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Showing NP-Card for 3-Dehydrocarnitine (NP0091948)

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Record Information
Version2.0
Created at2022-05-11 18:52:51 UTC
Updated at2022-05-11 18:52:51 UTC
NP-MRD IDNP0091948
Secondary Accession NumbersNone
Natural Product Identification
Common Name3-Dehydrocarnitine
Description3-Dehydrocarnitine 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. 3-Dehydrocarnitine is an extremely weak basic (essentially neutral) compound (based on its pKa). 3-Dehydrocarnitine is found in Apis cerana. 3-Dehydrocarnitine was first documented in 1967 (PMID: 4968678). An ammonium betaine that is the conjugate base of 3-dehydrocarnitinium; major species at pH 7.3 (PMID: 25037050).
Structure
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MOL3D MOLSDFPDBSMILESInChI

MOL for NP0091948 (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 NP0091948 (3-Dehydrocarnitine)

     RDKit          3D

 24 23  0  0  0  0  0  0  0  0999 V2000
   -1.1612    1.0095    1.0811 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1481   -0.0132    0.0359 N   0  0  0  0  0  4  0  0  0  0  0  0
   -1.5027    0.6434   -1.1954 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1812   -0.9827    0.4170 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.1215   -0.6873   -0.0271 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.1770    0.1291   -0.6661 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.8801    1.2459   -1.0430 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.5666   -0.3866   -0.8489 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.4796    0.0910    0.2019 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.4632   -0.4543    1.3301 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.3642    1.1304   -0.0143 O   0  0  0  0  0  1  0  0  0  0  0  0
   -0.7761    0.6000    2.0285 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2364    1.3081    1.1861 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6328    1.9345    0.7499 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3997    1.7548   -1.1022 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6109    0.4708   -1.3401 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9658    0.2544   -2.0837 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6291   -0.7582    1.4060 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7280   -2.0086    0.4945 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9935   -1.0394   -0.3211 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.4414   -1.0386    0.9960 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.0022   -1.6168   -0.6286 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.9302   -0.0792   -1.8507 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.5395   -1.5069   -0.8498 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 11  1  0
  9 10  2  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 NP0091948 (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>
NP0091948

> <DATABASE_NAME>
NP-MRD

> <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

$$$$
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3D-SDF for NP0091948 (3-Dehydrocarnitine)

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PDB for NP0091948 (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 NP0091948 (3-Dehydrocarnitine)
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SMILES for NP0091948 (3-Dehydrocarnitine)
C[N+](C)(C)CC(=O)CC([O-])=O
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INCHI for NP0091948 (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 JSmol
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 Mass159.1830 Da
Monoisotopic Mass159.08954 Da
IUPAC Name3-oxo-4-(trimethylazaniumyl)butanoate
Traditional Name3-dehydrocarnitine
CAS Registry NumberNot Available
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
Experimental Spectra
Not Available
Predicted Spectra
Spectrum TypeDescriptionDepositor IDDepositor OrganizationDepositorDeposition DateView
1D NMR13C NMR Spectrum (1D, 25 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 100 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 252 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 1000 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 50 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 200 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 75 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 300 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 101 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 400 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 126 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 500 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 151 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 600 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 176 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 700 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 201 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 800 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 226 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 900 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
Chemical Shift Submissions
Not Available
Species
Species of Origin
Species NameSourceReference
Anas platyrhynchosFooDB
AnatidaeFooDB
Anser anserFooDB
Apis ceranaLOTUS Database
Bison bisonFooDB
Bos taurusFooDB
Bos taurus X Bison bisonFooDB
Bubalus bubalisFooDB
Capra aegagrus hircusFooDB
CervidaeFooDB
Cervus canadensisFooDB
ColumbaFooDB
ColumbidaeFooDB
Dromaius novaehollandiaeFooDB
Equus caballusFooDB
Gallus gallusFooDB
Lagopus mutaFooDB
LeporidaeFooDB
Lepus timidusFooDB
Melanitta fuscaFooDB
Meleagris gallopavoFooDB
Numida meleagrisFooDB
OdocoileusFooDB
OryctolagusFooDB
Ovis ariesFooDB
PhasianidaeFooDB
Phasianus colchicusFooDB
Struthio camelusFooDB
Sus scrofaFooDB
Sus scrofa domesticaFooDB
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
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-2.2ALOGPS
logP-4.3ChemAxon
logS-2.3ALOGPS
pKa (Strongest Acidic)3.94ChemAxon
pKa (Strongest Basic)-8.7ChemAxon
Physiological Charge0ChemAxon
Hydrogen Acceptor Count3ChemAxon
Hydrogen Donor Count0ChemAxon
Polar Surface Area57.2 ŲChemAxon
Rotatable Bond Count4ChemAxon
Refractivity62.72 m³·mol⁻¹ChemAxon
Polarizability16.08 ųChemAxon
Number of Rings0ChemAxon
BioavailabilityYesChemAxon
Rule of FiveYesChemAxon
Ghose FilterNoChemAxon
Veber's RuleNoChemAxon
MDDR-like RuleNoChemAxon
HMDB IDHMDB0012154  
DrugBank IDNot Available
Phenol Explorer Compound IDNot Available
FoodDB 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  
Good Scents IDNot Available
References
General References
  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. Kleber HP, Schopp W, Sorger H, Tauchert H, Aurich H: [Formation of 3-dehydrocarnitine from L-carnitine through the action of a Pseudomonas aeruginosa enzyme]. Acta Biol Med Ger. 1967;19(5):659-67. [PubMed:4968678  ]