MiMeDB: Showing metabocard for Pimelylcarnitine (MMDBc0033541)

Record Information

Version

1.0

Status

Detected and Quantified

Creation Date

2021-11-19 04:52:51 UTC

Update Date

2024-04-30 20:12:15 UTC

Metabolite ID

MMDBc0033541

Metabolite Identification

Common Name

Pimelylcarnitine

Description

Pimelylcarnitine is an acylcarnitine. More specifically, it is an pimelic 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. Pimelylcarnitine is therefore classified as a medium chain AC. As a medium-chain acylcarnitine pimelylcarnitine is somewhat less abundant than short-chain acylcarnitines. These are formed either through esterification with L-carnitine or through the peroxisomal metabolism of longer chain acylcarnitines (PMID: 30540494 ). Many medium-chain acylcarnitines can serve as useful markers for inherited disorders of fatty acid metabolism. Carnitine octanoyltransferase (CrOT, EC:2.3.1.137) is responsible for the synthesis of all medium-chain (MCAC, C5-C12) and medium-length branched-chain acylcarnitines in peroxisomes (PMID: 10486279 ). 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


  Mrv0541 02241223162D          

 21 20  0  0  1  0            999 V2000
    1.4586    1.3184    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.2836    1.3184    0.0000 N   0  3  0  0  0  0  0  0  0  0  0  0
    3.1086    1.3184    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.2836    0.4934    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.2836    2.1434    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    1.5691    2.5559    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.8546    2.1434    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.1401    2.5559    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5743    2.1434    0.0000 O   0  5  0  0  0  0  0  0  0  0  0  0
    0.1401    3.3809    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.9980    2.5559    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.7125    2.1434    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.7125    1.3184    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.4270    2.5559    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.1414    2.1434    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.8559    2.5559    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.5704    2.1434    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.2849    2.5559    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.9993    2.1434    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    8.7138    2.5559    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    7.9993    1.3184    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
  2  4  1  0  0  0  0
  2  5  1  0  0  0  0
  5  6  1  0  0  0  0
  6  7  1  0  0  0  0
  7  8  1  0  0  0  0
  8  9  1  0  0  0  0
  8 10  2  0  0  0  0
  5 11  1  6  0  0  0
 11 12  1  0  0  0  0
 12 13  2  0  0  0  0
 12 14  1  0  0  0  0
 14 15  1  0  0  0  0
 15 16  1  0  0  0  0
 16 17  1  0  0  0  0
 17 18  1  0  0  0  0
 18 19  1  0  0  0  0
 19 20  1  0  0  0  0
 19 21  2  0  0  0  0
M  CHG  2   2   1   9  -1
M  END
> <DATABASE_ID>
MMDBc0033541

> <DATABASE_NAME>
MIME

> <SMILES>
C[N+](C)(C)[C@H](CCC([O-])=O)OC(=O)CCCCCC(O)=O

> <INCHI_IDENTIFIER>
InChI=1S/C14H25NO6/c1-15(2,3)11(9-10-13(18)19)21-14(20)8-6-4-5-7-12(16)17/h11H,4-10H2,1-3H3,(H-,16,17,18,19)/t11-/m0/s1

> <INCHI_KEY>
AUWRHMAICBSXMC-NSHDSACASA-N

> <FORMULA>
C14H25NO6

> <MOLECULAR_WEIGHT>
303.3514

> <EXACT_MASS>
303.168187537

> <JCHEM_ACCEPTOR_COUNT>
5

> <JCHEM_AVERAGE_POLARIZABILITY>
32.37079163994415

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
1

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(4S)-4-[(6-carboxyhexanoyl)oxy]-4-(trimethylazaniumyl)butanoate

> <ALOGPS_LOGP>
-0.84

> <JCHEM_LOGP>
-2.9617411564717457

> <ALOGPS_LOGS>
-4.26

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
0

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-1

> <JCHEM_PKA>
4.285740034769975

> <JCHEM_PKA_STRONGEST_ACIDIC>
3.528016653366708

> <JCHEM_PKA_STRONGEST_BASIC>
-7.1850416064831055

> <JCHEM_POLAR_SURFACE_AREA>
103.73000000000002

> <JCHEM_REFRACTIVITY>
97.26589999999999

> <JCHEM_ROTATABLE_BOND_COUNT>
12

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
1.95e-02 g/l

> <JCHEM_TRADITIONAL_IUPAC>
(4S)-4-[(6-carboxyhexanoyl)oxy]-4-(trimethylammonio)butanoate

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 24-FEB-12   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   24-FEB-12         0                                  
HETATM    1  C   UNK     0       2.723   2.461   0.000  0.00  0.00           C+0
HETATM    2  N   UNK     0       4.263   2.461   0.000  0.00  0.00           N+1
HETATM    3  C   UNK     0       5.803   2.461   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       4.263   0.921   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       4.263   4.001   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       2.929   4.771   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       1.595   4.001   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0       0.262   4.771   0.000  0.00  0.00           C+0
HETATM    9  O   UNK     0      -1.072   4.001   0.000  0.00  0.00           O-1
HETATM   10  O   UNK     0       0.262   6.311   0.000  0.00  0.00           O+0
HETATM   11  O   UNK     0       5.596   4.771   0.000  0.00  0.00           O+0
HETATM   12  C   UNK     0       6.930   4.001   0.000  0.00  0.00           C+0
HETATM   13  O   UNK     0       6.930   2.461   0.000  0.00  0.00           O+0
HETATM   14  C   UNK     0       8.264   4.771   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0       9.597   4.001   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0      10.931   4.771   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0      12.265   4.001   0.000  0.00  0.00           C+0
HETATM   18  C   UNK     0      13.598   4.771   0.000  0.00  0.00           C+0
HETATM   19  C   UNK     0      14.932   4.001   0.000  0.00  0.00           C+0
HETATM   20  O   UNK     0      16.266   4.771   0.000  0.00  0.00           O+0
HETATM   21  O   UNK     0      14.932   2.461   0.000  0.00  0.00           O+0
CONECT    1    2                                                            
CONECT    2    1    3    4    5                                             
CONECT    3    2                                                            
CONECT    4    2                                                            
CONECT    5    2    6   11                                                  
CONECT    6    5    7                                                       
CONECT    7    6    8                                                       
CONECT    8    7    9   10                                                  
CONECT    9    8                                                            
CONECT   10    8                                                            
CONECT   11    5   12                                                       
CONECT   12   11   13   14                                                  
CONECT   13   12                                                            
CONECT   14   12   15                                                       
CONECT   15   14   16                                                       
CONECT   16   15   17                                                       
CONECT   17   16   18                                                       
CONECT   18   17   19                                                       
CONECT   19   18   20   21                                                  
CONECT   20   19                                                            
CONECT   21   19                                                            
MASTER        0    0    0    0    0    0    0    0   21    0   40    0
END

Synonyms

Value	Source
Heptanedioylcarnitine	HMDB
Pimelyl-L-carnitine	HMDB
(4S)-4-[(6-Carboxyhexanoyl)oxy]-4-(trimethylazaniumyl)butanoic acid	Generator

Molecular Formula

C₁₄H₂₅NO₆

Average Mass

303.3514

Monoisotopic Mass

303.168187537

IUPAC Name

(4S)-4-[(6-carboxyhexanoyl)oxy]-4-(trimethylazaniumyl)butanoate

Traditional Name

(4S)-4-[(6-carboxyhexanoyl)oxy]-4-(trimethylammonio)butanoate

CAS Registry Number

Not Available

SMILES

C[N+](C)(C)[C@H](CCC([O-])=O)OC(=O)CCCCCC(O)=O

InChI Identifier

InChI=1S/C14H25NO6/c1-15(2,3)11(9-10-13(18)19)21-14(20)8-6-4-5-7-12(16)17/h11H,4-10H2,1-3H3,(H-,16,17,18,19)/t11-/m0/s1

InChI Key

AUWRHMAICBSXMC-NSHDSACASA-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.

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
Fatty acid ester
Fatty acyl
Tetraalkylammonium salt
Carboxylic acid salt
Carboxylic acid ester
Carboxylic acid
Hydrocarbon derivative
Organopnictogen compound
Organic salt
Organic oxygen compound
Organooxygen compound
Organonitrogen compound
Organic nitrogen compound
Carbonyl group
Organic oxide
Aliphatic acyclic compound

Molecular Framework

Aliphatic acyclic compounds

External Descriptors

Not Available

Functional Ontology

Not Available

Physical Properties

State

Solid

Predicted Properties

Property	Value	Source
Water Solubility	0.02 g/L	ALOGPS
logP	-0.84	ALOGPS
logP	-3	ChemAxon
logS	-4.3	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	1	ChemAxon
Polar Surface Area	103.73 Å²	ChemAxon
Rotatable Bond Count	12	ChemAxon
Refractivity	97.27 m³·mol⁻¹	ChemAxon
Polarizability	32.37 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	splash10-0006-4930000000-ec7de156d9cda9bb7aad	2016-09-22	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (1 TMS) - 70eV, Positive	splash10-0fdx-8911000000-348d3cccc277e4437e3c	2017-10-06	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Positive	splash10-000i-0191000000-43d3a4bf3589560b2b44	2017-09-01	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Positive	splash10-0006-3920000000-242e09cd487fc5dab13e	2017-09-01	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Positive	splash10-0abc-9410000000-85ab5b4e84825faec47b	2017-09-01	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Negative	splash10-0udl-0519000000-6a81df14b2da7386d262	2017-09-01	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Negative	splash10-0006-1931000000-1b0421fd494e69fb090f	2017-09-01	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Negative	splash10-0a4l-9700000000-b4d9a88cb8065ca13aa0	2017-09-01	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 100 MHz, H₂O, predicted)		2022-08-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 100 MHz, H₂O, predicted)		2022-08-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 1000 MHz, H₂O, predicted)		2022-08-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 1000 MHz, H₂O, predicted)		2022-08-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 200 MHz, H₂O, predicted)		2022-08-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 200 MHz, H₂O, predicted)		2022-08-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 300 MHz, H₂O, predicted)		2022-08-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 300 MHz, H₂O, predicted)		2022-08-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 400 MHz, H₂O, predicted)		2022-08-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 400 MHz, H₂O, predicted)		2022-08-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 500 MHz, H₂O, predicted)		2022-08-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 500 MHz, H₂O, predicted)		2022-08-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 600 MHz, H₂O, predicted)		2022-08-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 600 MHz, H₂O, predicted)		2022-08-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 700 MHz, H₂O, predicted)		2022-08-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 700 MHz, H₂O, predicted)		2022-08-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 800 MHz, H₂O, predicted)		2022-08-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 800 MHz, H₂O, predicted)		2022-08-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 900 MHz, H₂O, predicted)		2022-08-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 900 MHz, H₂O, predicted)		2022-08-20	View Spectrum

Biological Properties

Cellular Locations

Not Available

Biospecimen Locations

Blood
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

Not Available

Health Effects and Bioactivity

Health Outcome/Bioactivity	Metabolite Response/Effect	Evidence Type	Host and Biospecimen	Data Source	Reference
Obesity		Association	Human Blood	HMDB	Metabolomics reveals determinants of weight loss during lifestyle intervention in obese children
Obesity		Association	Human Blood	HMDB	Metabolomics reveals determinants of weight loss during lifestyle intervention in obese children

Microbial Sources

Superkingdom/Kingdom	Phylum	Total species	Hosts and Body Sites	Microbial Links
Eukaryota/Fungi	Ascomycota	1	Human feces; Human saliva	Unknown

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 Urine	Detected and Quantified			0.02	0.09	umol/mmol creatinine	Newborn (0-30 days old)	Both	Normal	HMDB	32340350
Human Urine	Detected and Quantified	0.03		0.01	0.11	umol/mmol creatinine	Adult (>18 years old)	Both	Normal	HMDB	24023812
Human Blood	Detected and Quantified	0.03	0.02			uM	Adult (>18 years old)	Both	Normal	HMDB	28278231
Human Urine	Detected and Quantified	0.04	0.02			umol/mmol creatinine	Newborn (0-30 days old)	Female	Normal	HMDB	32340350
Human Urine	Detected and Quantified	0.05	0.02			umol/mmol creatinine	Newborn (0-30 days old)	Male	Normal	HMDB	32340350
Human Feces	Detected and Quantified	0.15	0.05			nmol/g wet feces	Adult (>18 years old)	Both	Normal	HMDB	27624970
Human Feces	Detected and Quantified	0.15	0.07			nmol/g wet feces	Adult (>18 years old)	Both	Normal	HMDB	27624970
Human Blood	Detected and Quantified	0.033	0.011			uM	Children (1-13 years old)	Both	Obesity	HMDB	Metabolomics reveals determinants of weight loss during lifestyle intervention in obese children
Human Blood	Detected and Quantified	0.034	0.012			uM	Children (1-13 years old)	Both	Obesity	HMDB	Metabolomics reveals determinants of weight loss during lifestyle intervention in obese children
Human Blood	Detected and Quantified			0.035	0.120	uM	Adult (>18 years old)	Both	Normal	HMDB	Molecular You (https://molecularyou.com)
Human Urine	Detected but not Quantified						Adult (>18 years old)	Both	Normal	HMDB	32966057
Human Blood	Detected but not Quantified						Adult (>18 years old)	Both	Normal	HMDB	32966057

External Links

HMDB ID

Not Available

DrugBank ID

Not Available

Phenol Explorer Compound ID

Not Available

FooDB ID

FDB029388

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

53481675

PDB ID

Not Available

ChEBI ID

Not Available

Food Biomarker Ontology

Not Available

References

Synthesis Reference

Not Available

General References

Ferdinandusse S, Mulders J, IJlst L, Denis S, Dacremont G, Waterham HR, Wanders RJ: Molecular cloning and expression of human carnitine octanoyltransferase: evidence for its role in the peroxisomal beta-oxidation of branched-chain fatty acids. Biochem Biophys Res Commun. 1999 Sep 16;263(1):213-8. doi: 10.1006/bbrc.1999.1340. [PubMed:10486279 ]
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 ]
Violante S, Achetib N, van Roermund CWT, Hagen J, Dodatko T, Vaz FM, Waterham HR, Chen H, Baes M, Yu C, Argmann CA, Houten SM: Peroxisomes can oxidize medium- and long-chain fatty acids through a pathway involving ABCD3 and HSD17B4. FASEB J. 2019 Mar;33(3):4355-4364. doi: 10.1096/fj.201801498R. Epub 2018 Dec 12. [PubMed:30540494 ]

Showing metabocard for Pimelylcarnitine (MMDBc0033541)

MOL for #<Metabolite:0x00007fd0f74a5c20>

3D MOL for #<Metabolite:0x00007fd0f74a5c20>

3D SDF for #<Metabolite:0x00007fd0f74a5c20>

3D-SDF for #<Metabolite:0x00007fd0f74a5c20>

PDB for #<Metabolite:0x00007fd0f74a5c20>

3D PDB for #<Metabolite:0x00007fd0f74a5c20>

SMILES for #<Metabolite:0x00007fd0f74a5c20>

INCHI for #<Metabolite:0x00007fd0f74a5c20>

Structure for #<Metabolite:0x00007fd0f74a5c20>

3D Structure for #<Metabolite:0x00007fd0f74a5c20>