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Record Information

Version

5.0

Status

Detected and Quantified

Creation Date

2006-05-22 14:17:36 UTC

Update Date

2022-03-07 02:49:12 UTC

HMDB ID

HMDB0002095

Secondary Accession Numbers

HMDB0062496
HMDB0062592
HMDB02095
HMDB62496
HMDB62592

Metabolite Identification

Common Name

Malonylcarnitine

Description

Malonylcarnitine is a metabolite that accumulates with specific disruption of fatty-acid oxidation caused by the impaired entry of long-chain acylcarnitine esters into the mitochondria and failure of the mitochondrial respiratory chain at complex 11 and malonyl-CoA decarboxylase (EC 4.1.1.9) deficiency (OMIM: 248360 ). Malonylcarnitine has also been found to accumulate in some newborns with medium-chain acyl-CoA dehydrogenase (EC 1.3.99.3) deficiency (OMIM: 201450 ). (PMID:11558490 , 15303003 , 12651823 ).

Structure

MOL 3D MOL SDF 3D SDF PDB 3D PDB SMILES InChI

HMDB0002095
     RDKit          3D
Malonylcarnitine
 34 33  0  0  0  0  0  0  0  0999 V2000
   -2.8374   -1.9144    0.5063 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2819   -0.6223    0.0702 N   0  0  0  0  0  4  0  0  0  0  0  0
   -2.3372   -0.6107   -1.3722 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.1831    0.3919    0.5752 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9633   -0.5515    0.6037 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0251    0.3774   -0.0771 C   0  0  1  0  0  0  0  0  0  0  0  0
   -0.4357    1.8273    0.0251 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.5582    2.6787   -0.6804 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.6785    2.8272   -0.1099 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.3449    3.3011   -1.8832 O   0  0  0  0  0  1  0  0  0  0  0  0
    1.2250    0.2798    0.6240 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.4028   -0.0427   -0.0294 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.3049   -0.2435   -1.2755 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.7129   -0.1496    0.6836 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.7853   -0.4987   -0.2499 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.5125   -0.6646   -1.4654 O   0  0  0  0  0  0  0  0  0  0  0  0
    6.0758   -0.6350    0.2515 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.9278   -1.9097    0.5433 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4485   -2.1041    1.5415 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4126   -2.7499   -0.1132 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.1165   -1.3224   -1.7290 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3918   -0.9195   -1.8478 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6850    0.4001   -1.7006 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5848    1.0110   -0.2588 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.0631   -0.0340    1.0857 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6594    1.0259    1.3372 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5146   -1.5712    0.5807 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0276   -0.2673    1.6740 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.1825    0.1575   -1.1250 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4584    2.1825    1.0780 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4081    1.9975   -0.4741 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.8616    0.8036    1.2190 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.6401   -0.9593    1.4444 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.4770   -1.4910    0.5482 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  1  0
  7  8  1  0
  8  9  2  0
  8 10  1  0
  6 11  1  0
 11 12  1  0
 12 13  2  0
 12 14  1  0
 14 15  1  0
 15 16  2  0
 15 17  1  0
  1 18  1  0
  1 19  1  0
  1 20  1  0
  3 21  1  0
  3 22  1  0
  3 23  1  0
  4 24  1  0
  4 25  1  0
  4 26  1  0
  5 27  1  0
  5 28  1  0
  6 29  1  6
  7 30  1  0
  7 31  1  0
 14 32  1  0
 14 33  1  0
 17 34  1  0
M  CHG  2   2   1  10  -1
M  END

      
  Mrv1652305271900202D          

 17 16  0  0  1  0            999 V2000
   -0.9059    2.7770    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9059    1.9520    0.0000 N   0  3  0  0  0  0  0  0  0  0  0  0
   -1.7309    1.9520    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0809    1.9520    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9059    1.1270    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1913    0.7145    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   -0.1913   -0.1105    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9059   -0.5230    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6204   -0.1105    0.0000 O   0  5  0  0  0  0  0  0  0  0  0  0
   -0.9059   -1.3480    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.5230    1.1270    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.2374    0.7145    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.2374   -0.1105    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.9520    1.1270    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.6664    0.7145    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.3809    1.1270    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.6664   -0.1105    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  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
  5  6  1  0  0  0  0
  6  7  1  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
  6 11  1  6  0  0  0
 11 12  1  0  0  0  0
 12 13  2  0  0  0  0
 12 14  1  0  0  0  0
 14 15  1  0  0  0  0
 15 16  1  0  0  0  0
 15 17  2  0  0  0  0
M  CHG  2   2   1   9  -1
M  END
> <DATABASE_ID>
HMDB0002095

> <DATABASE_NAME>
hmdb

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

> <INCHI_IDENTIFIER>
InChI=1S/C10H17NO6/c1-11(2,3)6-7(4-8(12)13)17-10(16)5-9(14)15/h7H,4-6H2,1-3H3,(H-,12,13,14,15)/t7-/m1/s1

> <INCHI_KEY>
ZGNBLKBZJBJFDG-SSDOTTSWSA-N

> <FORMULA>
C10H17NO6

> <MOLECULAR_WEIGHT>
247.247

> <EXACT_MASS>
247.105587271

> <JCHEM_ACCEPTOR_COUNT>
5

> <JCHEM_ATOM_COUNT>
34

> <JCHEM_AVERAGE_POLARIZABILITY>
23.67588410523618

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
1

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(3R)-3-[(2-carboxyacetyl)oxy]-4-(trimethylazaniumyl)butanoate

> <ALOGPS_LOGP>
-1.98

> <JCHEM_LOGP>
-4.554152191805079

> <ALOGPS_LOGS>
-2.95

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
0

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-1

> <JCHEM_PKA>
4.169537385693162

> <JCHEM_PKA_STRONGEST_ACIDIC>
3.4676356359550904

> <JCHEM_PKA_STRONGEST_BASIC>
-7.172258267685226

> <JCHEM_POLAR_SURFACE_AREA>
103.73000000000002

> <JCHEM_REFRACTIVITY>
78.98089999999999

> <JCHEM_ROTATABLE_BOND_COUNT>
8

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
3.41e-01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
(3R)-3-[(2-carboxyacetyl)oxy]-4-(trimethylammonio)butanoate

> <JCHEM_VEBER_RULE>
0

$$$$

HMDB0002095
     RDKit          3D
Malonylcarnitine
 34 33  0  0  0  0  0  0  0  0999 V2000
   -2.8374   -1.9144    0.5063 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2819   -0.6223    0.0702 N   0  0  0  0  0  4  0  0  0  0  0  0
   -2.3372   -0.6107   -1.3722 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.1831    0.3919    0.5752 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9633   -0.5515    0.6037 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0251    0.3774   -0.0771 C   0  0  1  0  0  0  0  0  0  0  0  0
   -0.4357    1.8273    0.0251 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.5582    2.6787   -0.6804 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.6785    2.8272   -0.1099 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.3449    3.3011   -1.8832 O   0  0  0  0  0  1  0  0  0  0  0  0
    1.2250    0.2798    0.6240 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.4028   -0.0427   -0.0294 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.3049   -0.2435   -1.2755 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.7129   -0.1496    0.6836 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.7853   -0.4987   -0.2499 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.5125   -0.6646   -1.4654 O   0  0  0  0  0  0  0  0  0  0  0  0
    6.0758   -0.6350    0.2515 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.9278   -1.9097    0.5433 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4485   -2.1041    1.5415 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4126   -2.7499   -0.1132 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.1165   -1.3224   -1.7290 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3918   -0.9195   -1.8478 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6850    0.4001   -1.7006 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5848    1.0110   -0.2588 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.0631   -0.0340    1.0857 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6594    1.0259    1.3372 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5146   -1.5712    0.5807 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0276   -0.2673    1.6740 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.1825    0.1575   -1.1250 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4584    2.1825    1.0780 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4081    1.9975   -0.4741 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.8616    0.8036    1.2190 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.6401   -0.9593    1.4444 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.4770   -1.4910    0.5482 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  1  0
  7  8  1  0
  8  9  2  0
  8 10  1  0
  6 11  1  0
 11 12  1  0
 12 13  2  0
 12 14  1  0
 14 15  1  0
 15 16  2  0
 15 17  1  0
  1 18  1  0
  1 19  1  0
  1 20  1  0
  3 21  1  0
  3 22  1  0
  3 23  1  0
  4 24  1  0
  4 25  1  0
  4 26  1  0
  5 27  1  0
  5 28  1  0
  6 29  1  6
  7 30  1  0
  7 31  1  0
 14 32  1  0
 14 33  1  0
 17 34  1  0
M  CHG  2   2   1  10  -1
M  END

HEADER    PROTEIN                                 27-MAY-19   NONE
TITLE     NULL                                                        
COMPND    MOLECULE:                                                   
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   27-MAY-19         0                                  
HETATM    1  C   UNK     0      -1.691   5.184   0.000  0.00  0.00           C+0
HETATM    2  N   UNK     0      -1.691   3.644   0.000  0.00  0.00           N+1
HETATM    3  C   UNK     0      -3.231   3.644   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0      -0.151   3.644   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0      -1.691   2.104   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0      -0.357   1.334   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0      -0.357  -0.206   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0      -1.691  -0.976   0.000  0.00  0.00           C+0
HETATM    9  O   UNK     0      -3.025  -0.206   0.000  0.00  0.00           O-1
HETATM   10  O   UNK     0      -1.691  -2.516   0.000  0.00  0.00           O+0
HETATM   11  O   UNK     0       0.976   2.104   0.000  0.00  0.00           O+0
HETATM   12  C   UNK     0       2.310   1.334   0.000  0.00  0.00           C+0
HETATM   13  O   UNK     0       2.310  -0.206   0.000  0.00  0.00           O+0
HETATM   14  C   UNK     0       3.644   2.104   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0       4.977   1.334   0.000  0.00  0.00           C+0
HETATM   16  O   UNK     0       6.311   2.104   0.000  0.00  0.00           O+0
HETATM   17  O   UNK     0       4.977  -0.206   0.000  0.00  0.00           O+0
CONECT    1    2                                                            
CONECT    2    1    3    4    5                                             
CONECT    3    2                                                            
CONECT    4    2                                                            
CONECT    5    2    6                                                       
CONECT    6    5    7   11                                                  
CONECT    7    6    8                                                       
CONECT    8    7    9   10                                                  
CONECT    9    8                                                            
CONECT   10    8                                                            
CONECT   11    6   12                                                       
CONECT   12   11   13   14                                                  
CONECT   13   12                                                            
CONECT   14   12   15                                                       
CONECT   15   14   16   17                                                  
CONECT   16   15                                                            
CONECT   17   15                                                            
MASTER        0    0    0    0    0    0    0    0   17    0   32    0
END

COMPND    HMDB0002095
HETATM    1  C1  UNL     1      -2.837  -1.914   0.506  1.00  0.00           C  
HETATM    2  N1  UNL     1      -2.282  -0.622   0.070  1.00  0.00           N1+
HETATM    3  C2  UNL     1      -2.337  -0.611  -1.372  1.00  0.00           C  
HETATM    4  C3  UNL     1      -3.183   0.392   0.575  1.00  0.00           C  
HETATM    5  C4  UNL     1      -0.963  -0.551   0.604  1.00  0.00           C  
HETATM    6  C5  UNL     1      -0.025   0.377  -0.077  1.00  0.00           C  
HETATM    7  C6  UNL     1      -0.436   1.827   0.025  1.00  0.00           C  
HETATM    8  C7  UNL     1       0.558   2.679  -0.680  1.00  0.00           C  
HETATM    9  O1  UNL     1       1.678   2.827  -0.110  1.00  0.00           O  
HETATM   10  O2  UNL     1       0.345   3.301  -1.883  1.00  0.00           O1-
HETATM   11  O3  UNL     1       1.225   0.280   0.624  1.00  0.00           O  
HETATM   12  C8  UNL     1       2.403  -0.043  -0.029  1.00  0.00           C  
HETATM   13  O4  UNL     1       2.305  -0.243  -1.275  1.00  0.00           O  
HETATM   14  C9  UNL     1       3.713  -0.150   0.684  1.00  0.00           C  
HETATM   15  C10 UNL     1       4.785  -0.499  -0.250  1.00  0.00           C  
HETATM   16  O5  UNL     1       4.513  -0.665  -1.465  1.00  0.00           O  
HETATM   17  O6  UNL     1       6.076  -0.635   0.252  1.00  0.00           O  
HETATM   18  H1  UNL     1      -3.928  -1.910   0.543  1.00  0.00           H  
HETATM   19  H2  UNL     1      -2.449  -2.104   1.542  1.00  0.00           H  
HETATM   20  H3  UNL     1      -2.413  -2.750  -0.113  1.00  0.00           H  
HETATM   21  H4  UNL     1      -3.116  -1.322  -1.729  1.00  0.00           H  
HETATM   22  H5  UNL     1      -1.392  -0.919  -1.848  1.00  0.00           H  
HETATM   23  H6  UNL     1      -2.685   0.400  -1.701  1.00  0.00           H  
HETATM   24  H7  UNL     1      -3.585   1.011  -0.259  1.00  0.00           H  
HETATM   25  H8  UNL     1      -4.063  -0.034   1.086  1.00  0.00           H  
HETATM   26  H9  UNL     1      -2.659   1.026   1.337  1.00  0.00           H  
HETATM   27  H10 UNL     1      -0.515  -1.571   0.581  1.00  0.00           H  
HETATM   28  H11 UNL     1      -1.028  -0.267   1.674  1.00  0.00           H  
HETATM   29  H12 UNL     1       0.183   0.158  -1.125  1.00  0.00           H  
HETATM   30  H13 UNL     1      -0.458   2.183   1.078  1.00  0.00           H  
HETATM   31  H14 UNL     1      -1.408   1.997  -0.474  1.00  0.00           H  
HETATM   32  H15 UNL     1       3.862   0.804   1.219  1.00  0.00           H  
HETATM   33  H16 UNL     1       3.640  -0.959   1.444  1.00  0.00           H  
HETATM   34  H17 UNL     1       6.477  -1.491   0.548  1.00  0.00           H  
CONECT    1    2   18   19   20
CONECT    2    3    4    5
CONECT    3   21   22   23
CONECT    4   24   25   26
CONECT    5    6   27   28
CONECT    6    7   11   29
CONECT    7    8   30   31
CONECT    8    9    9   10
CONECT   11   12
CONECT   12   13   13   14
CONECT   14   15   32   33
CONECT   15   16   16   17
CONECT   17   34
END

HMDB0002095
     RDKit          3D
Malonylcarnitine
 34 33  0  0  0  0  0  0  0  0999 V2000
   -2.8374   -1.9144    0.5063 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2819   -0.6223    0.0702 N   0  0  0  0  0  4  0  0  0  0  0  0
   -2.3372   -0.6107   -1.3722 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.1831    0.3919    0.5752 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9633   -0.5515    0.6037 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0251    0.3774   -0.0771 C   0  0  1  0  0  0  0  0  0  0  0  0
   -0.4357    1.8273    0.0251 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.5582    2.6787   -0.6804 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.6785    2.8272   -0.1099 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.3449    3.3011   -1.8832 O   0  0  0  0  0  1  0  0  0  0  0  0
    1.2250    0.2798    0.6240 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.4028   -0.0427   -0.0294 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.3049   -0.2435   -1.2755 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.7129   -0.1496    0.6836 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.7853   -0.4987   -0.2499 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.5125   -0.6646   -1.4654 O   0  0  0  0  0  0  0  0  0  0  0  0
    6.0758   -0.6350    0.2515 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.9278   -1.9097    0.5433 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4485   -2.1041    1.5415 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4126   -2.7499   -0.1132 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.1165   -1.3224   -1.7290 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3918   -0.9195   -1.8478 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6850    0.4001   -1.7006 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5848    1.0110   -0.2588 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.0631   -0.0340    1.0857 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6594    1.0259    1.3372 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5146   -1.5712    0.5807 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0276   -0.2673    1.6740 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.1825    0.1575   -1.1250 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4584    2.1825    1.0780 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4081    1.9975   -0.4741 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.8616    0.8036    1.2190 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.6401   -0.9593    1.4444 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.4770   -1.4910    0.5482 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  1  0
  7  8  1  0
  8  9  2  0
  8 10  1  0
  6 11  1  0
 11 12  1  0
 12 13  2  0
 12 14  1  0
 14 15  1  0
 15 16  2  0
 15 17  1  0
  1 18  1  0
  1 19  1  0
  1 20  1  0
  3 21  1  0
  3 22  1  0
  3 23  1  0
  4 24  1  0
  4 25  1  0
  4 26  1  0
  5 27  1  0
  5 28  1  0
  6 29  1  6
  7 30  1  0
  7 31  1  0
 14 32  1  0
 14 33  1  0
 17 34  1  0
M  CHG  2   2   1  10  -1
M  END

View in JSmol View NMR Assignments View Stereo Labels

Synonyms

Value	Source
Malonyl-carnitin	HMDB
Malonyl-carnitine	HMDB
Malonyl-L-carnitine	HMDB
O-Malonyl-L-carnitine	HMDB
O-Malonylcarnitine	HMDB
Malonylcarnitine	HMDB

Chemical Formula

C₁₀H₁₇NO₆

Average Molecular Weight

247.247

Monoisotopic Molecular Weight

247.105587271

IUPAC Name

(3R)-3-[(2-carboxyacetyl)oxy]-4-(trimethylazaniumyl)butanoate

Traditional Name

(3R)-3-[(2-carboxyacetyl)oxy]-4-(trimethylammonio)butanoate

CAS Registry Number

910825-21-7

SMILES

C[N+](C)(C)C[C@@H](CC([O-])=O)OC(=O)CC(O)=O

InChI Identifier

InChI=1S/C10H17NO6/c1-11(2,3)6-7(4-8(12)13)17-10(16)5-9(14)15/h7H,4-6H2,1-3H3,(H-,12,13,14,15)/t7-/m1/s1

InChI Key

ZGNBLKBZJBJFDG-SSDOTTSWSA-N

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as acyl carnitines. These are organic compounds containing a fatty acid with the carboxylic acid attached to carnitine through an ester bond.

Kingdom

Organic compounds

Super Class

Lipids and lipid-like molecules

Class

Fatty Acyls

Sub Class

Fatty acid esters

Direct Parent

Acyl carnitines

Alternative Parents

Substituents

Acyl-carnitine
Tricarboxylic acid or derivatives
1,3-dicarbonyl compound
Quaternary ammonium salt
Tetraalkylammonium salt
Carboxylic acid salt
Carboxylic acid ester
Carboxylic acid
Carboxylic acid derivative
Hydrocarbon derivative
Organic salt
Organopnictogen compound
Organic oxygen compound
Organic nitrogen compound
Organooxygen compound
Organonitrogen compound
Carbonyl group
Amine
Organic oxide
Aliphatic acyclic compound

Molecular Framework

Aliphatic acyclic compounds

External Descriptors

O-acyl-L-carnitine (CHEBI:85470 )

Ontology

Physiological effect

Not Available

Disposition

Biological location

Non-excretory biofluid

Biofluid or Excreta

Blood (PMID: 11558490)

Organ

Placenta (HMDB: HMDB0002095)

Excreta

Biofluid or Excreta

Urine (PMID: 24023812)

Cellular substructure

Extracellular (HMDB: HMDB0002095)
Membrane (HMDB: HMDB0002095)

Source

Exogenous

Exogenous (HMDB: HMDB0002095)

Food

Animal origin

Poultry

Pheasant (FooDB: FOOD00430)
Squab (FooDB: FOOD00481)
Turkey (FooDB: FOOD00494)
Quail (FooDB: FOOD00541)
Anatidae (FooDB: FOOD00576)
Rock ptarmigan (FooDB: FOOD00597)
Columbidae (Dove, Pigeon) (FooDB: FOOD00610)
Chicken (FooDB: FOOD00329)
Mallard duck (FooDB: FOOD00353)
Emu (FooDB: FOOD00360)
Greylag goose (FooDB: FOOD00368)
Guinea hen (FooDB: FOOD00373)
Ostrich (FooDB: FOOD00422)
Velvet duck (FooDB: FOOD00427)

Lagomorph

Ovis

Sheep (Mutton, Lamb) (FooDB: FOOD00473)

Bovine

Venison

Deer (FooDB: FOOD00524)
Mule deer (FooDB: FOOD00348)
Elk (FooDB: FOOD00359)

Caprae

Domestic goat (FooDB: FOOD00529)

Swine

Domestic pig (FooDB: FOOD00536)
Wild boar (FooDB: FOOD00307)

Equine

Horse (FooDB: FOOD00378)

Endogenous

Endogenous (HMDB: HMDB0002095)

Process

Not Available

Role

Industrial application

Pharmaceutical industry

Biomarker

Pregnancy (MarkerDB: MDB00000376)
Malonyl Co A Decarboxylase Deficiency (MarkerDB: MDB00000376)

Physical Properties

State

Solid

Experimental Molecular Properties

Property	Value	Reference
Melting Point	Not Available	Not Available
Boiling Point	Not Available	Not Available
Water Solubility	Not Available	Not Available
LogP	Not Available	Not Available

Experimental Chromatographic Properties

Not Available

Predicted Molecular Properties

Property	Value	Source
Water Solubility	0.34 g/L	ALOGPS
logP	-2	ALOGPS
logP	-4.6	ChemAxon
logS	-3	ALOGPS
pKa (Strongest Acidic)	3.47	ChemAxon
pKa (Strongest Basic)	-7.2	ChemAxon
Physiological Charge	-1	ChemAxon
Hydrogen Acceptor Count	5	ChemAxon
Hydrogen Donor Count	1	ChemAxon
Polar Surface Area	103.73 Å²	ChemAxon
Rotatable Bond Count	8	ChemAxon
Refractivity	78.98 m³·mol⁻¹	ChemAxon
Polarizability	23.68 Å³	ChemAxon
Number of Rings	0	ChemAxon
Bioavailability	Yes	ChemAxon
Rule of Five	Yes	ChemAxon
Ghose Filter	No	ChemAxon
Veber's Rule	No	ChemAxon
MDDR-like Rule	No	ChemAxon

Predicted Chromatographic Properties

Predicted Collision Cross Sections

Predictor	Adduct Type	CCS Value (Å²)	Reference
DeepCCS	[M+H]+	158.361	30932474
DeepCCS	[M-H]-	155.966	30932474
DeepCCS	[M-2H]-	188.984	30932474
DeepCCS	[M+Na]+	164.401	30932474
AllCCS	[M+H]+	155.1	32859911
AllCCS	[M+H-H2O]+	152.0	32859911
AllCCS	[M+NH4]+	158.0	32859911
AllCCS	[M+Na]+	158.9	32859911
AllCCS	[M-H]-	160.9	32859911
AllCCS	[M+Na-2H]-	161.7	32859911
AllCCS	[M+HCOO]-	162.7	32859911

Predicted Retention Times

Underivatized

Chromatographic Method	Retention Time	Reference
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.	2.12 minutes	32390414
Predicted by Siyang on May 30, 2022	9.5378 minutes	33406817
Predicted by Siyang using ReTip algorithm on June 8, 2022	6.71 minutes	32390414
AjsUoB = Accucore 150 Amide HILIC with 10mM Ammonium Formate, 0.1% Formic Acid	347.7 seconds	40023050
Fem_Long = Waters ACQUITY UPLC HSS T3 C18 with Water:MeOH and 0.1% Formic Acid	560.6 seconds	40023050
Fem_Lipids = Ascentis Express C18 with (60:40 water:ACN):(90:10 IPA:ACN) and 10mM NH4COOH + 0.1% Formic Acid	221.6 seconds	40023050
Life_Old = Waters ACQUITY UPLC BEH C18 with Water:(20:80 acetone:ACN) and 0.1% Formic Acid	80.5 seconds	40023050
Life_New = RP Waters ACQUITY UPLC HSS T3 C18 with Water:(30:70 MeOH:ACN) and 0.1% Formic Acid	156.0 seconds	40023050
RIKEN = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid	48.6 seconds	40023050
Eawag_XBridgeC18 = XBridge C18 3.5u 2.1x50 mm with Water:MeOH and 0.1% Formic Acid	236.0 seconds	40023050
BfG_NTS_RP1 =Agilent Zorbax Eclipse Plus C18 (2.1 mm x 150 mm, 3.5 um) with Water:ACN and 0.1% Formic Acid	288.7 seconds	40023050
HILIC_BDD_2 = Merck SeQuant ZIC-HILIC with ACN(0.1% formic acid):water(16 mM ammonium formate)	842.5 seconds	40023050
UniToyama_Atlantis = RP Waters Atlantis T3 (2.1 x 150 mm, 5 um) with ACN:Water and 0.1% Formic Acid	676.6 seconds	40023050
BDD_C18 = Hypersil Gold 1.9µm C18 with Water:ACN and 0.1% Formic Acid	54.8 seconds	40023050
UFZ_Phenomenex = Kinetex Core-Shell C18 2.6 um, 3.0 x 100 mm, Phenomenex with Water:MeOH and 0.1% Formic Acid	1181.9 seconds	40023050
SNU_RIKEN_POS = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid	188.9 seconds	40023050
RPMMFDA = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid	192.7 seconds	40023050
MTBLS87 = Merck SeQuant ZIC-pHILIC column with ACN:Water and :ammonium carbonate	573.5 seconds	40023050
KI_GIAR_zic_HILIC_pH2_7 = Merck SeQuant ZIC-HILIC with ACN:Water and 0.1% FA	317.2 seconds	40023050
Meister zic-pHILIC pH9.3 = Merck SeQuant ZIC-pHILIC column with ACN:Water 5mM NH4Ac pH9.3 and 5mM ammonium acetate in water	226.1 seconds	40023050

Predicted Kovats Retention Indices

Underivatized

Metabolite	SMILES	Kovats RI Value	Column Type	Reference
Malonylcarnitine	C[N+](C)(C)C[C@@H](CC([O-])=O)OC(=O)CC(O)=O	2841.1	Standard polar	33892256
Malonylcarnitine	C[N+](C)(C)C[C@@H](CC([O-])=O)OC(=O)CC(O)=O	1311.1	Standard non polar	33892256
Malonylcarnitine	C[N+](C)(C)C[C@@H](CC([O-])=O)OC(=O)CC(O)=O	1754.7	Semi standard non polar	33892256

Derivatized

Derivative Name / Structure	SMILES	Kovats RI Value	Column Type	Reference
Malonylcarnitine,1TMS,isomer #1	C[N+](C)(C)C[C@@H](CC(=O)[O-])OC(=O)CC(=O)O[Si](C)(C)C	1719.2	Semi standard non polar	33892256
Malonylcarnitine,1TBDMS,isomer #1	CC(C)(C)[Si](C)(C)OC(=O)CC(=O)O[C@H](CC(=O)[O-])C[N+](C)(C)C	1961.6	Semi standard non polar	33892256

Spectra

Biological Properties

Cellular Locations

Extracellular
Membrane

Biospecimen Locations

Blood
Urine

Tissue Locations

Placenta

Pathways

Not Available

Name	SMPDB/PathBank	KEGG

Normal Concentrations

Biospecimen	Status	Value	Age	Sex	Condition	Reference	Details
Blood	Detected and Quantified	0.1 (0 - 0.2) uM	Children (1-13 years old)	Not Specified	Normal	11558490	details
Blood	Detected and Quantified	0.030-0.090 uM	Adult (>18 years old)	Both	Normal	Molecular You	details
Blood	Detected and Quantified	<0.30 uM	Newborn (0-30 days old)	Both	Normal	12651823	details
Blood	Detected but not Quantified	Not Quantified	Adult (>18 years old)	Both	Normal	32966057	details
Urine	Detected and Quantified	0.02 (0.01-0.04) umol/mmol creatinine	Adult (>18 years old)	Both	Normal	24023812	details
Urine	Detected and Quantified	0.01-0.08 umol/mmol creatinine	Newborn (0-30 days old)	Both	Normal	32340350	details
Urine	Detected and Quantified	0.04 +/- 0.02 umol/mmol creatinine	Newborn (0-30 days old)	Female	Normal	32340350	details
Urine	Detected and Quantified	0.04 +/- 0.02 umol/mmol creatinine	Newborn (0-30 days old)	Male	Normal	32340350	details
Urine	Detected but not Quantified	Not Quantified	Adult (>18 years old)	Both	Normal	32966057	details

Abnormal Concentrations

Biospecimen	Status	Value	Age	Sex	Condition	Reference	Details
Blood	Detected and Quantified	2.7 (1.6 - 3.8) uM	Newborn (0-30 days old)	Not Specified	Malonyl-CoA decarboxylase deficiency	12651823	details
Blood	Detected and Quantified	0.2 (0.13 - 0.3) uM	Infant (0-1 year old)	Not Specified	Malonyl-CoA decarboxylase deficiency	16078122	details
Blood	Detected and Quantified	46.8 (24.8) uM	Adult (>18 years old)	Female	Late-onset preeclampsia	23159745	details
Blood	Detected and Quantified	27.8 (20.0) uM	Adult (>18 years old)	Female	Pregnancy	23159745	details
Blood	Detected and Quantified	50.65(14.14) uM	Adult (>18 years old)	Both	Heart failure with preserved ejection fraction	26010610	details

Associated Disorders and Diseases

Disease References

Malonyl-Coa decarboxylase deficiency
Santer R, Fingerhut R, Lassker U, Wightman PJ, Fitzpatrick DR, Olgemoller B, Roscher AA: Tandem mass spectrometric determination of malonylcarnitine: diagnosis and neonatal screening of malonyl-CoA decarboxylase deficiency. Clin Chem. 2003 Apr;49(4):660-2. [PubMed:12651823 ] Ficicioglu C, Chrisant MR, Payan I, Chace DH: Cardiomyopathy and hypotonia in a 5-month-old infant with malonyl-coa decarboxylase deficiency: potential for preclinical diagnosis with expanded newborn screening. Pediatr Cardiol. 2005 Nov-Dec;26(6):881-3. [PubMed:16078122 ]
Late-onset preeclampsia
Bahado-Singh RO, Akolekar R, Mandal R, Dong E, Xia J, Kruger M, Wishart DS, Nicolaides K: First-trimester metabolomic detection of late-onset preeclampsia. Am J Obstet Gynecol. 2013 Jan;208(1):58.e1-7. doi: 10.1016/j.ajog.2012.11.003. Epub 2012 Nov 13. [PubMed:23159745 ]
Pregnancy
Bahado-Singh RO, Akolekar R, Mandal R, Dong E, Xia J, Kruger M, Wishart DS, Nicolaides K: First-trimester metabolomic detection of late-onset preeclampsia. Am J Obstet Gynecol. 2013 Jan;208(1):58.e1-7. doi: 10.1016/j.ajog.2012.11.003. Epub 2012 Nov 13. [PubMed:23159745 ]

Associated OMIM IDs

248360 (Malonyl-Coa decarboxylase deficiency)

External Links

DrugBank ID

Not Available

Phenol Explorer Compound ID

Not Available

FooDB ID

FDB022843

KNApSAcK ID

Not Available

Chemspider ID

34999703

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

6484

PubChem Compound

91825606

PDB ID

Not Available

ChEBI ID

85470

Food Biomarker Ontology

Not Available

VMH ID

HC10859

MarkerDB ID

MDB00000376

Good Scents ID

Not Available

References

Synthesis Reference

Not Available

Material Safety Data Sheet (MSDS)

Not Available

General References

Johnson DW, Trinh MU: Stability of malonylcarnitine and glutarylcarnitine in stored blood spots. J Inherit Metab Dis. 2004;27(6):789-90. [PubMed:15617193 ]
Santer R, Fingerhut R, Lassker U, Wightman PJ, Fitzpatrick DR, Olgemoller B, Roscher AA: Tandem mass spectrometric determination of malonylcarnitine: diagnosis and neonatal screening of malonyl-CoA decarboxylase deficiency. Clin Chem. 2003 Apr;49(4):660-2. [PubMed:12651823 ]
Napolitano N, Wiley V, Pitt JJ: Pseudo-glutarylcarnitinaemia in medium-chain acyl-CoA dehydrogenase deficiency detected by tandem mass spectrometry newborn screening. J Inherit Metab Dis. 2004;27(4):465-71. [PubMed:15303003 ]
Wolf A, Weir P, Segar P, Stone J, Shield J: Impaired fatty acid oxidation in propofol infusion syndrome. Lancet. 2001 Feb 24;357(9256):606-7. [PubMed:11558490 ]
Ficicioglu C, Chrisant MR, Payan I, Chace DH: Cardiomyopathy and hypotonia in a 5-month-old infant with malonyl-coa decarboxylase deficiency: potential for preclinical diagnosis with expanded newborn screening. Pediatr Cardiol. 2005 Nov-Dec;26(6):881-3. [PubMed:16078122 ]
Simons K, Toomre D: Lipid rafts and signal transduction. Nat Rev Mol Cell Biol. 2000 Oct;1(1):31-9. [PubMed:11413487 ]
Watson AD: Thematic review series: systems biology approaches to metabolic and cardiovascular disorders. Lipidomics: a global approach to lipid analysis in biological systems. J Lipid Res. 2006 Oct;47(10):2101-11. Epub 2006 Aug 10. [PubMed:16902246 ]
Sethi JK, Vidal-Puig AJ: Thematic review series: adipocyte biology. Adipose tissue function and plasticity orchestrate nutritional adaptation. J Lipid Res. 2007 Jun;48(6):1253-62. Epub 2007 Mar 20. [PubMed:17374880 ]
Lingwood D, Simons K: Lipid rafts as a membrane-organizing principle. Science. 2010 Jan 1;327(5961):46-50. doi: 10.1126/science.1174621. [PubMed:20044567 ]
Elshenawy S, Pinney SE, Stuart T, Doulias PT, Zura G, Parry S, Elovitz MA, Bennett MJ, Bansal A, Strauss JF 3rd, Ischiropoulos H, Simmons RA: The Metabolomic Signature of the Placenta in Spontaneous Preterm Birth. Int J Mol Sci. 2020 Feb 4;21(3). pii: ijms21031043. doi: 10.3390/ijms21031043. [PubMed:32033212 ]
Gunstone, Frank D., John L. Harwood, and Albert J. Dijkstra (2007). The lipid handbook with CD-ROM. CRC Press.

Showing metabocard for Malonylcarnitine (HMDB0002095)

MOL for HMDB0002095 (Malonylcarnitine)

3D MOL for HMDB0002095 (Malonylcarnitine)

3D SDF for HMDB0002095 (Malonylcarnitine)

3D-SDF for HMDB0002095 (Malonylcarnitine)

PDB for HMDB0002095 (Malonylcarnitine)

3D PDB for HMDB0002095 (Malonylcarnitine)

SMILES for HMDB0002095 (Malonylcarnitine)

INCHI for HMDB0002095 (Malonylcarnitine)

Structure for HMDB0002095 (Malonylcarnitine)

3D Structure for HMDB0002095 (Malonylcarnitine)

Predicted Collision Cross Sections

Predicted Retention Times

Underivatized

Predicted Kovats Retention Indices

Underivatized

Derivatized