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Showing metabocard for Citramalic acid (HMDB0000426)

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Record Information
Version5.0
StatusDetected and Quantified
Creation Date2005-11-16 15:48:42 UTC
Update Date2023-02-21 17:14:49 UTC
HMDB IDHMDB0000426
Secondary Accession Numbers
  • HMDB00426
Metabolite Identification
Common NameCitramalic acid
DescriptionCitramalic acid, also known as 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
Data?1676999689
MOL3D MOLSDF3D SDFPDB3D PDBSMILESInChI

MOL for HMDB0000426 (Citramalic acid)

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
Download

3D MOL for HMDB0000426 (Citramalic acid)

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
Download

3D SDF for HMDB0000426 (Citramalic acid)

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>
HMDB0000426

> <DATABASE_NAME>
hmdb

> <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

$$$$
Download

3D-SDF for HMDB0000426 (Citramalic acid)

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 HMDB0000426 (Citramalic acid)

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 HMDB0000426 (Citramalic acid)

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 HMDB0000426 (Citramalic acid)

CC(O)(CC(O)=O)C(O)=O
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INCHI for HMDB0000426 (Citramalic acid)

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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View in JSmolView NMR AssignmentsView Stereo Labels
Synonyms
Chemical FormulaC5H8O5
Average Molecular Weight148.114
Monoisotopic Molecular Weight148.037173366
IUPAC Name2-hydroxy-2-methylbutanedioic acid
Traditional Namecitramalate, (+-)-
CAS Registry Number597-44-4
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
Chemical Taxonomy
Description Belongs to the class of organic compounds known as hydroxy fatty acids. These are fatty acids in which the chain bears a hydroxyl group.
KingdomOrganic compounds
Super ClassLipids and lipid-like molecules
ClassFatty Acyls
Sub ClassFatty acids and conjugates
Direct ParentHydroxy fatty acids
Alternative Parents
Substituents
  • Branched fatty acid
  • Methyl-branched fatty acid
  • Short-chain hydroxy acid
  • Hydroxy fatty acid
  • Alpha-hydroxy acid
  • Dicarboxylic acid or derivatives
  • Hydroxy acid
  • Tertiary alcohol
  • Carboxylic acid
  • Carboxylic acid derivative
  • Alcohol
  • Hydrocarbon derivative
  • Carbonyl group
  • Organic oxide
  • Organic oxygen compound
  • Organooxygen compound
  • Aliphatic acyclic compound
Molecular FrameworkAliphatic acyclic compounds
External Descriptors
Ontology
Physiological effectNot Available
Disposition
Biological locationRoute of exposureSource
Process
Naturally occurring process
Role
Biological role
Physical Properties
StateSolid
Experimental Molecular Properties
PropertyValueReference
Melting Point107 - 111 °CNot Available
Boiling PointNot AvailableNot Available
Water Solubility1000000 mg/L @ 25 °C (est)The Good Scents Company Information System
LogPNot AvailableNot Available
Experimental Chromatographic Properties

Experimental Collision Cross Sections

Adduct TypeData SourceCCS Value (Å2)Reference
[M-H]-Baker124.86730932474
[M-H]-Not Available123.2http://allccs.zhulab.cn/database/detail?ID=AllCCS00001898
Predicted Molecular Properties
Predicted Chromatographic Properties
Spectra
Biological Properties
Cellular Locations
  • Cytoplasm
Biospecimen Locations
  • Blood
  • Feces
  • Saliva
  • Urine
Tissue LocationsNot Available
Pathways
Normal Concentrations
Abnormal Concentrations
BiospecimenStatusValueAgeSexConditionReferenceDetails
FecesDetected but not QuantifiedNot QuantifiedAdult (>18 years old)Both
Colorectal cancer		 details
Associated Disorders and Diseases
Disease References
Colorectal cancer
  1. Goedert JJ, Sampson JN, Moore SC, Xiao Q, Xiong X, Hayes RB, Ahn J, Shi J, Sinha R: Fecal metabolomics: assay performance and association with colorectal cancer. Carcinogenesis. 2014 Sep;35(9):2089-96. doi: 10.1093/carcin/bgu131. Epub 2014 Jul 18. [PubMed:25037050 ]
Associated OMIM IDs
DrugBank IDNot Available
Phenol Explorer Compound IDNot Available
FooDB IDFDB002815
KNApSAcK IDC00001181
Chemspider ID1051
KEGG Compound IDC00815
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkNot Available
METLIN ID5415
PubChem Compound1081
PDB IDNot Available
ChEBI ID15584
Food Biomarker OntologyNot Available
VMH IDCITMAL
MarkerDB IDNot Available
Good Scents IDrw1390651
References
Synthesis ReferenceBarker, H. A. Chemical synthesis and resolution of (±)-citramalic acid. Biochemical Preparations (1962), 9 25-9.
Material Safety Data Sheet (MSDS)Download (PDF)
General References
  1. Shaw W, Kassen E, Chaves E: Increased urinary excretion of analogs of Krebs cycle metabolites and arabinose in two brothers with autistic features. Clin Chem. 1995 Aug;41(8 Pt 1):1094-104. [PubMed:7628083 ]
  2. HULME AC: The oxidation of citramalic acid and beta-hydroxyglutaric acid to acetoacetic acid and the possible significance of citramalic acid in plant metabolism. Biochim Biophys Acta. 1954 May;14(1):44-51. [PubMed:13160012 ]
  3. Castrillo JI, Zeef LA, Hoyle DC, Zhang N, Hayes A, Gardner DC, Cornell MJ, Petty J, Hakes L, Wardleworth L, Rash B, Brown M, Dunn WB, Broadhurst D, O'Donoghue K, Hester SS, Dunkley TP, Hart SR, Swainston N, Li P, Gaskell SJ, Paton NW, Lilley KS, Kell DB, Oliver SG: Growth control of the eukaryote cell: a systems biology study in yeast. J Biol. 2007;6(2):4. doi: 10.1186/jbiol54. [PubMed:17439666 ]
  4. Perlman S, Carr SA: Citramalic acid in cerebrospinal fluid of patients with bacterial meningitis. Clin Chem. 1984 Jul;30(7):1209-12. [PubMed:6145530 ]
  5. Greter J, Lindstedt S, Seeman H, Steen G: 2-hydroxy-2-methylsuccinic acid--a urinary metabolite in propionyl-CoA carboxylase deficiency. Clin Chim Acta. 1980 Sep 8;106(1):103-6. [PubMed:7408203 ]
  6. HULME AC: The isolation of l-citramalic acid from the peel of the apple fruit. Biochim Biophys Acta. 1954 May;14(1):36-43. doi: 10.1016/0006-3002(54)90127-4. [PubMed:13160011 ]
  7. CARLES J: [On the decarboxylations in wine and the appearance of citramalic acid]. Rev Esp Fisiol. 1959 Sep;15:193-9. [PubMed:13807713 ]
  8. Hossain AH, Hendrikx A, Punt PJ: Identification of novel citramalate biosynthesis pathways in Aspergillus niger. Fungal Biol Biotechnol. 2019 Nov 19;6:19. doi: 10.1186/s40694-019-0084-7. eCollection 2019. [PubMed:31827810 ]