MiMeDB: Showing metabocard for Methylmalonylcarnitine (MMDBc0000783)

Record Information

Version

1.0

Status

Detected and Quantified

Creation Date

2020-12-10 21:51:42 UTC

Update Date

2024-04-30 19:33:42 UTC

Metabolite ID

MMDBc0000783

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 [Dambrova et al. 2021, Physiological Reviews], 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 at [Dambrova et al. 2021, Physiological Reviews].

Structure

MOL SDF PDB SMILES InChI


  Mrv1652309172008452D          

 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  0  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  1   9   1
M  END
> <DATABASE_ID>
MMDBc0000783

> <DATABASE_NAME>
MIME

> <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

> <FORMULA>
C11H20NO6

> <MOLECULAR_WEIGHT>
262.281

> <EXACT_MASS>
262.128513788

> <JCHEM_ACCEPTOR_COUNT>
5

> <JCHEM_ATOM_COUNT>
38

> <JCHEM_AVERAGE_POLARIZABILITY>
25.99170819702714

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
2

> <JCHEM_FORMAL_CHARGE>
1

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
[(2R)-3-carboxy-2-{[(2R)-2-carboxy-2-methylacetyl]oxy}propyl]trimethylazanium

> <ALOGPS_LOGP>
-1.09

> <JCHEM_LOGP>
-4.0111659134717454

> <ALOGPS_LOGS>
-2.97

> <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>
100.9

> <JCHEM_REFRACTIVITY>
72.7183

> <JCHEM_ROTATABLE_BOND_COUNT>
8

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
3.21e-01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
[(2R)-3-carboxy-2-{[(2R)-2-carboxy-2-methylacetyl]oxy}propyl]trimethylazanium

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 17-SEP-20   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   17-SEP-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+0
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

Synonyms

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

Molecular Formula

C₁₁H₂₀NO₆

Average Mass

262.281

Monoisotopic Mass

262.128513788

IUPAC Name

[(2R)-3-carboxy-2-{[(2R)-2-carboxy-2-methylacetyl]oxy}propyl]trimethylazanium

Traditional Name

[(2R)-3-carboxy-2-{[(2R)-2-carboxy-2-methylacetyl]oxy}propyl]trimethylazanium

CAS Registry Number

Not Available

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 tricarboxylic acids and derivatives. These are carboxylic acids containing exactly three carboxyl groups.

Kingdom

Organic compounds

Super Class

Organic acids and derivatives

Class

Carboxylic acids and derivatives

Sub Class

Tricarboxylic acids and derivatives

Direct Parent

Tricarboxylic acids and derivatives

Alternative Parents

Substituents

Tricarboxylic acid or derivatives
1,3-dicarbonyl compound
Quaternary ammonium salt
Tetraalkylammonium salt
Carboxylic acid ester
Carboxylic acid
Hydrocarbon derivative
Organic oxygen compound
Organic nitrogen compound
Organooxygen compound
Organonitrogen compound
Carbonyl group
Amine
Organic oxide
Organic cation
Aliphatic acyclic compound

Molecular Framework

Aliphatic acyclic compounds

External Descriptors

Not Available

Functional Ontology

Not Available

Physical Properties

State

Expected Solid

Predicted Properties

Property	Value	Source
Water Solubility	0.32 g/L	ALOGPS
logP	-1.1	ALOGPS
logP	-4	ChemAxon
logS	-3	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	2	ChemAxon
Polar Surface Area	100.9 Å²	ChemAxon
Rotatable Bond Count	8	ChemAxon
Refractivity	72.72 m³·mol⁻¹	ChemAxon
Polarizability	25.99 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	Deposition Date	View
1D NMR	¹³C NMR Spectrum (1D, 100 MHz, H₂O, predicted)	2022-08-22	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 100 MHz, H₂O, predicted)	2022-08-22	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 1000 MHz, H₂O, predicted)	2022-08-22	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 1000 MHz, H₂O, predicted)	2022-08-22	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 200 MHz, H₂O, predicted)	2022-08-22	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 200 MHz, H₂O, predicted)	2022-08-22	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 300 MHz, H₂O, predicted)	2022-08-22	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 300 MHz, H₂O, predicted)	2022-08-22	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 400 MHz, H₂O, predicted)	2022-08-22	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 400 MHz, H₂O, predicted)	2022-08-22	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 500 MHz, H₂O, predicted)	2022-08-22	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 500 MHz, H₂O, predicted)	2022-08-22	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 600 MHz, H₂O, predicted)	2022-08-22	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 600 MHz, H₂O, predicted)	2022-08-22	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 700 MHz, H₂O, predicted)	2022-08-22	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 700 MHz, H₂O, predicted)	2022-08-22	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 800 MHz, H₂O, predicted)	2022-08-22	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 800 MHz, H₂O, predicted)	2022-08-22	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 900 MHz, H₂O, predicted)	2022-08-22	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 900 MHz, H₂O, predicted)	2022-08-22	View Spectrum

Biological Properties

Cellular Locations

Extracellular
Membrane

Biospecimen Locations

Blood
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

Not Available

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	Bacteroidetes	1	Human feces; Human stool; Human	Indirect association between microbiota composition and metabolites measured in host biospecimen

Exposure Sources

Source Type	Source Sub-type	Species	Data Source	Reference

Host Biospecimen and Location

Host and Biospecimen	Status	Mean	Std	Min	Max	Units	Age	Sex	Health Condition	Data Source	Reference
Human Blood	Detected and Quantified	<0.110				uM	Not Specified	Not Specified	Normal	HMDB	16148061
Human Urine	Detected and Quantified	0.09		0.05	0.16	umol/mmol creatinine	Adult (>18 years old)	Both	Normal	HMDB	24023812

External Links

HMDB ID

HMDB0013133

DrugBank ID

Not Available

Phenol Explorer Compound ID

Not Available

FooDB ID

FDB029306

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

96365703

PDB ID

Not Available

ChEBI ID

Not Available

Food Biomarker Ontology

Not Available

References

Synthesis Reference

Not Available

General References

Simons K, Toomre D: Lipid rafts and signal transduction. Nat Rev Mol Cell Biol. 2000 Oct;1(1):31-9. doi: 10.1038/35036052. [PubMed:11413487 ]
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 ]
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. doi: 10.1194/jlr.R600022-JLR200. Epub 2006 Aug 10. [PubMed:16902246 ]
Maeda Y, Ito T, Suzuki A, Kurono Y, Ueta A, Yokoi K, Sumi S, Togari H, Sugiyama N: Simultaneous quantification of acylcarnitine isomers containing dicarboxylic acylcarnitines in human serum and urine by high-performance liquid chromatography/electrospray ionization tandem mass spectrometry. Rapid Commun Mass Spectrom. 2007;21(5):799-806. doi: 10.1002/rcm.2905. [PubMed:17279485 ]
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. doi: 10.1194/jlr.R700005-JLR200. 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 ]
Rahmandar MH, Bawcom A, Romano ME, Hamid R: Cobalamin C deficiency in an adolescent with altered mental status and anorexia. Pediatrics. 2014 Dec;134(6):e1709-14. doi: 10.1542/peds.2013-2711. Epub 2014 Nov 3. [PubMed:25367534 ]
Waters PJ, Thuriot F, Clarke JT, Gravel S, Watkins D, Rosenblatt DS, Levesque S: Methylmalonyl-coA epimerase deficiency: A new case, with an acute metabolic presentation and an intronic splicing mutation in the MCEE gene. Mol Genet Metab Rep. 2016 Sep 24;9:19-24. doi: 10.1016/j.ymgmr.2016.09.001. eCollection 2016 Dec. [PubMed:27699154 ]
Zhang X, Li Y, Liang Y, Sun P, Wu X, Song J, Sun X, Hong M, Gao P, Deng D: Distinguishing Intracerebral Hemorrhage from Acute Cerebral Infarction through Metabolomics. Rev Invest Clin. 2017 Nov-Dec;69(6):319-328. doi: 10.24875/RIC.17002348. [PubMed:29265114 ]
Kiykim E, Aktuglu Zeybek AC, Barut K, Zubarioglu T, Cansever MS, Alsancak S, Kasapcopur O: Screening of Free Carnitine and Acylcarnitine Status in Children With Familial Mediterranean Fever. Arch Rheumatol. 2016 Mar 10;31(2):133-138. doi: 10.5606/ArchRheumatol.2016.5696. eCollection 2016 Jun. [PubMed:29900937 ]
Bayci AWL, Baker DA, Somerset AE, Turkoglu O, Hothem Z, Callahan RE, Mandal R, Han B, Bjorndahl T, Wishart D, Bahado-Singh R, Graham SF, Keidan R: Metabolomic identification of diagnostic serum-based biomarkers for advanced stage melanoma. Metabolomics. 2018 Aug 3;14(8):105. doi: 10.1007/s11306-018-1398-9. [PubMed:30830422 ]
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 ]
Gunstone, Frank D., John L. Harwood, and Albert J. Dijkstra (2007). The lipid handbook with CD-ROM. CRC Press.

Showing metabocard for Methylmalonylcarnitine (MMDBc0000783)

MOL for #<Metabolite:0x00007fd0c8717aa0>

3D MOL for #<Metabolite:0x00007fd0c8717aa0>

3D SDF for #<Metabolite:0x00007fd0c8717aa0>

3D-SDF for #<Metabolite:0x00007fd0c8717aa0>

PDB for #<Metabolite:0x00007fd0c8717aa0>

3D PDB for #<Metabolite:0x00007fd0c8717aa0>

SMILES for #<Metabolite:0x00007fd0c8717aa0>

INCHI for #<Metabolite:0x00007fd0c8717aa0>

Structure for #<Metabolite:0x00007fd0c8717aa0>

3D Structure for #<Metabolite:0x00007fd0c8717aa0>