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Record Information

Version

5.0

Status

Detected and Quantified

Creation Date

2009-11-03 15:30:49 UTC

Update Date

2022-10-24 19:44:11 UTC

HMDB ID

HMDB0013133

Secondary Accession Numbers

HMDB13133

Metabolite Identification

Common Name

Methylmalonylcarnitine

Description

Methylmalonylcarnitine is an acylcarnitine. More specifically, it is an methylmalonic acid ester of carnitine. Acylcarnitines were first discovered more than 70 year ago (PMID: 13825279 ). It is believed that there are more than 1000 types of acylcarnitines in the human body. The general role of acylcarnitines is to transport acyl-groups (organic acids and fatty acids) from the cytoplasm into the mitochondria so that they can be broken down to produce energy. This process is known as beta-oxidation. According to a recent review (PMID: 35710135 ), acylcarnitines (ACs) can be classified into 9 different categories depending on the type and size of their acyl-group: 1) short-chain ACs; 2) medium-chain ACs; 3) long-chain ACs; 4) very long-chain ACs; 5) hydroxy ACs; 6) branched chain ACs; 7) unsaturated ACs; 8) dicarboxylic ACs and 9) miscellaneous ACs. Short-chain ACs have acyl-groups with two to five carbons (C2-C5), medium-chain ACs have acyl-groups with six to thirteen carbons (C6-C13), long-chain ACs have acyl-groups with fourteen to twenty once carbons (C14-C21) and very long-chain ACs have acyl groups with more than 22 carbons. Methylmalonylcarnitine is therefore classified as a short chain AC. As a short-chain acylcarnitine methylmalonylcarnitine is a member of the most abundant group of carnitines in the body, comprising more than 50% of all acylcarnitines quantified in tissues and biofluids (PMID: 31920980 ). Some short-chain carnitines have been studied as supplements or treatments for a number of diseases, including neurological disorders and inborn errors of metabolism. In particular methylmalonylcarnitine is elevated in the blood or plasma of individuals with methylmalonyl-coa epimerase deficiency/methylmalonic acidemia (PMID: 27699154 , PMID: 17279485 ), familial mediterranean fever (PMID: 29900937 ), and cobalamin C deficiency (PMID: 25367534 ). It is also decreased in the blood or plasma of individuals with melanoma (PMID: 30830422 ) and intracerebral hemorrhage (PMID: 29265114 ). Methylmalonylcarnitine is elevated in the urine of individuals with methylmalonyl-coa epimerase deficiency/methylmalonic acidemia (PMID: 27699154 , PMID: 17279485 ). Carnitine acetyltransferase (CrAT, EC:2.3.1.7) is responsible for the synthesis of all short-chain and short branched-chain acylcarnitines (PMID: 23485643 ). The study of acylcarnitines is an active area of research and it is likely that many novel acylcarnitines will be discovered in the coming years. It is also likely that many novel roles in health and disease will be uncovered. An excellent review of the current state of knowledge for acylcarnitines is available (PMID: 35710135 ).

Structure

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

HMDB0013133
     RDKit          3D
Methylmalonylcarnitine
 38 37  0  0  0  0  0  0  0  0999 V2000
    3.6215   -1.9772   -0.5065 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.9643   -0.8645    0.2528 C   0  0  2  0  0  0  0  0  0  0  0  0
    2.7098   -1.1915    1.6626 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.2140   -0.5054    2.5852 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.9101   -2.2607    2.0536 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.7679   -0.3964   -0.4618 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4573   -0.9541   -1.5446 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.9425    0.6297   -0.0263 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1911    0.9963   -0.8027 C   0  0  2  0  0  0  0  0  0  0  0  0
    0.1082    2.3980   -1.2801 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9016    3.0089   -2.1266 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9344    2.4518   -2.5071 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6638    4.3355   -2.5309 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4659    0.9170   -0.0446 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8155   -0.3533    0.4841 N   0  0  0  0  0  4  0  0  0  0  0  0
   -3.2552   -0.2702    0.8089 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6818   -1.4678   -0.3905 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1855   -0.6027    1.7920 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.7233   -1.9238   -0.4333 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.3105   -1.8774   -1.5812 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.2551   -2.9654   -0.1586 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.6955   -0.0031    0.2211 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.9376   -2.6652    2.9601 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2632    0.3557   -1.6988 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.0812    2.3236   -1.8388 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.3343    3.0332   -0.3917 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7337    5.0755   -1.8363 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3371    1.3153   -0.5905 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3535    1.6117    0.8425 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.6451   -1.2664    1.0930 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.7883    0.0105   -0.1374 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.4484    0.4321    1.6198 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7281   -2.0193   -0.2834 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4689   -2.2106   -0.1451 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8629   -1.1395   -1.4303 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1127   -0.4250    1.7669 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4804   -1.6324    2.0870 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7162    0.0774    2.5175 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  1  0
  3  4  2  0
  3  5  1  0
  2  6  1  0
  6  7  2  0
  6  8  1  0
  8  9  1  0
  9 10  1  0
 10 11  1  0
 11 12  2  0
 11 13  1  0
  9 14  1  0
 14 15  1  0
 15 16  1  0
 15 17  1  0
 15 18  1  0
  1 19  1  0
  1 20  1  0
  1 21  1  0
  2 22  1  1
  5 23  1  0
  9 24  1  6
 10 25  1  0
 10 26  1  0
 13 27  1  0
 14 28  1  0
 14 29  1  0
 16 30  1  0
 16 31  1  0
 16 32  1  0
 17 33  1  0
 17 34  1  0
 17 35  1  0
 18 36  1  0
 18 37  1  0
 18 38  1  0
M  CHG  1  15   1
M  END


  Mrv1652304202021252D          

 18 17  0  0  0  0            999 V2000
 2493.9443 2499.8005    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
 2494.6583 2499.3872    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
 2495.3723 2499.8005    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
 2496.0863 2499.3872    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
 2496.8003 2499.8005    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
 2497.5143 2499.3872    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
 2495.3723 2500.6248    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
 2493.9443 2500.6248    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
 2493.2303 2501.0360    0.0000 N   0  3  0  0  0  0  0  0  0  0  0  0
 2492.5122 2500.6230    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
 2493.2303 2501.8607    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
 2492.3773 2501.5292    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
 2493.2365 2499.3769    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
 2493.2365 2498.5526    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
 2493.9526 2498.1392    0.0000 O   0  5  0  0  0  0  0  0  0  0  0  0
 2492.5246 2498.1392    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
 2496.8003 2500.6255    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
 2496.0863 2498.5621    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  1  8  1  6  0  0  0
  1 13  1  0  0  0  0
  2  3  1  0  0  0  0
  3  4  1  0  0  0  0
  3  7  2  0  0  0  0
  4  5  1  0  0  0  0
  8  9  1  0  0  0  0
  9 10  1  0  0  0  0
  9 11  1  0  0  0  0
  9 12  1  0  0  0  0
 13 14  1  0  0  0  0
 14 15  1  0  0  0  0
 14 16  2  0  0  0  0
  5 17  2  0  0  0  0
  4 18  1  1  0  0  0
  5  6  1  0  0  0  0
M  CHG  2   9   1  15  -1
M  END
> <DATABASE_ID>
HMDB0013133

> <DATABASE_NAME>
hmdb

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

> <INCHI_IDENTIFIER>
InChI=1S/C11H19NO6/c1-7(10(15)16)11(17)18-8(5-9(13)14)6-12(2,3)4/h7-8H,5-6H2,1-4H3,(H-,13,14,15,16)/t7-,8-/m1/s1

> <INCHI_KEY>
XROYFEWIXXCPAW-HTQZYQBOSA-N

> <FORMULA>
C11H19NO6

> <MOLECULAR_WEIGHT>
261.274

> <EXACT_MASS>
261.121237336

> <JCHEM_ACCEPTOR_COUNT>
5

> <JCHEM_ATOM_COUNT>
37

> <JCHEM_AVERAGE_POLARIZABILITY>
25.619008029173237

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
1

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(3R)-3-{[(2R)-2-carboxy-2-methylacetyl]oxy}-4-(trimethylazaniumyl)butanoate

> <ALOGPS_LOGP>
-1.62

> <JCHEM_LOGP>
-4.0111659134717454

> <ALOGPS_LOGS>
-3.07

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
0

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-1

> <JCHEM_PKA>
4.23841297010917

> <JCHEM_PKA_STRONGEST_ACIDIC>
3.534250036378786

> <JCHEM_PKA_STRONGEST_BASIC>
-7.208415042403216

> <JCHEM_POLAR_SURFACE_AREA>
103.72999999999999

> <JCHEM_REFRACTIVITY>
83.55539999999999

> <JCHEM_ROTATABLE_BOND_COUNT>
8

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
2.66e-01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
(3R)-3-{[(2R)-2-carboxy-2-methylacetyl]oxy}-4-(trimethylammonio)butanoate

> <JCHEM_VEBER_RULE>
0

$$$$

HMDB0013133
     RDKit          3D
Methylmalonylcarnitine
 38 37  0  0  0  0  0  0  0  0999 V2000
    3.6215   -1.9772   -0.5065 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.9643   -0.8645    0.2528 C   0  0  2  0  0  0  0  0  0  0  0  0
    2.7098   -1.1915    1.6626 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.2140   -0.5054    2.5852 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.9101   -2.2607    2.0536 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.7679   -0.3964   -0.4618 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4573   -0.9541   -1.5446 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.9425    0.6297   -0.0263 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1911    0.9963   -0.8027 C   0  0  2  0  0  0  0  0  0  0  0  0
    0.1082    2.3980   -1.2801 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9016    3.0089   -2.1266 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9344    2.4518   -2.5071 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6638    4.3355   -2.5309 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4659    0.9170   -0.0446 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8155   -0.3533    0.4841 N   0  0  0  0  0  4  0  0  0  0  0  0
   -3.2552   -0.2702    0.8089 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6818   -1.4678   -0.3905 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1855   -0.6027    1.7920 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.7233   -1.9238   -0.4333 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.3105   -1.8774   -1.5812 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.2551   -2.9654   -0.1586 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.6955   -0.0031    0.2211 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.9376   -2.6652    2.9601 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2632    0.3557   -1.6988 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.0812    2.3236   -1.8388 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.3343    3.0332   -0.3917 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7337    5.0755   -1.8363 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3371    1.3153   -0.5905 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3535    1.6117    0.8425 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.6451   -1.2664    1.0930 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.7883    0.0105   -0.1374 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.4484    0.4321    1.6198 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7281   -2.0193   -0.2834 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4689   -2.2106   -0.1451 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8629   -1.1395   -1.4303 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1127   -0.4250    1.7669 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4804   -1.6324    2.0870 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7162    0.0774    2.5175 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  1  0
  3  4  2  0
  3  5  1  0
  2  6  1  0
  6  7  2  0
  6  8  1  0
  8  9  1  0
  9 10  1  0
 10 11  1  0
 11 12  2  0
 11 13  1  0
  9 14  1  0
 14 15  1  0
 15 16  1  0
 15 17  1  0
 15 18  1  0
  1 19  1  0
  1 20  1  0
  1 21  1  0
  2 22  1  1
  5 23  1  0
  9 24  1  6
 10 25  1  0
 10 26  1  0
 13 27  1  0
 14 28  1  0
 14 29  1  0
 16 30  1  0
 16 31  1  0
 16 32  1  0
 17 33  1  0
 17 34  1  0
 17 35  1  0
 18 36  1  0
 18 37  1  0
 18 38  1  0
M  CHG  1  15   1
M  END

HEADER    PROTEIN                                 20-APR-20   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   20-APR-20         0                                  
HETATM    1  C   UNK     0    4655.3634666.294   0.000  0.00  0.00           C+0
HETATM    2  O   UNK     0    4656.6954665.523   0.000  0.00  0.00           O+0
HETATM    3  C   UNK     0    4658.0284666.294   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0    4659.3614665.523   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0    4660.6944666.294   0.000  0.00  0.00           C+0
HETATM    6  O   UNK     0    4662.0274665.523   0.000  0.00  0.00           O+0
HETATM    7  O   UNK     0    4658.0284667.833   0.000  0.00  0.00           O+0
HETATM    8  C   UNK     0    4655.3634667.833   0.000  0.00  0.00           C+0
HETATM    9  N   UNK     0    4654.0304668.601   0.000  0.00  0.00           N+1
HETATM   10  C   UNK     0    4652.6894667.830   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0    4654.0304670.140   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0    4652.4384669.521   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0    4654.0414665.504   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0    4654.0414663.965   0.000  0.00  0.00           C+0
HETATM   15  O   UNK     0    4655.3784663.193   0.000  0.00  0.00           O-1
HETATM   16  O   UNK     0    4652.7134663.193   0.000  0.00  0.00           O+0
HETATM   17  O   UNK     0    4660.6944667.834   0.000  0.00  0.00           O+0
HETATM   18  C   UNK     0    4659.3614663.983   0.000  0.00  0.00           C+0
CONECT    1    2    8   13                                                  
CONECT    2    1    3                                                       
CONECT    3    2    4    7                                                  
CONECT    4    3    5   18                                                  
CONECT    5    4   17    6                                                  
CONECT    6    5                                                            
CONECT    7    3                                                            
CONECT    8    1    9                                                       
CONECT    9    8   10   11   12                                             
CONECT   10    9                                                            
CONECT   11    9                                                            
CONECT   12    9                                                            
CONECT   13    1   14                                                       
CONECT   14   13   15   16                                                  
CONECT   15   14                                                            
CONECT   16   14                                                            
CONECT   17    5                                                            
CONECT   18    4                                                            
MASTER        0    0    0    0    0    0    0    0   18    0   34    0
END

COMPND    HMDB0013133
HETATM    1  C1  UNL     1       3.621  -1.977  -0.506  1.00  0.00           C  
HETATM    2  C2  UNL     1       2.964  -0.865   0.253  1.00  0.00           C  
HETATM    3  C3  UNL     1       2.710  -1.192   1.663  1.00  0.00           C  
HETATM    4  O1  UNL     1       3.214  -0.505   2.585  1.00  0.00           O  
HETATM    5  O2  UNL     1       1.910  -2.261   2.054  1.00  0.00           O  
HETATM    6  C4  UNL     1       1.768  -0.396  -0.462  1.00  0.00           C  
HETATM    7  O3  UNL     1       1.457  -0.954  -1.545  1.00  0.00           O  
HETATM    8  O4  UNL     1       0.943   0.630  -0.026  1.00  0.00           O  
HETATM    9  C5  UNL     1      -0.191   0.996  -0.803  1.00  0.00           C  
HETATM   10  C6  UNL     1       0.108   2.398  -1.280  1.00  0.00           C  
HETATM   11  C7  UNL     1      -0.902   3.009  -2.127  1.00  0.00           C  
HETATM   12  O5  UNL     1      -1.934   2.452  -2.507  1.00  0.00           O  
HETATM   13  O6  UNL     1      -0.664   4.336  -2.531  1.00  0.00           O  
HETATM   14  C8  UNL     1      -1.466   0.917  -0.045  1.00  0.00           C  
HETATM   15  N1  UNL     1      -1.815  -0.353   0.484  1.00  0.00           N1+
HETATM   16  C9  UNL     1      -3.255  -0.270   0.809  1.00  0.00           C  
HETATM   17  C10 UNL     1      -1.682  -1.468  -0.390  1.00  0.00           C  
HETATM   18  C11 UNL     1      -1.186  -0.603   1.792  1.00  0.00           C  
HETATM   19  H1  UNL     1       4.723  -1.924  -0.433  1.00  0.00           H  
HETATM   20  H2  UNL     1       3.311  -1.877  -1.581  1.00  0.00           H  
HETATM   21  H3  UNL     1       3.255  -2.965  -0.159  1.00  0.00           H  
HETATM   22  H4  UNL     1       3.696  -0.003   0.221  1.00  0.00           H  
HETATM   23  H5  UNL     1       1.938  -2.665   2.960  1.00  0.00           H  
HETATM   24  H6  UNL     1      -0.263   0.356  -1.699  1.00  0.00           H  
HETATM   25  H7  UNL     1       1.081   2.324  -1.839  1.00  0.00           H  
HETATM   26  H8  UNL     1       0.334   3.033  -0.392  1.00  0.00           H  
HETATM   27  H9  UNL     1      -0.734   5.075  -1.836  1.00  0.00           H  
HETATM   28  H10 UNL     1      -2.337   1.315  -0.590  1.00  0.00           H  
HETATM   29  H11 UNL     1      -1.353   1.612   0.842  1.00  0.00           H  
HETATM   30  H12 UNL     1      -3.645  -1.266   1.093  1.00  0.00           H  
HETATM   31  H13 UNL     1      -3.788   0.011  -0.137  1.00  0.00           H  
HETATM   32  H14 UNL     1      -3.448   0.432   1.620  1.00  0.00           H  
HETATM   33  H15 UNL     1      -0.728  -2.019  -0.283  1.00  0.00           H  
HETATM   34  H16 UNL     1      -2.469  -2.211  -0.145  1.00  0.00           H  
HETATM   35  H17 UNL     1      -1.863  -1.140  -1.430  1.00  0.00           H  
HETATM   36  H18 UNL     1      -0.113  -0.425   1.767  1.00  0.00           H  
HETATM   37  H19 UNL     1      -1.480  -1.632   2.087  1.00  0.00           H  
HETATM   38  H20 UNL     1      -1.716   0.077   2.517  1.00  0.00           H  
CONECT    1    2   19   20   21
CONECT    2    3    6   22
CONECT    3    4    4    5
CONECT    5   23
CONECT    6    7    7    8
CONECT    8    9
CONECT    9   10   14   24
CONECT   10   11   25   26
CONECT   11   12   12   13
CONECT   13   27
CONECT   14   15   28   29
CONECT   15   16   17   18
CONECT   16   30   31   32
CONECT   17   33   34   35
CONECT   18   36   37   38
END

HMDB0013133
     RDKit          3D
Methylmalonylcarnitine
 38 37  0  0  0  0  0  0  0  0999 V2000
    3.6215   -1.9772   -0.5065 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.9643   -0.8645    0.2528 C   0  0  2  0  0  0  0  0  0  0  0  0
    2.7098   -1.1915    1.6626 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.2140   -0.5054    2.5852 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.9101   -2.2607    2.0536 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.7679   -0.3964   -0.4618 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4573   -0.9541   -1.5446 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.9425    0.6297   -0.0263 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1911    0.9963   -0.8027 C   0  0  2  0  0  0  0  0  0  0  0  0
    0.1082    2.3980   -1.2801 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9016    3.0089   -2.1266 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9344    2.4518   -2.5071 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6638    4.3355   -2.5309 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4659    0.9170   -0.0446 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8155   -0.3533    0.4841 N   0  0  0  0  0  4  0  0  0  0  0  0
   -3.2552   -0.2702    0.8089 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6818   -1.4678   -0.3905 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1855   -0.6027    1.7920 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.7233   -1.9238   -0.4333 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.3105   -1.8774   -1.5812 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.2551   -2.9654   -0.1586 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.6955   -0.0031    0.2211 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.9376   -2.6652    2.9601 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2632    0.3557   -1.6988 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.0812    2.3236   -1.8388 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.3343    3.0332   -0.3917 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7337    5.0755   -1.8363 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3371    1.3153   -0.5905 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3535    1.6117    0.8425 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.6451   -1.2664    1.0930 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.7883    0.0105   -0.1374 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.4484    0.4321    1.6198 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7281   -2.0193   -0.2834 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4689   -2.2106   -0.1451 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8629   -1.1395   -1.4303 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1127   -0.4250    1.7669 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4804   -1.6324    2.0870 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7162    0.0774    2.5175 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  1  0
  3  4  2  0
  3  5  1  0
  2  6  1  0
  6  7  2  0
  6  8  1  0
  8  9  1  0
  9 10  1  0
 10 11  1  0
 11 12  2  0
 11 13  1  0
  9 14  1  0
 14 15  1  0
 15 16  1  0
 15 17  1  0
 15 18  1  0
  1 19  1  0
  1 20  1  0
  1 21  1  0
  2 22  1  1
  5 23  1  0
  9 24  1  6
 10 25  1  0
 10 26  1  0
 13 27  1  0
 14 28  1  0
 14 29  1  0
 16 30  1  0
 16 31  1  0
 16 32  1  0
 17 33  1  0
 17 34  1  0
 17 35  1  0
 18 36  1  0
 18 37  1  0
 18 38  1  0
M  CHG  1  15   1
M  END

View in JSmol View NMR Assignments View Stereo Labels

Synonyms

Value	Source
(2R)-3-{[(2R)-1-carboxy-3-(trimethylazaniumyl)propan-2-yl]oxy}-2-methyl-3-oxopropanoic acid	HMDB
Methylmalonyl-L-carnitine	HMDB
Methylmalonylcarnitine	HMDB

Chemical Formula

C₁₁H₂₀NO₆

Average Molecular Weight

262.281

Monoisotopic Molecular Weight

262.128513788

IUPAC Name

(3R)-3-{[(2R)-2-carboxy-2-methylacetyl]oxy}-4-(trimethylazaniumyl)butanoate

Traditional Name

(3R)-3-{[(2R)-2-carboxy-2-methylacetyl]oxy}-4-(trimethylammonio)butanoate

CAS Registry Number

256928-70-8

SMILES

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

InChI Identifier

InChI=1S/C11H19NO6/c1-7(10(15)16)11(17)18-8(5-9(13)14)6-12(2,3)4/h7-8H,5-6H2,1-4H3,(H-,13,14,15,16)/p+1/t7-,8-/m1/s1

InChI Key

XROYFEWIXXCPAW-HTQZYQBOSA-O

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
Tetraalkylammonium salt
Quaternary ammonium salt
Carboxylic acid salt
Carboxylic acid ester
Carboxylic acid
Carboxylic acid derivative
Organic nitrogen compound
Organic oxygen compound
Organopnictogen compound
Organic oxide
Hydrocarbon derivative
Organic salt
Organooxygen compound
Organonitrogen compound
Carbonyl group
Amine
Aliphatic acyclic compound

Molecular Framework

Aliphatic acyclic compounds

External Descriptors

Not Available

Ontology

Physiological effect

Disposition

Biological location

Non-excretory biofluid

Biofluid or Excreta

Blood (PMID: 24704061)

Excreta

Biofluid or Excreta

Urine (PMID: 24023812)

Cellular substructure

Organelle

Peroxisome (PMID: 35710135)

Cell

All cells and tissues (PMID: 35710135)

Source

Exogenous

Exogenous (HMDB: HMDB0013133)

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: HMDB0013133)

Process

Not Available

Role

Biological role

Energy source (PMID: 35710135)

Industrial application

Pharmaceutical industry

Biomarker

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	0.27 g/L	ALOGPS
logP	-1.6	ALOGPS
logP	-4	ChemAxon
logS	-3.1	ALOGPS
pKa (Strongest Acidic)	3.53	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	83.56 m³·mol⁻¹	ChemAxon
Polarizability	25.62 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]+	160.239	30932474
DeepCCS	[M-H]-	156.776	30932474
DeepCCS	[M-2H]-	192.993	30932474
DeepCCS	[M+Na]+	168.641	30932474

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	9.5935 minutes	33406817
Predicted by Siyang using ReTip algorithm on June 8, 2022	6.15 minutes	32390414
AjsUoB = Accucore 150 Amide HILIC with 10mM Ammonium Formate, 0.1% Formic Acid	370.0 seconds	40023050
Fem_Long = Waters ACQUITY UPLC HSS T3 C18 with Water:MeOH and 0.1% Formic Acid	473.4 seconds	40023050
Fem_Lipids = Ascentis Express C18 with (60:40 water:ACN):(90:10 IPA:ACN) and 10mM NH4COOH + 0.1% Formic Acid	218.4 seconds	40023050
Life_Old = Waters ACQUITY UPLC BEH C18 with Water:(20:80 acetone:ACN) and 0.1% Formic Acid	79.2 seconds	40023050
Life_New = RP Waters ACQUITY UPLC HSS T3 C18 with Water:(30:70 MeOH:ACN) and 0.1% Formic Acid	159.0 seconds	40023050
RIKEN = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid	47.8 seconds	40023050
Eawag_XBridgeC18 = XBridge C18 3.5u 2.1x50 mm with Water:MeOH and 0.1% Formic Acid	242.2 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	282.5 seconds	40023050
HILIC_BDD_2 = Merck SeQuant ZIC-HILIC with ACN(0.1% formic acid):water(16 mM ammonium formate)	859.1 seconds	40023050
UniToyama_Atlantis = RP Waters Atlantis T3 (2.1 x 150 mm, 5 um) with ACN:Water and 0.1% Formic Acid	640.5 seconds	40023050
BDD_C18 = Hypersil Gold 1.9µm C18 with Water:ACN and 0.1% Formic Acid	56.6 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	1107.5 seconds	40023050
SNU_RIKEN_POS = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid	190.4 seconds	40023050
RPMMFDA = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid	191.8 seconds	40023050
MTBLS87 = Merck SeQuant ZIC-pHILIC column with ACN:Water and :ammonium carbonate	524.7 seconds	40023050
KI_GIAR_zic_HILIC_pH2_7 = Merck SeQuant ZIC-HILIC with ACN:Water and 0.1% FA	379.3 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	212.4 seconds	40023050

Predicted Kovats Retention Indices

Underivatized

Metabolite	SMILES	Kovats RI Value	Column Type	Reference
Methylmalonylcarnitine	C[C@H](C(O)=O)C(=O)O[C@H](CC(O)=O)C[N+](C)(C)C	2950.1	Standard polar	33892256
Methylmalonylcarnitine	C[C@H](C(O)=O)C(=O)O[C@H](CC(O)=O)C[N+](C)(C)C	1571.2	Standard non polar	33892256
Methylmalonylcarnitine	C[C@H](C(O)=O)C(=O)O[C@H](CC(O)=O)C[N+](C)(C)C	1879.9	Semi standard non polar	33892256

Derivatized

Derivative Name / Structure	SMILES	Kovats RI Value	Column Type	Reference
Methylmalonylcarnitine,1TMS,isomer #1	C[C@@H](C(=O)O[C@H](CC(=O)O)C[N+](C)(C)C)C(=O)O[Si](C)(C)C	1784.6	Semi standard non polar	33892256
Methylmalonylcarnitine,1TMS,isomer #2	C[C@H](C(=O)O)C(=O)O[C@H](CC(=O)O[Si](C)(C)C)C[N+](C)(C)C	1779.0	Semi standard non polar	33892256
Methylmalonylcarnitine,2TMS,isomer #1	C[C@@H](C(=O)O[C@H](CC(=O)O[Si](C)(C)C)C[N+](C)(C)C)C(=O)O[Si](C)(C)C	1845.3	Semi standard non polar	33892256
Methylmalonylcarnitine,1TBDMS,isomer #1	C[C@@H](C(=O)O[C@H](CC(=O)O)C[N+](C)(C)C)C(=O)O[Si](C)(C)C(C)(C)C	2015.0	Semi standard non polar	33892256
Methylmalonylcarnitine,1TBDMS,isomer #2	C[C@H](C(=O)O)C(=O)O[C@H](CC(=O)O[Si](C)(C)C(C)(C)C)C[N+](C)(C)C	2004.0	Semi standard non polar	33892256
Methylmalonylcarnitine,2TBDMS,isomer #1	C[C@@H](C(=O)O[C@H](CC(=O)O[Si](C)(C)C(C)(C)C)C[N+](C)(C)C)C(=O)O[Si](C)(C)C(C)(C)C	2292.8	Semi standard non polar	33892256

Spectra

Biological Properties

Cellular Locations

Extracellular
Membrane

Biospecimen Locations

Blood
Urine

Tissue Locations

Not Available

Pathways

Not Available

Name	SMPDB/PathBank	KEGG

Normal Concentrations

Biospecimen	Status	Value	Age	Sex	Condition	Reference	Details
Blood	Expected but not Quantified	Not Quantified	Not Available	Not Available	Normal	Not Available	details
Blood	Detected and Quantified	<0.110 uM	Not Specified	Not Specified	Normal	16148061	details
Urine	Detected and Quantified	0.09 (0.05-0.16) umol/mmol creatinine	Adult (>18 years old)	Both	Normal	24023812	details

Abnormal Concentrations

Biospecimen	Status	Value	Age	Sex	Condition	Reference	Details
Blood	Detected and Quantified	0.0602 (0.0527) uM	Adult (>18 years old)	Female	Pregnancy with fetus having congenital heart defect	24704061	details

Associated Disorders and Diseases

Disease References

None

Associated OMIM IDs

None

External Links

DrugBank ID

Not Available

Phenol Explorer Compound ID

Not Available

FooDB ID

FDB112307

KNApSAcK ID

Not Available

Chemspider ID

Not Available

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

156908004

PDB ID

Not Available

ChEBI ID

Not Available

Food Biomarker Ontology

Not Available

VMH ID

Not Available

MarkerDB ID

Not Available

Good Scents ID

Not Available

References

Synthesis Reference

Not Available

Material Safety Data Sheet (MSDS)

Not Available

General References

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 ]
Violante S, Ijlst L, Ruiter J, Koster J, van Lenthe H, Duran M, de Almeida IT, Wanders RJ, Houten SM, Ventura FV: Substrate specificity of human carnitine acetyltransferase: Implications for fatty acid and branched-chain amino acid metabolism. Biochim Biophys Acta. 2013 Jun;1832(6):773-9. doi: 10.1016/j.bbadis.2013.02.012. Epub 2013 Feb 24. [PubMed:23485643 ]
FRITZ IB: Action of carnitine on long chain fatty acid oxidation by liver. Am J Physiol. 1959 Aug;197:297-304. doi: 10.1152/ajplegacy.1959.197.2.297. [PubMed:13825279 ]
Makarova E, Makrecka-Kuka M, Vilks K, Volska K, Sevostjanovs E, Grinberga S, Zarkova-Malkova O, Dambrova M, Liepinsh E: Decreases in Circulating Concentrations of Long-Chain Acylcarnitines and Free Fatty Acids During the Glucose Tolerance Test Represent Tissue-Specific Insulin Sensitivity. Front Endocrinol (Lausanne). 2019 Dec 17;10:870. doi: 10.3389/fendo.2019.00870. eCollection 2019. [PubMed:31920980 ]
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Showing metabocard for Methylmalonylcarnitine (HMDB0013133)

MOL for HMDB0013133 (Methylmalonylcarnitine)

3D MOL for HMDB0013133 (Methylmalonylcarnitine)

3D SDF for HMDB0013133 (Methylmalonylcarnitine)

3D-SDF for HMDB0013133 (Methylmalonylcarnitine)

PDB for HMDB0013133 (Methylmalonylcarnitine)

3D PDB for HMDB0013133 (Methylmalonylcarnitine)

SMILES for HMDB0013133 (Methylmalonylcarnitine)

INCHI for HMDB0013133 (Methylmalonylcarnitine)

Structure for HMDB0013133 (Methylmalonylcarnitine)

3D Structure for HMDB0013133 (Methylmalonylcarnitine)

Predicted Collision Cross Sections

Predicted Retention Times

Underivatized

Predicted Kovats Retention Indices

Underivatized

Derivatized