Showing metabocard for 2-Hydroxy-2-methylbutanedioic acid (MMDBc0033556)

Record Information
Version1.0
StatusDetected and Quantified
Creation Date2021-11-19 04:53:27 UTC
Update Date2022-08-31 22:36:44 UTC
Metabolite IDMMDBc0033556
Metabolite Identification
Common Name2-Hydroxy-2-methylbutanedioic acid
Description2-Hydroxy-2-methylbutanedioic acid, also known as citramalic acid, 2-Methylmalic acid, is an analog of malic acid. The structure of citramalic acid is similar to the structure of malic acid except it has an extra CH3 group on position 2. It is also classified as a 2-hydroxydicarboxylic acid. Citramalic acid exists in two isomers, L-citramalic acid and D-citramalic acid. The L-isomer is more biologically relevant isomer. Citramalic acid is found in almost all living organisms from microbes to plants to humans although citramalate is primarily produced from bacteria. L-citramalic acid was first isolated from the peel of apples in 1954 (PMID: 13160011 ). It has also been isolated in wine and other ripening fruit (PMID: 13807713 ). Citramalic acid can inhibit the production of malic acid. Citramalic acid is also an important microbial metabolite and has been found to be a byproduct of Saccharomyces yeast species, as well as Propionibacterium acnes and Aspergillus niger (PMID: 31827810 ) (http://drweyrich.weyrich.com/labs/oat.html) (PMID: 7628083 ). Citramalic acid is a component of the C5-branched dibasic acid metabolism pathway. It can be broken down by the enzyme citramalate lyase, which converts citramalate to acetate and pyruvate. Citramalate synthase is an enzyme found in bacteria that synthesizes citramalic acid from acetyl-CoA, pyruvate and water. Citramalic acid may have a useful role in medical diagnoses. It has been found in the urine of two brothers with autistic features (PMID: 7628083 ). Citramalic acid can also be used as a urinary marker for gut dysbiosis (PMID: 31669633 ). Dysbiosis is a disorder of the bacterial flora of the human digestive tract. It is usually diagnosed clinically by direct detection of an abnormal pattern of the intestinal microbiota.
Structure
MOL3D MOLSDF3D SDFPDB3D PDBSMILESInChI

MOL for #<Metabolite:0x0000560be1afcce0>

2-Hydroxy-2-methyl-butanedioic acid.mol
  Mrv1652305271900062D          

 10  9  0  0  0  0            999 V2000
    0.9809   -0.2237    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.2526    0.2613    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4293   -0.1324    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1110    0.2613    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.9695   -1.0486    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.7929    0.2645    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1110    1.0486    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7929   -0.1324    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3726    0.8850    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.9541    0.9502    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
  3  4  1  0  0  0  0
  1  5  2  0  0  0  0
  1  6  1  0  0  0  0
  4  7  2  0  0  0  0
  4  8  1  0  0  0  0
  2  9  1  0  0  0  0
  2 10  1  0  0  0  0
M  END
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3D MOL for #<Metabolite:0x0000560be1afcce0>

HMDB0000426
     RDKit          3D
Citramalic acid
 18 17  0  0  0  0  0  0  0  0999 V2000
   -1.4722   -0.8551    1.0073 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5923   -0.1695   -0.0484 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1226   -0.3891   -1.3045 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.7666   -0.8142    0.0661 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.7428   -0.2606   -0.8930 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.9063   -0.7390   -0.8699 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.4602    0.7373   -1.8021 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5947    1.2571    0.2694 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0386    2.0658   -0.5564 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1147    1.7183    1.4653 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3688   -0.2872    1.9521 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1185   -1.8920    1.1656 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5283   -0.8800    0.6406 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6649   -1.1197   -1.8078 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.6136   -1.8910   -0.2235 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.1273   -0.8303    1.1062 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.9491    1.6415   -1.8054 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.0498    2.7077    1.6384 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
  4  5  1  0
  5  6  2  0
  5  7  1  0
  2  8  1  0
  8  9  2  0
  8 10  1  0
  1 11  1  0
  1 12  1  0
  1 13  1  0
  3 14  1  0
  4 15  1  0
  4 16  1  0
  7 17  1  0
 10 18  1  0
M  END
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3D SDF for #<Metabolite:0x0000560be1afcce0>

2-Hydroxy-2-methyl-butanedioic acid.mol
  Mrv1652305271900062D          

 10  9  0  0  0  0            999 V2000
    0.9809   -0.2237    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.2526    0.2613    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4293   -0.1324    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1110    0.2613    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.9695   -1.0486    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.7929    0.2645    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1110    1.0486    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7929   -0.1324    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3726    0.8850    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.9541    0.9502    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
  3  4  1  0  0  0  0
  1  5  2  0  0  0  0
  1  6  1  0  0  0  0
  4  7  2  0  0  0  0
  4  8  1  0  0  0  0
  2  9  1  0  0  0  0
  2 10  1  0  0  0  0
M  END
> <DATABASE_ID>
MMDBc0033556

> <DATABASE_NAME>
MIME

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

> <INCHI_IDENTIFIER>
InChI=1S/C5H8O5/c1-5(10,4(8)9)2-3(6)7/h10H,2H2,1H3,(H,6,7)(H,8,9)

> <INCHI_KEY>
XFTRTWQBIOMVPK-UHFFFAOYSA-N

> <FORMULA>
C5H8O5

> <MOLECULAR_WEIGHT>
148.114

> <EXACT_MASS>
148.037173366

> <JCHEM_ACCEPTOR_COUNT>
5

> <JCHEM_ATOM_COUNT>
18

> <JCHEM_AVERAGE_POLARIZABILITY>
12.68540259019519

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
3

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
2-hydroxy-2-methylbutanedioic acid

> <ALOGPS_LOGP>
-0.91

> <JCHEM_LOGP>
-0.6808755420000001

> <ALOGPS_LOGS>
0.30

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
0

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-2

> <JCHEM_PKA>
5.3015290068332295

> <JCHEM_PKA_STRONGEST_ACIDIC>
3.3477157472119226

> <JCHEM_PKA_STRONGEST_BASIC>
-3.967730895376275

> <JCHEM_POLAR_SURFACE_AREA>
94.83

> <JCHEM_REFRACTIVITY>
29.5885

> <JCHEM_ROTATABLE_BOND_COUNT>
3

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
2.97e+02 g/l

> <JCHEM_TRADITIONAL_IUPAC>
citramalate, (+-)-

> <JCHEM_VEBER_RULE>
0

$$$$
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3D-SDF for #<Metabolite:0x0000560be1afcce0>

HMDB0000426
     RDKit          3D
Citramalic acid
 18 17  0  0  0  0  0  0  0  0999 V2000
   -1.4722   -0.8551    1.0073 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5923   -0.1695   -0.0484 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1226   -0.3891   -1.3045 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.7666   -0.8142    0.0661 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.7428   -0.2606   -0.8930 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.9063   -0.7390   -0.8699 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.4602    0.7373   -1.8021 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5947    1.2571    0.2694 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0386    2.0658   -0.5564 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1147    1.7183    1.4653 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3688   -0.2872    1.9521 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1185   -1.8920    1.1656 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5283   -0.8800    0.6406 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6649   -1.1197   -1.8078 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.6136   -1.8910   -0.2235 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.1273   -0.8303    1.1062 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.9491    1.6415   -1.8054 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.0498    2.7077    1.6384 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
  4  5  1  0
  5  6  2  0
  5  7  1  0
  2  8  1  0
  8  9  2  0
  8 10  1  0
  1 11  1  0
  1 12  1  0
  1 13  1  0
  3 14  1  0
  4 15  1  0
  4 16  1  0
  7 17  1  0
 10 18  1  0
M  END
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PDB for #<Metabolite:0x0000560be1afcce0>

HEADER    PROTEIN                                 27-MAY-19   NONE
TITLE     NULL                                                        
COMPND    MOLECULE: 2-Hydroxy-2-methyl-butanedioic acid.mol           
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   27-MAY-19         0                                  
HETATM    1  C   UNK     0       1.831  -0.418   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       0.472   0.488   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0      -0.801  -0.247   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0      -2.074   0.488   0.000  0.00  0.00           C+0
HETATM    5  O   UNK     0       1.810  -1.957   0.000  0.00  0.00           O+0
HETATM    6  O   UNK     0       3.347   0.494   0.000  0.00  0.00           O+0
HETATM    7  O   UNK     0      -2.074   1.957   0.000  0.00  0.00           O+0
HETATM    8  O   UNK     0      -3.347  -0.247   0.000  0.00  0.00           O+0
HETATM    9  C   UNK     0      -0.696   1.652   0.000  0.00  0.00           C+0
HETATM   10  O   UNK     0       1.781   1.774   0.000  0.00  0.00           O+0
CONECT    1    2    5    6                                                  
CONECT    2    1    3    9   10                                             
CONECT    3    2    4                                                       
CONECT    4    3    7    8                                                  
CONECT    5    1                                                            
CONECT    6    1                                                            
CONECT    7    4                                                            
CONECT    8    4                                                            
CONECT    9    2                                                            
CONECT   10    2                                                            
MASTER        0    0    0    0    0    0    0    0   10    0   18    0
END
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3D PDB for #<Metabolite:0x0000560be1afcce0>

COMPND    HMDB0000426
HETATM    1  C1  UNL     1      -1.472  -0.855   1.007  1.00  0.00           C  
HETATM    2  C2  UNL     1      -0.592  -0.169  -0.048  1.00  0.00           C  
HETATM    3  O1  UNL     1      -1.123  -0.389  -1.305  1.00  0.00           O  
HETATM    4  C3  UNL     1       0.767  -0.814   0.066  1.00  0.00           C  
HETATM    5  C4  UNL     1       1.743  -0.261  -0.893  1.00  0.00           C  
HETATM    6  O2  UNL     1       2.906  -0.739  -0.870  1.00  0.00           O  
HETATM    7  O3  UNL     1       1.460   0.737  -1.802  1.00  0.00           O  
HETATM    8  C5  UNL     1      -0.595   1.257   0.269  1.00  0.00           C  
HETATM    9  O4  UNL     1      -1.039   2.066  -0.556  1.00  0.00           O  
HETATM   10  O5  UNL     1      -0.115   1.718   1.465  1.00  0.00           O  
HETATM   11  H1  UNL     1      -1.369  -0.287   1.952  1.00  0.00           H  
HETATM   12  H2  UNL     1      -1.119  -1.892   1.166  1.00  0.00           H  
HETATM   13  H3  UNL     1      -2.528  -0.880   0.641  1.00  0.00           H  
HETATM   14  H4  UNL     1      -0.665  -1.120  -1.808  1.00  0.00           H  
HETATM   15  H5  UNL     1       0.614  -1.891  -0.224  1.00  0.00           H  
HETATM   16  H6  UNL     1       1.127  -0.830   1.106  1.00  0.00           H  
HETATM   17  H7  UNL     1       1.949   1.642  -1.805  1.00  0.00           H  
HETATM   18  H8  UNL     1       0.050   2.708   1.638  1.00  0.00           H  
CONECT    1    2   11   12   13
CONECT    2    3    4    8
CONECT    3   14
CONECT    4    5   15   16
CONECT    5    6    6    7
CONECT    7   17
CONECT    8    9    9   10
CONECT   10   18
END
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SMILES for #<Metabolite:0x0000560be1afcce0>

CC(O)(CC(O)=O)C(O)=O
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INCHI for #<Metabolite:0x0000560be1afcce0>

InChI=1S/C5H8O5/c1-5(10,4(8)9)2-3(6)7/h10H,2H2,1H3,(H,6,7)(H,8,9)
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Synonyms
ValueSource
(+-)-2-Hydroxy-2-methylsuccinic acidChEBI
2-Hydroxy-2-methylbutanedioic acidChEBI
2-Hydroxy-2-methylsuccinic acidChEBI
2-Methylmalic acidChEBI
alpha-Hydroxypyrotartaric acidChEBI
Citramalic acidsChEBI
(+-)-2-Hydroxy-2-methylsuccinateGenerator
2-Hydroxy-2-methylbutanedioateGenerator
2-Hydroxy-2-methylsuccinateGenerator
2-MethylmalateGenerator
a-HydroxypyrotartarateGenerator
a-Hydroxypyrotartaric acidGenerator
alpha-HydroxypyrotartarateGenerator
Α-hydroxypyrotartarateGenerator
Α-hydroxypyrotartaric acidGenerator
CitramalateGenerator
(b)-2-MethylmalateHMDB
(b)-2-Methylmalic acidHMDB
(b)-CitramalateHMDB
(b)-Citramalic acidHMDB
(R,S)-(b)-CitramalateHMDB
(R,S)-(b)-Citramalic acidHMDB
(R,S)-b-MethylmalateHMDB
(R,S)-b-Methylmalic acidHMDB
(R,S)-beta-MethylmalateHMDB
(R,S)-beta-Methylmalic acidHMDB
2-Deoxy-3-C-methyltetrarateHMDB
2-Deoxy-3-C-methyltetraric acidHMDB
2-Hydroxy-2-methyl-(b)-butanedioateHMDB
2-Hydroxy-2-methyl-(b)-butanedioic acidHMDB
2-Hydroxy-2-methyl-butanedioateHMDB
2-Hydroxy-2-methyl-butanedioic acidHMDB
2-Methyl-(b)-malateHMDB
2-Methyl-(b)-malic acidHMDB
DL-CitramalateHMDB
DL-Citramalic acidHMDB
Citramalate, (+-)-isomerHMDB
Citramalate, (R)-isomerHMDB
Citramalate, (S)-isomerHMDB
alpha-MethylmalateHMDB
(R)-2-Hydroxy-2-methylbutanedioateHMDB
Citramalic acidKEGG
Molecular FormulaC5H8O5
Average Mass148.114
Monoisotopic Mass148.037173366
IUPAC Name2-hydroxy-2-methylbutanedioic acid
Traditional Namecitramalate, (+-)-
CAS Registry Number2306-22-1
SMILES
CC(O)(CC(O)=O)C(O)=O
InChI Identifier
InChI=1S/C5H8O5/c1-5(10,4(8)9)2-3(6)7/h10H,2H2,1H3,(H,6,7)(H,8,9)
InChI KeyXFTRTWQBIOMVPK-UHFFFAOYSA-N