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Showing metabocard for 2-Methylcitric acid (HMDB0000379)

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Record Information
Version5.0
StatusDetected and Quantified
Creation Date2005-11-16 15:48:42 UTC
Update Date2021-09-14 15:19:34 UTC
HMDB IDHMDB0000379
Secondary Accession Numbers
  • HMDB0003610
  • HMDB00379
  • HMDB03610
Metabolite Identification
Common Name2-Methylcitric acid
Description2-Methylcitric acid, also known as 2-methylcitrate, belongs to the class of organic compounds known as tricarboxylic acids and derivatives. These are carboxylic acids containing exactly three carboxyl groups. 2-Methylcitric acid exists in all living organisms, ranging from bacteria to humans. 2-Methylcitric acid has been detected, but not quantified in, several different foods, such as anatidaes (Anatidae), chickens (Gallus gallus), domestic pigs (Sus scrofa domestica), and milk (cow). This could make 2-methylcitric acid a potential biomarker for the consumption of these foods. 2-Methylcitric acid is a primary metabolite. Primary metabolites are metabolically or physiologically essential metabolites. They are directly involved in an organism’s growth, development or reproduction. 2-Methylcitric acid, with regard to humans, has been found to be associated with the diseases such as crohn's disease; 2-methylcitric acid has also been linked to several inborn metabolic disorders including propionic acidemia, isovaleric acidemia, vitamin B12 deficiency, and biotinidase deficiency. Based on a literature review a significant number of articles have been published on 2-Methylcitric acid.
Structure
Data?1582752127
MOL3D MOLSDF3D SDFPDB3D PDBSMILESInChI

MOL for HMDB0000379 (2-Methylcitric acid)


  Mrv0541 02231218292D          

 14 13  0  0  0  0            999 V2000
    8.8380   -4.9115    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   10.9005   -5.6260    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    9.2505   -5.6260    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   11.3130   -6.3404    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    8.8380   -6.3404    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   10.0755   -4.8009    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   10.0755   -5.6260    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   10.9005   -7.0549    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   12.1379   -6.3404    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    8.0130   -6.3404    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    9.2505   -7.0549    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   10.7900   -4.3885    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    9.3610   -4.3885    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   10.0755   -6.4509    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  1  3  1  0  0  0  0
  2  7  1  0  0  0  0
  2  4  1  0  0  0  0
  3  5  1  0  0  0  0
  3  7  1  0  0  0  0
  4  8  1  0  0  0  0
  4  9  2  0  0  0  0
  5 10  1  0  0  0  0
  5 11  2  0  0  0  0
  6  7  1  0  0  0  0
  6 12  1  0  0  0  0
  6 13  2  0  0  0  0
  7 14  1  0  0  0  0
M  END
Download

3D MOL for HMDB0000379 (2-Methylcitric acid)

HMDB0000379
     RDKit          3D
2-Methylcitric acid
 24 23  0  0  0  0  0  0  0  0999 V2000
   -1.5243   -0.4652   -1.6390 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2867    0.1251   -0.2745 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0965   -0.5965    0.7687 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8439   -1.5478    0.5024 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9550   -0.1281    2.0612 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.1703    0.1676    0.1154 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.2317    0.7328    1.3878 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.8617    1.1246   -0.8353 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.3176    1.2331   -0.5251 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.9849    2.0078   -1.2614 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.8980    0.5193    0.5161 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.8042   -1.1493    0.1574 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.9148   -1.9178   -0.8394 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.3507   -1.6636    1.3512 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6474   -0.4894   -1.7591 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1701    0.2467   -2.3927 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1887   -1.4923   -1.7544 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7100    1.1514   -0.2936 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1951    0.8016    2.3583 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.3759    0.0107    2.0459 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.4076    2.1223   -0.6609 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.7216    0.7993   -1.8794 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.3150    1.0569    1.2904 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.2638   -2.6494    1.5601 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  1  0
  6  8  1  0
  8  9  1  0
  9 10  2  0
  9 11  1  0
  6 12  1  0
 12 13  2  0
 12 14  1  0
  1 15  1  0
  1 16  1  0
  1 17  1  0
  2 18  1  0
  5 19  1  0
  7 20  1  0
  8 21  1  0
  8 22  1  0
 11 23  1  0
 14 24  1  0
M  END
Download

3D SDF for HMDB0000379 (2-Methylcitric acid)


  Mrv0541 02231218292D          

 14 13  0  0  0  0            999 V2000
    8.8380   -4.9115    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   10.9005   -5.6260    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    9.2505   -5.6260    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   11.3130   -6.3404    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    8.8380   -6.3404    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   10.0755   -4.8009    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   10.0755   -5.6260    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   10.9005   -7.0549    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   12.1379   -6.3404    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    8.0130   -6.3404    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    9.2505   -7.0549    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   10.7900   -4.3885    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    9.3610   -4.3885    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   10.0755   -6.4509    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  1  3  1  0  0  0  0
  2  7  1  0  0  0  0
  2  4  1  0  0  0  0
  3  5  1  0  0  0  0
  3  7  1  0  0  0  0
  4  8  1  0  0  0  0
  4  9  2  0  0  0  0
  5 10  1  0  0  0  0
  5 11  2  0  0  0  0
  6  7  1  0  0  0  0
  6 12  1  0  0  0  0
  6 13  2  0  0  0  0
  7 14  1  0  0  0  0
M  END
> <DATABASE_ID>
HMDB0000379

> <DATABASE_NAME>
hmdb

> <SMILES>
CC(C(O)=O)C(O)(CC(O)=O)C(O)=O

> <INCHI_IDENTIFIER>
InChI=1S/C7H10O7/c1-3(5(10)11)7(14,6(12)13)2-4(8)9/h3,14H,2H2,1H3,(H,8,9)(H,10,11)(H,12,13)

> <INCHI_KEY>
YNOXCRMFGMSKIJ-UHFFFAOYSA-N

> <FORMULA>
C7H10O7

> <MOLECULAR_WEIGHT>
206.1501

> <EXACT_MASS>
206.042652674

> <JCHEM_ACCEPTOR_COUNT>
7

> <JCHEM_AVERAGE_POLARIZABILITY>
17.21399595260961

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
4

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
2-hydroxy-1-methylpropane-1,2,3-tricarboxylic acid

> <ALOGPS_LOGP>
-0.89

> <JCHEM_LOGP>
-0.7797011736666666

> <ALOGPS_LOGS>
-0.07

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
0

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-3

> <JCHEM_PKA>
4.7852796669207125

> <JCHEM_PKA_STRONGEST_ACIDIC>
3.18324322639043

> <JCHEM_PKA_STRONGEST_BASIC>
-4.260390633991254

> <JCHEM_POLAR_SURFACE_AREA>
132.13

> <JCHEM_REFRACTIVITY>
40.19840000000001

> <JCHEM_ROTATABLE_BOND_COUNT>
5

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
1.75e+02 g/l

> <JCHEM_TRADITIONAL_IUPAC>
methylcitric acid

> <JCHEM_VEBER_RULE>
0

$$$$
Download

3D-SDF for HMDB0000379 (2-Methylcitric acid)

HMDB0000379
     RDKit          3D
2-Methylcitric acid
 24 23  0  0  0  0  0  0  0  0999 V2000
   -1.5243   -0.4652   -1.6390 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2867    0.1251   -0.2745 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0965   -0.5965    0.7687 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8439   -1.5478    0.5024 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9550   -0.1281    2.0612 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.1703    0.1676    0.1154 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.2317    0.7328    1.3878 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.8617    1.1246   -0.8353 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.3176    1.2331   -0.5251 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.9849    2.0078   -1.2614 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.8980    0.5193    0.5161 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.8042   -1.1493    0.1574 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.9148   -1.9178   -0.8394 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.3507   -1.6636    1.3512 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6474   -0.4894   -1.7591 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1701    0.2467   -2.3927 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1887   -1.4923   -1.7544 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7100    1.1514   -0.2936 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1951    0.8016    2.3583 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.3759    0.0107    2.0459 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.4076    2.1223   -0.6609 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.7216    0.7993   -1.8794 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.3150    1.0569    1.2904 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.2638   -2.6494    1.5601 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  1  0
  6  8  1  0
  8  9  1  0
  9 10  2  0
  9 11  1  0
  6 12  1  0
 12 13  2  0
 12 14  1  0
  1 15  1  0
  1 16  1  0
  1 17  1  0
  2 18  1  0
  5 19  1  0
  7 20  1  0
  8 21  1  0
  8 22  1  0
 11 23  1  0
 14 24  1  0
M  END
Download

PDB for HMDB0000379 (2-Methylcitric acid)

HEADER    PROTEIN                                 23-FEB-12   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   23-FEB-12         0                                  
HETATM    1  C   UNK     0      16.498  -9.168   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0      20.348 -10.502   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0      17.268 -10.502   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0      21.118 -11.835   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0      16.498 -11.835   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0      18.808  -8.962   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0      18.808 -10.502   0.000  0.00  0.00           C+0
HETATM    8  O   UNK     0      20.348 -13.169   0.000  0.00  0.00           O+0
HETATM    9  O   UNK     0      22.657 -11.835   0.000  0.00  0.00           O+0
HETATM   10  O   UNK     0      14.958 -11.835   0.000  0.00  0.00           O+0
HETATM   11  O   UNK     0      17.268 -13.169   0.000  0.00  0.00           O+0
HETATM   12  O   UNK     0      20.141  -8.192   0.000  0.00  0.00           O+0
HETATM   13  O   UNK     0      17.474  -8.192   0.000  0.00  0.00           O+0
HETATM   14  O   UNK     0      18.808 -12.042   0.000  0.00  0.00           O+0
CONECT    1    3                                                            
CONECT    2    7    4                                                       
CONECT    3    1    5    7                                                  
CONECT    4    2    8    9                                                  
CONECT    5    3   10   11                                                  
CONECT    6    7   12   13                                                  
CONECT    7    2    3    6   14                                             
CONECT    8    4                                                            
CONECT    9    4                                                            
CONECT   10    5                                                            
CONECT   11    5                                                            
CONECT   12    6                                                            
CONECT   13    6                                                            
CONECT   14    7                                                            
MASTER        0    0    0    0    0    0    0    0   14    0   26    0
END
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3D PDB for HMDB0000379 (2-Methylcitric acid)

COMPND    HMDB0000379
HETATM    1  C1  UNL     1      -1.524  -0.465  -1.639  1.00  0.00           C  
HETATM    2  C2  UNL     1      -1.287   0.125  -0.274  1.00  0.00           C  
HETATM    3  C3  UNL     1      -2.097  -0.597   0.769  1.00  0.00           C  
HETATM    4  O1  UNL     1      -2.844  -1.548   0.502  1.00  0.00           O  
HETATM    5  O2  UNL     1      -1.955  -0.128   2.061  1.00  0.00           O  
HETATM    6  C4  UNL     1       0.170   0.168   0.115  1.00  0.00           C  
HETATM    7  O3  UNL     1       0.232   0.733   1.388  1.00  0.00           O  
HETATM    8  C5  UNL     1       0.862   1.125  -0.835  1.00  0.00           C  
HETATM    9  C6  UNL     1       2.318   1.233  -0.525  1.00  0.00           C  
HETATM   10  O4  UNL     1       2.985   2.008  -1.261  1.00  0.00           O  
HETATM   11  O5  UNL     1       2.898   0.519   0.516  1.00  0.00           O  
HETATM   12  C7  UNL     1       0.804  -1.149   0.157  1.00  0.00           C  
HETATM   13  O6  UNL     1       0.915  -1.918  -0.839  1.00  0.00           O  
HETATM   14  O7  UNL     1       1.351  -1.664   1.351  1.00  0.00           O  
HETATM   15  H1  UNL     1      -2.647  -0.489  -1.759  1.00  0.00           H  
HETATM   16  H2  UNL     1      -1.170   0.247  -2.393  1.00  0.00           H  
HETATM   17  H3  UNL     1      -1.189  -1.492  -1.754  1.00  0.00           H  
HETATM   18  H4  UNL     1      -1.710   1.151  -0.294  1.00  0.00           H  
HETATM   19  H5  UNL     1      -2.195   0.802   2.358  1.00  0.00           H  
HETATM   20  H6  UNL     1       0.376   0.011   2.046  1.00  0.00           H  
HETATM   21  H7  UNL     1       0.408   2.122  -0.661  1.00  0.00           H  
HETATM   22  H8  UNL     1       0.722   0.799  -1.879  1.00  0.00           H  
HETATM   23  H9  UNL     1       3.315   1.057   1.290  1.00  0.00           H  
HETATM   24  H10 UNL     1       1.264  -2.649   1.560  1.00  0.00           H  
CONECT    1    2   15   16   17
CONECT    2    3    6   18
CONECT    3    4    4    5
CONECT    5   19
CONECT    6    7    8   12
CONECT    7   20
CONECT    8    9   21   22
CONECT    9   10   10   11
CONECT   11   23
CONECT   12   13   13   14
CONECT   14   24
END
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SMILES for HMDB0000379 (2-Methylcitric acid)

CC(C(O)=O)C(O)(CC(O)=O)C(O)=O
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INCHI for HMDB0000379 (2-Methylcitric acid)

InChI=1S/C7H10O7/c1-3(5(10)11)7(14,6(12)13)2-4(8)9/h3,14H,2H2,1H3,(H,8,9)(H,10,11)(H,12,13)
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View in JSmolView NMR AssignmentsView Stereo Labels
Synonyms
ValueSource
2-Hydroxy-1,2,3-butanetricarboxylic acidChEBI
2-Hydroxy-1,2,3-butanetricarboxylateGenerator
2-MethylcitrateGenerator
(2S,3S)-2-MethylcitrateHMDB
2-Hydroxybutane-1,2,3-tricarboxylateHMDB
2-Hydroxybutane-1,2,3-tricarboxylic acidHMDB
2-Methylcitric acid, 3H-labeledHMDB
3-Carboxy-3-hydroxy-2-methylpentanedioic acidHMDB
Methylcitric acidHMDB
Chemical FormulaC7H10O7
Average Molecular Weight206.1501
Monoisotopic Molecular Weight206.042652674
IUPAC Name2-hydroxy-1-methylpropane-1,2,3-tricarboxylic acid
Traditional Namemethylcitric acid
CAS Registry Number6061-96-7
SMILES
CC(C(O)=O)C(O)(CC(O)=O)C(O)=O
InChI Identifier
InChI=1S/C7H10O7/c1-3(5(10)11)7(14,6(12)13)2-4(8)9/h3,14H,2H2,1H3,(H,8,9)(H,10,11)(H,12,13)
InChI KeyYNOXCRMFGMSKIJ-UHFFFAOYSA-N
Chemical Taxonomy
Description Belongs to the class of organic compounds known as tricarboxylic acids and derivatives. These are carboxylic acids containing exactly three carboxyl groups.
KingdomOrganic compounds
Super ClassOrganic acids and derivatives
ClassCarboxylic acids and derivatives
Sub ClassTricarboxylic acids and derivatives
Direct ParentTricarboxylic acids and derivatives
Alternative Parents
Substituents
  • Tricarboxylic acid or derivatives
  • Hydroxy acid
  • Alpha-hydroxy acid
  • Tertiary alcohol
  • Carboxylic acid
  • Organic oxygen compound
  • Organic oxide
  • Hydrocarbon derivative
  • Organooxygen compound
  • Carbonyl group
  • Alcohol
  • Aliphatic acyclic compound
Molecular FrameworkAliphatic acyclic compounds
External Descriptors
Ontology
Physiological effectNot Available
Disposition
Biological locationSource
Process
Naturally occurring process
Role
Industrial application
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
PropertyValueSource
Water Solubility175 g/LALOGPS
logP-0.89ALOGPS
logP-0.78ChemAxon
logS-0.07ALOGPS
pKa (Strongest Acidic)3.18ChemAxon
pKa (Strongest Basic)-4.3ChemAxon
Physiological Charge-3ChemAxon
Hydrogen Acceptor Count7ChemAxon
Hydrogen Donor Count4ChemAxon
Polar Surface Area132.13 ŲChemAxon
Rotatable Bond Count5ChemAxon
Refractivity40.2 m³·mol⁻¹ChemAxon
Polarizability17.21 ųChemAxon
Number of Rings0ChemAxon
BioavailabilityYesChemAxon
Rule of FiveYesChemAxon
Ghose FilterNoChemAxon
Veber's RuleNoChemAxon
MDDR-like RuleNoChemAxon
Predicted Chromatographic Properties

Predicted Collision Cross Sections

PredictorAdduct TypeCCS Value (Å2)Reference
DarkChem[M+H]+145.40731661259
DarkChem[M-H]-139.72531661259
AllCCS[M+H]+144.3732859911
AllCCS[M-H]-137.90632859911
DeepCCS[M+H]+133.63430932474
DeepCCS[M-H]-130.62930932474
DeepCCS[M-2H]-167.14930932474
DeepCCS[M+Na]+142.68730932474
AllCCS[M+H]+144.432859911
AllCCS[M+H-H2O]+140.732859911
AllCCS[M+NH4]+147.732859911
AllCCS[M+Na]+148.732859911
AllCCS[M-H]-137.932859911
AllCCS[M+Na-2H]-138.932859911
AllCCS[M+HCOO]-140.132859911

Predicted Retention Times

Underivatized

Chromatographic MethodRetention TimeReference
Measured using a Waters Acquity ultraperformance liquid chromatography (UPLC) ethylene-bridged hybrid (BEH) C18 column (100 mm × 2.1 mm; 1.7 μmparticle diameter). Predicted by Afia on May 17, 2022. Predicted by Afia on May 17, 2022.1.76 minutes32390414
Predicted by Siyang on May 30, 202210.2852 minutes33406817
Predicted by Siyang using ReTip algorithm on June 8, 20226.68 minutes32390414
AjsUoB = Accucore 150 Amide HILIC with 10mM Ammonium Formate, 0.1% Formic Acid331.6 seconds40023050
Fem_Long = Waters ACQUITY UPLC HSS T3 C18 with Water:MeOH and 0.1% Formic Acid628.1 seconds40023050
Fem_Lipids = Ascentis Express C18 with (60:40 water:ACN):(90:10 IPA:ACN) and 10mM NH4COOH + 0.1% Formic Acid322.8 seconds40023050
Life_Old = Waters ACQUITY UPLC BEH C18 with Water:(20:80 acetone:ACN) and 0.1% Formic Acid40.4 seconds40023050
Life_New = RP Waters ACQUITY UPLC HSS T3 C18 with Water:(30:70 MeOH:ACN) and 0.1% Formic Acid177.5 seconds40023050
RIKEN = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid67.3 seconds40023050
Eawag_XBridgeC18 = XBridge C18 3.5u 2.1x50 mm with Water:MeOH and 0.1% Formic Acid276.1 seconds40023050
BfG_NTS_RP1 =Agilent Zorbax Eclipse Plus C18 (2.1 mm x 150 mm, 3.5 um) with Water:ACN and 0.1% Formic Acid263.6 seconds40023050
HILIC_BDD_2 = Merck SeQuant ZIC-HILIC with ACN(0.1% formic acid):water(16 mM ammonium formate)625.1 seconds40023050
UniToyama_Atlantis = RP Waters Atlantis T3 (2.1 x 150 mm, 5 um) with ACN:Water and 0.1% Formic Acid618.1 seconds40023050
BDD_C18 = Hypersil Gold 1.9µm C18 with Water:ACN and 0.1% Formic Acid56.8 seconds40023050
UFZ_Phenomenex = Kinetex Core-Shell C18 2.6 um, 3.0 x 100 mm, Phenomenex with Water:MeOH and 0.1% Formic Acid827.9 seconds40023050
SNU_RIKEN_POS = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid191.8 seconds40023050
RPMMFDA = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid242.2 seconds40023050
MTBLS87 = Merck SeQuant ZIC-pHILIC column with ACN:Water and :ammonium carbonate701.5 seconds40023050
KI_GIAR_zic_HILIC_pH2_7 = Merck SeQuant ZIC-HILIC with ACN:Water and 0.1% FA269.0 seconds40023050
Meister zic-pHILIC pH9.3 = Merck SeQuant ZIC-pHILIC column with ACN:Water 5mM NH4Ac pH9.3 and 5mM ammonium acetate in water524.4 seconds40023050

Predicted Kovats Retention Indices

Underivatized

MetaboliteSMILESKovats RI ValueColumn TypeReference
2-Methylcitric acidCC(C(O)=O)C(O)(CC(O)=O)C(O)=O2881.4Standard polar33892256
2-Methylcitric acidCC(C(O)=O)C(O)(CC(O)=O)C(O)=O1239.5Standard non polar33892256
2-Methylcitric acidCC(C(O)=O)C(O)(CC(O)=O)C(O)=O1733.2Semi standard non polar33892256

Derivatized

Derivative Name / StructureSMILESKovats RI ValueColumn TypeReference
2-Methylcitric acid,1TMS,isomer #1CC(C(=O)O[Si](C)(C)C)C(O)(CC(=O)O)C(=O)O1738.0Semi standard non polar33892256
2-Methylcitric acid,1TMS,isomer #2CC(C(=O)O)C(CC(=O)O)(O[Si](C)(C)C)C(=O)O1768.2Semi standard non polar33892256
2-Methylcitric acid,1TMS,isomer #3CC(C(=O)O)C(O)(CC(=O)O[Si](C)(C)C)C(=O)O1741.3Semi standard non polar33892256
2-Methylcitric acid,1TMS,isomer #4CC(C(=O)O)C(O)(CC(=O)O)C(=O)O[Si](C)(C)C1707.6Semi standard non polar33892256
2-Methylcitric acid,2TMS,isomer #1CC(C(=O)O[Si](C)(C)C)C(CC(=O)O)(O[Si](C)(C)C)C(=O)O1787.3Semi standard non polar33892256
2-Methylcitric acid,2TMS,isomer #2CC(C(=O)O[Si](C)(C)C)C(O)(CC(=O)O[Si](C)(C)C)C(=O)O1773.3Semi standard non polar33892256
2-Methylcitric acid,2TMS,isomer #3CC(C(=O)O[Si](C)(C)C)C(O)(CC(=O)O)C(=O)O[Si](C)(C)C1749.9Semi standard non polar33892256
2-Methylcitric acid,2TMS,isomer #4CC(C(=O)O)C(CC(=O)O[Si](C)(C)C)(O[Si](C)(C)C)C(=O)O1789.1Semi standard non polar33892256
2-Methylcitric acid,2TMS,isomer #5CC(C(=O)O)C(CC(=O)O)(O[Si](C)(C)C)C(=O)O[Si](C)(C)C1776.1Semi standard non polar33892256
2-Methylcitric acid,2TMS,isomer #6CC(C(=O)O)C(O)(CC(=O)O[Si](C)(C)C)C(=O)O[Si](C)(C)C1743.7Semi standard non polar33892256
2-Methylcitric acid,3TMS,isomer #1CC(C(=O)O[Si](C)(C)C)C(CC(=O)O[Si](C)(C)C)(O[Si](C)(C)C)C(=O)O1797.7Semi standard non polar33892256
2-Methylcitric acid,3TMS,isomer #2CC(C(=O)O[Si](C)(C)C)C(CC(=O)O)(O[Si](C)(C)C)C(=O)O[Si](C)(C)C1815.1Semi standard non polar33892256
2-Methylcitric acid,3TMS,isomer #3CC(C(=O)O[Si](C)(C)C)C(O)(CC(=O)O[Si](C)(C)C)C(=O)O[Si](C)(C)C1796.4Semi standard non polar33892256
2-Methylcitric acid,3TMS,isomer #4CC(C(=O)O)C(CC(=O)O[Si](C)(C)C)(O[Si](C)(C)C)C(=O)O[Si](C)(C)C1809.1Semi standard non polar33892256
2-Methylcitric acid,4TMS,isomer #1CC(C(=O)O[Si](C)(C)C)C(CC(=O)O[Si](C)(C)C)(O[Si](C)(C)C)C(=O)O[Si](C)(C)C1884.7Semi standard non polar33892256
2-Methylcitric acid,1TBDMS,isomer #1CC(C(=O)O[Si](C)(C)C(C)(C)C)C(O)(CC(=O)O)C(=O)O1979.3Semi standard non polar33892256
2-Methylcitric acid,1TBDMS,isomer #2CC(C(=O)O)C(CC(=O)O)(O[Si](C)(C)C(C)(C)C)C(=O)O1987.8Semi standard non polar33892256
2-Methylcitric acid,1TBDMS,isomer #3CC(C(=O)O)C(O)(CC(=O)O[Si](C)(C)C(C)(C)C)C(=O)O1994.3Semi standard non polar33892256
2-Methylcitric acid,1TBDMS,isomer #4CC(C(=O)O)C(O)(CC(=O)O)C(=O)O[Si](C)(C)C(C)(C)C1977.2Semi standard non polar33892256
2-Methylcitric acid,2TBDMS,isomer #1CC(C(=O)O[Si](C)(C)C(C)(C)C)C(CC(=O)O)(O[Si](C)(C)C(C)(C)C)C(=O)O2210.2Semi standard non polar33892256
2-Methylcitric acid,2TBDMS,isomer #2CC(C(=O)O[Si](C)(C)C(C)(C)C)C(O)(CC(=O)O[Si](C)(C)C(C)(C)C)C(=O)O2227.3Semi standard non polar33892256
2-Methylcitric acid,2TBDMS,isomer #3CC(C(=O)O[Si](C)(C)C(C)(C)C)C(O)(CC(=O)O)C(=O)O[Si](C)(C)C(C)(C)C2227.9Semi standard non polar33892256
2-Methylcitric acid,2TBDMS,isomer #4CC(C(=O)O)C(CC(=O)O[Si](C)(C)C(C)(C)C)(O[Si](C)(C)C(C)(C)C)C(=O)O2214.4Semi standard non polar33892256
2-Methylcitric acid,2TBDMS,isomer #5CC(C(=O)O)C(CC(=O)O)(O[Si](C)(C)C(C)(C)C)C(=O)O[Si](C)(C)C(C)(C)C2211.9Semi standard non polar33892256
2-Methylcitric acid,2TBDMS,isomer #6CC(C(=O)O)C(O)(CC(=O)O[Si](C)(C)C(C)(C)C)C(=O)O[Si](C)(C)C(C)(C)C2236.0Semi standard non polar33892256
2-Methylcitric acid,3TBDMS,isomer #1CC(C(=O)O[Si](C)(C)C(C)(C)C)C(CC(=O)O[Si](C)(C)C(C)(C)C)(O[Si](C)(C)C(C)(C)C)C(=O)O2464.1Semi standard non polar33892256
2-Methylcitric acid,3TBDMS,isomer #2CC(C(=O)O[Si](C)(C)C(C)(C)C)C(CC(=O)O)(O[Si](C)(C)C(C)(C)C)C(=O)O[Si](C)(C)C(C)(C)C2454.5Semi standard non polar33892256
2-Methylcitric acid,3TBDMS,isomer #3CC(C(=O)O[Si](C)(C)C(C)(C)C)C(O)(CC(=O)O[Si](C)(C)C(C)(C)C)C(=O)O[Si](C)(C)C(C)(C)C2437.2Semi standard non polar33892256
2-Methylcitric acid,3TBDMS,isomer #4CC(C(=O)O)C(CC(=O)O[Si](C)(C)C(C)(C)C)(O[Si](C)(C)C(C)(C)C)C(=O)O[Si](C)(C)C(C)(C)C2455.0Semi standard non polar33892256
2-Methylcitric acid,4TBDMS,isomer #1CC(C(=O)O[Si](C)(C)C(C)(C)C)C(CC(=O)O[Si](C)(C)C(C)(C)C)(O[Si](C)(C)C(C)(C)C)C(=O)O[Si](C)(C)C(C)(C)C2665.4Semi standard non polar33892256
Spectra
Biological Properties
Cellular Locations
  • Extracellular
Biospecimen Locations
  • Blood
  • Cerebrospinal Fluid (CSF)
  • Feces
  • Urine
Tissue Locations
  • Placenta
Pathways
Normal Concentrations
BiospecimenStatusValueAgeSexConditionReferenceDetails
BloodDetected and Quantified0.1 (0.08-0.26) uMAdult (>18 years old)BothNormal details
BloodDetected and Quantified0.059 (0.021-0.097) uMAdult (>18 years old)BothNormal details
Cerebrospinal Fluid (CSF)Detected and Quantified0.50 (0.24-0.80) uMAdult (>18 years old)BothNormal details
Cerebrospinal Fluid (CSF)Detected and Quantified0.323-1.07 uMNot SpecifiedNot SpecifiedNormal details
FecesDetected but not QuantifiedNot QuantifiedAdult (>18 years old)Both
Normal		 details
FecesDetected but not QuantifiedNot QuantifiedAdult (>18 years old)Both
Normal		 details
UrineDetected and Quantified6.7 (0.7-19.6) umol/mmol creatinineNewborn (0-30 days old)BothNormal details
UrineDetected and Quantified7.7 (3.3-28.6) umol/mmol creatinineInfant (0-1 year old)BothNormal details
UrineDetected and Quantified3.4 (1.4-8.5) umol/mmol creatinineChildren (1-13 years old)Both
Normal		 details
UrineDetected and Quantified3.2 (2.0-8.1) umol/mmol creatinineChildren (1-13 years old)Both
Normal		 details
UrineDetected and Quantified2.6 (1.6-6.2) umol/mmol creatinineAdolescent (13-18 years old)BothNormal details
UrineDetected and Quantified0.59 (0.05-1.15) umol/mmol creatinineAdult (>18 years old)BothNormal details
UrineDetected and Quantified<6.09 umol/mmol creatinineChildren (1 - 18 years old)Both
Normal
    • BC Children's Hos...
 details
UrineDetected and Quantified1.4-2.9 umol/mmol creatinineAdult (>18 years old)FemaleNormal details
UrineDetected and Quantified1.2-1.8 umol/mmol creatinineAdult (>18 years old)MaleNormal details
UrineDetected and Quantified<15 umol/mmol creatinineAdult (>18 years old)BothNormal details
Abnormal Concentrations
BiospecimenStatusValueAgeSexConditionReferenceDetails
Cerebrospinal Fluid (CSF)Detected and Quantified1.37-16.3 uMNot SpecifiedNot Specifiedcobalamin deficiency details
FecesDetected but not QuantifiedNot QuantifiedAdult (>18 years old)BothCrohns disease details
FecesDetected but not QuantifiedNot QuantifiedAdult (>18 years old)BothIron deficiency details
UrineDetected and Quantified7.0 (2.0-12.0) umol/mmol creatinineAdult (>18 years old)BothBiotinidase deficiency
    • MetaGene: Metabol...
 details
UrineDetected and Quantified30.0 (10.0-50.0) umol/mmol creatinineChildren (1-13 years old)BothBiotinidase deficiency
    • MetaGene: Metabol...
 details
UrineDetected and Quantified31 umol/mmol creatinineAdult (>18 years old)Not Specified
Propionic acidemia		 details
UrineDetected and Quantified0.780-3.600 umol/mmol creatinineChildren (1 - 13 years old)Not Specified
isovaleric acidemia		 details
UrineDetected and Quantified1.470-1.560 umol/mmol creatinineChildren (1 - 13 years old)Not Specified
isovaleric acidemia		 details
UrineDetected but not QuantifiedNot QuantifiedAdult (>18 years old)BothBladder cancer details
Associated Disorders and Diseases
Disease References
Vitamin B12 deficiency
  1. Allen RH, Stabler SP, Savage DG, Lindenbaum J: Elevation of 2-methylcitric acid I and II levels in serum, urine, and cerebrospinal fluid of patients with cobalamin deficiency. Metabolism. 1993 Aug;42(8):978-88. [PubMed:8345822 ]
Crohn's disease
  1. Lee T, Clavel T, Smirnov K, Schmidt A, Lagkouvardos I, Walker A, Lucio M, Michalke B, Schmitt-Kopplin P, Fedorak R, Haller D: Oral versus intravenous iron replacement therapy distinctly alters the gut microbiota and metabolome in patients with IBD. Gut. 2017 May;66(5):863-871. doi: 10.1136/gutjnl-2015-309940. Epub 2016 Feb 4. [PubMed:26848182 ]
Iron deficiency
  1. Lee T, Clavel T, Smirnov K, Schmidt A, Lagkouvardos I, Walker A, Lucio M, Michalke B, Schmitt-Kopplin P, Fedorak R, Haller D: Oral versus intravenous iron replacement therapy distinctly alters the gut microbiota and metabolome in patients with IBD. Gut. 2017 May;66(5):863-871. doi: 10.1136/gutjnl-2015-309940. Epub 2016 Feb 4. [PubMed:26848182 ]
Biotinidase deficiency
  1. G.Frauendienst-Egger, Friedrich K. Trefz (2017). MetaGene: Metabolic & Genetic Information Center (MIC: http://www.metagene.de). METAGENE consortium.
Propionic acidemia
  1. Riemersma M, Hazebroek MR, Helderman-van den Enden ATJM, Salomons GS, Ferdinandusse S, Brouwers MCGJ, van der Ploeg L, Heymans S, Glatz JFC, van den Wijngaard A, Krapels IPC, Bierau J, Brunner HG: Propionic acidemia as a cause of adult-onset dilated cardiomyopathy. Eur J Hum Genet. 2017 Nov;25(11):1195-1201. doi: 10.1038/ejhg.2017.127. Epub 2017 Aug 30. [PubMed:28853722 ]
Isovaleric acidemia
  1. Loots DT: Abnormal tricarboxylic acid cycle metabolites in isovaleric acidaemia. J Inherit Metab Dis. 2009 Jun;32(3):403-11. doi: 10.1007/s10545-009-1071-6. Epub 2009 Apr 5. [PubMed:19343532 ]
Associated OMIM IDs
DrugBank IDNot Available
Phenol Explorer Compound IDNot Available
FooDB IDFDB021997
KNApSAcK IDNot Available
Chemspider ID500
KEGG Compound IDNot Available
BioCyc IDNot Available
BiGG ID39369
Wikipedia LinkNot Available
METLIN ID5368
PubChem Compound515
PDB IDNot Available
ChEBI ID30835
Food Biomarker OntologyNot Available
VMH ID2MCIT
MarkerDB IDMDB00000155
Good Scents IDNot Available
References
Synthesis ReferenceEwering, Christian; Braemer, Christian Oliver; Steinbuechel, Alexander. Production of 2-methylcitric acid by a recombinant Ralstonia eutropha strain. PCT Int. Appl. (2007), 30pp. CODEN: PIXXD2 WO 2007101866 A2 20070913 CAN 147:363646 AN 2007:1033111
Material Safety Data Sheet (MSDS)Download (PDF)
General References
  1. Guneral F, Bachmann C: Age-related reference values for urinary organic acids in a healthy Turkish pediatric population. Clin Chem. 1994 Jun;40(6):862-6. [PubMed:8087979 ]
  2. Allen RH, Stabler SP, Savage DG, Lindenbaum J: Elevation of 2-methylcitric acid I and II levels in serum, urine, and cerebrospinal fluid of patients with cobalamin deficiency. Metabolism. 1993 Aug;42(8):978-88. [PubMed:8345822 ]
  3. Busch M, Stein G, Poppitz W, Hein G, Muller A: Validated capillary gas chromatographic-mass spectrometric assay to determine 2-methylcitric acid I and II levels in human serum by using a pulsed splitless injection procedure. J Chromatogr B Analyt Technol Biomed Life Sci. 2002 Aug 5;775(2):215-23. [PubMed:12113988 ]
  4. Bergstrom T, Greter J, Levin AH, Steen G, Tryding N, Wass U: Propionyl-CoA carboxylase deficiency: case report, effect of low-protein diet and identification of 3-oxo-2-methylvaleric acid 3-hydroxy-2-methylvaleric acid, and maleic acid in urine. Scand J Clin Lab Invest. 1981 Apr;41(2):117-26. [PubMed:7313494 ]
  5. Thompson GN, Chalmers RA: Increased urinary metabolite excretion during fasting in disorders of propionate metabolism. Pediatr Res. 1990 Apr;27(4 Pt 1):413-6. [PubMed:2342832 ]
  6. Krawczyk H, Gradowska W: 1H NMR spectra of methylcitric acid in urine. J Inherit Metab Dis. 2007 Apr;30(2):263. Epub 2007 Feb 14. [PubMed:17295121 ]
  7. 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 ]