)4-7(10)11/h4-5H2,1-3H3
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View in JSmolView Stereo Labels
Synonyms
ValueSource
3-oxo-4-(Trimethylammonio)butanoateChEBI
3-oxo-4-(Trimethylammonio)butanoic acidGenerator
3-Carboxy-N,N,N-trimethyl-2-oxo-1-propanaminiumHMDB
3-Carboxy-N,N,N-trimethyl-2-oxopropan-1-aminiumHMDB
Chemical FormulaC7H13NO3
Average Molecular Weight159.183
Monoisotopic Molecular Weight159.089543287
IUPAC Name3-oxo-4-(trimethylazaniumyl)butanoate
Traditional Name3-dehydrocarnitine
CAS Registry Number10457-99-5
SMILES
C[N+](C)(C)CC(=O)CC([O-])=O
InChI Identifier
InChI=1S/C7H13NO3/c1-8(2,3)5-6(9)4-7(10)11/h4-5H2,1-3H3
InChI KeyYNOWULSFLVIUDH-UHFFFAOYSA-N
Chemical Taxonomy
Description Belongs to the class of organic compounds known as short-chain keto acids and derivatives. These are keto acids with an alkyl chain the contains less than 6 carbon atoms.
KingdomOrganic compounds
Super ClassOrganic acids and derivatives
ClassKeto acids and derivatives
Sub ClassShort-chain keto acids and derivatives
Direct ParentShort-chain keto acids and derivatives
Alternative Parents
Substituents
  • Beta-keto acid
  • Short-chain keto acid
  • 1,3-dicarbonyl compound
  • Alpha-aminoketone
  • Tetraalkylammonium salt
  • Quaternary ammonium salt
  • Carboxylic acid salt
  • Ketone
  • Carboxylic acid derivative
  • Carboxylic acid
  • Monocarboxylic acid or derivatives
  • Organic nitrogen compound
  • Organonitrogen compound
  • Organooxygen compound
  • Organic salt
  • Hydrocarbon derivative
  • Organic oxide
  • Organopnictogen compound
  • Carbonyl group
  • Organic oxygen compound
  • Amine
  • Aliphatic acyclic compound
Molecular FrameworkAliphatic acyclic compounds
External Descriptors
Ontology
Physiological effectNot Available
Disposition
Biological locationSource
ProcessNot Available
RoleNot Available
Physical Properties
StateSolid
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
Predicted Chromatographic Properties
Spectra
Biological Properties
Cellular LocationsNot Available
Biospecimen Locations
  • Feces
  • Saliva
  • Urine
Tissue LocationsNot Available
Pathways
Normal Concentrations
Abnormal Concentrations
BiospecimenStatusValueAgeSexConditionReferenceDetails
FecesDetected but not QuantifiedNot QuantifiedAdult (>18 years old)Both
Colorectal cancer		 details
FecesDetected but not QuantifiedNot QuantifiedAdult (>18 years old)BothColorectal Cancer details
FecesDetected but not QuantifiedNot QuantifiedAdult (>18 years old)BothColorectal Cancer details
UrineDetected but not QuantifiedNot QuantifiedAdult (>18 years old)Both
Colorectal adenoma 		details
Associated Disorders and Diseases
Disease References
Colorectal cancer
  1. 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 ]
  2. 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 ]
  3. 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 ]
Associated OMIM IDs
DrugBank IDNot Available
Phenol Explorer Compound IDNot Available
FooDB IDFDB028811
KNApSAcK IDNot Available
Chemspider ID5360148
KEGG Compound IDC02636
BioCyc ID3-DE-H-CARNITINE
BiGG IDNot Available
Wikipedia Link3-Dehydrocarnitine
METLIN IDNot Available
PubChem Compound6991982
PDB IDNot Available
ChEBI ID57885
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