MiMeDB: Showing metabocard for (S)-Citramalate (MMDBc0049900)

Record Information

Version

1.0

Status

Detected and Quantified

Creation Date

2022-04-29 22:45:50 UTC

Update Date

2022-12-15 22:52:19 UTC

Metabolite ID

MMDBc0049900

Metabolite Identification

Common Name

(S)-Citramalate

Description

Citramalic 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

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

Synonyms

Value	Source
(+-)-2-Hydroxy-2-methylsuccinic acid	ChEBI
2-Hydroxy-2-methylbutanedioic acid	ChEBI
2-Hydroxy-2-methylsuccinic acid	ChEBI
2-Methylmalic acid	ChEBI
alpha-Hydroxypyrotartaric acid	ChEBI
Citramalic acids	ChEBI
(+-)-2-Hydroxy-2-methylsuccinate	Generator
2-Hydroxy-2-methylbutanedioate	Generator
2-Hydroxy-2-methylsuccinate	Generator
2-Methylmalate	Generator
a-Hydroxypyrotartarate	Generator
a-Hydroxypyrotartaric acid	Generator
alpha-Hydroxypyrotartarate	Generator
Α-hydroxypyrotartarate	Generator
Α-hydroxypyrotartaric acid	Generator
Citramalate	Generator
(b)-2-Methylmalate	HMDB
(b)-2-Methylmalic acid	HMDB
(b)-Citramalate	HMDB
(b)-Citramalic acid	HMDB
(R,S)-(b)-Citramalate	HMDB
(R,S)-(b)-Citramalic acid	HMDB
(R,S)-b-Methylmalate	HMDB
(R,S)-b-Methylmalic acid	HMDB
(R,S)-beta-Methylmalate	HMDB
(R,S)-beta-Methylmalic acid	HMDB
2-Deoxy-3-C-methyltetrarate	HMDB
2-Deoxy-3-C-methyltetraric acid	HMDB
2-Hydroxy-2-methyl-(b)-butanedioate	HMDB
2-Hydroxy-2-methyl-(b)-butanedioic acid	HMDB
2-Hydroxy-2-methyl-butanedioate	HMDB
2-Hydroxy-2-methyl-butanedioic acid	HMDB
2-Methyl-(b)-malate	HMDB
2-Methyl-(b)-malic acid	HMDB
DL-Citramalate	HMDB
DL-Citramalic acid	HMDB
Citramalate, (+-)-isomer	HMDB
Citramalate, (R)-isomer	HMDB
Citramalate, (S)-isomer	HMDB
alpha-Methylmalate	HMDB
(R)-2-Hydroxy-2-methylbutanedioate	HMDB
Citramalic acid	KEGG

Molecular Formula

C₅H₈O₅

Average Mass

148.114

Monoisotopic Mass

148.037173366

IUPAC Name

2-hydroxy-2-methylbutanedioic acid

Traditional Name

citramalate, (+-)-

CAS Registry Number

Not Available

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

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.

Kingdom

Organic compounds

Super Class

Lipids and lipid-like molecules

Class

Fatty Acyls

Sub Class

Fatty acids and conjugates

Direct Parent

Hydroxy 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 Framework

Aliphatic acyclic compounds

External Descriptors

3-hydroxy carboxylic acid (CHEBI:15584 )
2-hydroxydicarboxylic acid (CHEBI:15584 )

Functional Ontology

Not Available

Physical Properties

State

Expected Solid

Predicted Properties

Property	Value	Source
Water Solubility	297 g/L	ALOGPS
logP	-0.91	ALOGPS
logP	-0.68	ChemAxon
logS	0.3	ALOGPS
pKa (Strongest Acidic)	3.35	ChemAxon
pKa (Strongest Basic)	-4	ChemAxon
Physiological Charge	-2	ChemAxon
Hydrogen Acceptor Count	5	ChemAxon
Hydrogen Donor Count	3	ChemAxon
Polar Surface Area	94.83 Å²	ChemAxon
Rotatable Bond Count	3	ChemAxon
Refractivity	29.59 m³·mol⁻¹	ChemAxon
Polarizability	12.69 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

Spectra

Spectrum Type	Description	Splash Key	Deposition Date	View
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (Non-derivatized) - 70eV, Positive	splash10-000l-9200000000-d88cf81bb63b8badd74d	2016-09-22	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (3 TMS) - 70eV, Positive	splash10-00gs-8492000000-d1c8fb9235f1de536d15	2017-10-06	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (Non-derivatized) - 70eV, Positive	Not Available	2021-10-12	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_1_1) - 70eV, Positive	Not Available	2021-11-05	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_1_2) - 70eV, Positive	Not Available	2021-11-05	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_1_3) - 70eV, Positive	Not Available	2021-11-05	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_2_1) - 70eV, Positive	Not Available	2021-11-05	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_2_2) - 70eV, Positive	Not Available	2021-11-05	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_2_3) - 70eV, Positive	Not Available	2021-11-05	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TBDMS_1_1) - 70eV, Positive	Not Available	2021-11-05	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TBDMS_1_2) - 70eV, Positive	Not Available	2021-11-05	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TBDMS_1_3) - 70eV, Positive	Not Available	2021-11-05	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TBDMS_2_1) - 70eV, Positive	Not Available	2021-11-05	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TBDMS_2_2) - 70eV, Positive	Not Available	2021-11-05	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TBDMS_2_3) - 70eV, Positive	Not Available	2021-11-05	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TBDMS_3_1) - 70eV, Positive	Not Available	2021-11-05	View Spectrum
LC-MS/MS	LC-MS/MS Spectrum - Quattro_QQQ 10V, Negative (Annotated)	splash10-000j-7900000000-efbe2adf2c82decc64a6	2012-07-24	View Spectrum
LC-MS/MS	LC-MS/MS Spectrum - Quattro_QQQ 25V, Negative (Annotated)	splash10-052u-9000000000-3754186783f820cbff7c	2012-07-24	View Spectrum
LC-MS/MS	LC-MS/MS Spectrum - Quattro_QQQ 40V, Negative (Annotated)	splash10-052o-9000000000-0656e8e194378442727f	2012-07-24	View Spectrum
LC-MS/MS	LC-MS/MS Spectrum - LC-ESI-ITFT , negative	splash10-0002-2900000000-be1cc6b0ea685f5d7ac2	2017-09-14	View Spectrum
LC-MS/MS	LC-MS/MS Spectrum - LC-ESI-IT , negative	splash10-002r-8900000000-7dd192ed79cd2d306ea5	2017-09-14	View Spectrum
LC-MS/MS	LC-MS/MS Spectrum - , negative	splash10-000i-9500000000-c96a62314140c10f1245	2017-09-14	View Spectrum
LC-MS/MS	LC-MS/MS Spectrum - 50V, Negative	splash10-0002-2900000000-716fb416386753113137	2021-09-20	View Spectrum
LC-MS/MS	LC-MS/MS Spectrum - 40V, Negative	splash10-0a4l-9000000000-20ae5f1dfa6847e56e0d	2021-09-20	View Spectrum
LC-MS/MS	LC-MS/MS Spectrum - 20V, Negative	splash10-000i-9000000000-4bc688d98054e464cf07	2021-09-20	View Spectrum
LC-MS/MS	LC-MS/MS Spectrum - 30V, Negative	splash10-0a4r-9000000000-61294657ce4e2d5d6d05	2021-09-20	View Spectrum
LC-MS/MS	LC-MS/MS Spectrum - 10V, Negative	splash10-000i-9400000000-d027e4da9369388ea3c2	2021-09-20	View Spectrum
LC-MS/MS	LC-MS/MS Spectrum - 40V, Negative	splash10-0a4l-9000000000-e7930822f64c0c43d7c0	2021-09-20	View Spectrum
LC-MS/MS	LC-MS/MS Spectrum - 35V, Negative	splash10-000i-9500000000-2e922f07663d3c399240	2021-09-20	View Spectrum
LC-MS/MS	LC-MS/MS Spectrum - 10V, Negative	splash10-000i-9400000000-b372db83cd99e22fb0ac	2021-09-20	View Spectrum
LC-MS/MS	LC-MS/MS Spectrum - 20V, Negative	splash10-000i-9000000000-093483f4bf2d387fa405	2021-09-20	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Positive	splash10-001a-5900000000-437d36fe16a8d6f79c68	2016-09-12	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Positive	splash10-000i-9200000000-6aed3a8e654948bbd5e8	2016-09-12	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Positive	splash10-000i-9000000000-31c6a41b79f5b68fa431	2016-09-12	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Negative	splash10-0uds-4900000000-0d782e5134753ac75aeb	2016-09-12	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Negative	splash10-0zg0-9800000000-79154974b5c30f915ea5	2016-09-12	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Negative	splash10-0a4i-9100000000-16648250719da0016f96	2016-09-12	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Negative	splash10-0f79-7900000000-7ad97a16a3c93f065dc0	2021-09-22	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Negative	splash10-0pbi-9200000000-5a2fa29950e165d19eee	2021-09-22	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Negative	splash10-0006-9000000000-6e51c64fc7bc0e025373	2021-09-22	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Positive	splash10-0019-7900000000-8d007c21807d42c8e41b	2021-09-23	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 500 MHz, H₂O, experimental)		2012-12-04	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 100 MHz, D₂O, predicted)		2021-09-24	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 100 MHz, D₂O, predicted)		2021-09-24	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 1000 MHz, D₂O, predicted)		2021-09-24	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 1000 MHz, D₂O, predicted)		2021-09-24	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 200 MHz, D₂O, predicted)		2021-09-24	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 200 MHz, D₂O, predicted)		2021-09-24	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 300 MHz, D₂O, predicted)		2021-09-24	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 300 MHz, D₂O, predicted)		2021-09-24	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 400 MHz, D₂O, predicted)		2021-09-24	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 400 MHz, D₂O, predicted)		2021-09-24	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 500 MHz, D₂O, predicted)		2021-09-24	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 500 MHz, D₂O, predicted)		2021-09-24	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 600 MHz, D₂O, predicted)		2021-09-24	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 600 MHz, D₂O, predicted)		2021-09-24	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 700 MHz, D₂O, predicted)		2021-09-24	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 700 MHz, D₂O, predicted)		2021-09-24	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 800 MHz, D₂O, predicted)		2021-09-24	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 800 MHz, D₂O, predicted)		2021-09-24	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 900 MHz, D₂O, predicted)		2021-09-24	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 900 MHz, D₂O, predicted)		2021-09-24	View Spectrum
2D NMR	[¹H, ¹³C]-HSQC NMR Spectrum (2D, 400 MHz, H₂O, experimental)		2012-12-05	View Spectrum

Biological Properties

Cellular Locations

Cytoplasm

Biospecimen Locations

Feces
Urine

Tissue Locations

Not Available

Associated OMIM IDs

114500 (Colorectal cancer)
610247 (Eosinophilic esophagitis)

Human Proteins and Enzymes

Protein ID	Protein Name	Protein Type	Uniprot ID	Species

Human Pathways

Pathways

Name	SMPDB/PathBank

Metabolic Reactions

Reactions

Reaction ID	Precursor	Product	Enzyme	Reaction Type	Data Source	Reference
MMDBr0011029	(S)-Citramalate	Acetic acid	Not Available		VMH	30371894
MMDBr0012679	Mesaconic acid	(S)-Citramalate	Not Available		VMH	30371894

Health Effects and Bioactivity

Health Outcome/Bioactivity	Metabolite Response/Effect	Evidence Type	Host and Biospecimen	Data Source	Reference

Microbial Sources

Superkingdom/Kingdom	Phylum	Total species	Hosts and Body Sites	Microbial Links
Bacteria	Proteobacteria	9	Human feces; Human sputum; Human	Metabolic reconstruction
Bacteria	Bacteroidetes	2	Human ; Human feces	Metabolic reconstruction
Bacteria	Chloroflexi	2

Exposure Sources

Source Type	Source Sub-type	Species	Data Source	Reference

Host Biospecimen and Location

Host and Biospecimen	Status	Mean	Min	Max	Units	Age	Sex	Health Condition	Data Source	Reference
Human Feces	Detected but not Quantified								HMDB
Human Urine	Detected and Quantified	3.1			umol/mmol creatinine	Adult (>18 years old)	Both	Normal	HMDB	21388201
Human Urine	Detected and Quantified		0	100	umol/mmol creatinine	Newborn (0-30 days old)	Both	Normal	HMDB	31506554
Human Urine	Detected and Quantified	11.8	5.5	21.0	umol/mmol creatinine	Infant (0-1 year old)	Both	Normal	HMDB	8087979
Human Urine	Detected and Quantified	14.0	5.5	24.6	umol/mmol creatinine	Newborn (0-30 days old)	Not Specified	Normal	HMDB	8087979
Human Urine	Detected and Quantified	2.4	1.0	4.8	umol/mmol creatinine	Adult (>18 years old)	Both	Normal	HMDB	24023812
Human Urine	Detected and Quantified		2.5	3.4	umol/mmol creatinine	Adult (>18 years old)	Male	Normal	HMDB	27012787
Human Urine	Detected and Quantified		2.5	4.5	umol/mmol creatinine	Adult (>18 years old)	Female	Normal	HMDB	27012787
Human Urine	Detected and Quantified	4.7	1.3	11.2	umol/mmol creatinine	Adolescent (13-18 years old)	Both	Normal	HMDB	8087979
Human Urine	Detected and Quantified	5.5	4.2	8.9	umol/mmol creatinine	Children (1-13 years old)	Both	Normal	HMDB	8087979

External Links

HMDB ID

HMDB0000426

DrugBank ID

Not Available

Phenol Explorer Compound ID

Not Available

FooDB ID

KNApSAcK ID

Chemspider ID

KEGG Compound ID

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

5415

PubChem Compound

1081

PDB ID

Not Available

ChEBI ID

15584

Food Biomarker Ontology

Not Available

References

Synthesis Reference

Not Available

General References

Perlman S, Carr SA: Citramalic acid in cerebrospinal fluid of patients with bacterial meningitis. Clin Chem. 1984 Jul;30(7):1209-12. [PubMed:6145530 ]
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. doi: 10.1016/0009-8981(80)90380-0. [PubMed:7408203 ]
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 ]
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 ]
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. doi: 10.1016/0006-3002(54)90128-6. [PubMed:13160012 ]
CARLES J: [On the decarboxylations in wine and the appearance of citramalic acid]. Rev Esp Fisiol. 1959 Sep;15:193-9. [PubMed:13807713 ]
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 ]
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 ]

Showing metabocard for (S)-Citramalate (MMDBc0049900)

MOL for #<Metabolite:0x00007f66c81924f0>

3D MOL for #<Metabolite:0x00007f66c81924f0>

3D SDF for #<Metabolite:0x00007f66c81924f0>

3D-SDF for #<Metabolite:0x00007f66c81924f0>

PDB for #<Metabolite:0x00007f66c81924f0>

3D PDB for #<Metabolite:0x00007f66c81924f0>

SMILES for #<Metabolite:0x00007f66c81924f0>

INCHI for #<Metabolite:0x00007f66c81924f0>

Structure for #<Metabolite:0x00007f66c81924f0>

3D Structure for #<Metabolite:0x00007f66c81924f0>