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Record Information

Version

5.0

Status

Detected but not Quantified

Creation Date

2013-02-26 19:02:29 UTC

Update Date

2023-02-21 17:29:21 UTC

HMDB ID

HMDB0059757

Secondary Accession Numbers

HMDB59757

Metabolite Identification

Common Name

3-Methylpimelic acid

Description

3-Methylpimelic acid, also known as 3-methylpimelate, belongs to the class of organic compounds known as medium-chain fatty acids. These are fatty acids with an aliphatic tail that contains between 4 and 12 carbon atoms. 3-Methylpimelic acid is a weakly acidic compound (based on its pKa).

Structure

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

HEADER    PROTEIN                                 26-FEB-13   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   26-FEB-13         0                                  
HETATM    1  O   UNK     0       5.596   4.771   0.000  0.00  0.00           O+0
HETATM    2  C   UNK     0       6.930   4.001   0.000  0.00  0.00           C+0
HETATM    3  O   UNK     0       6.930   2.461   0.000  0.00  0.00           O+0
HETATM    4  C   UNK     0       8.264   4.771   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       9.597   4.001   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       9.597   2.461   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0      10.931   4.771   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0      12.265   4.001   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0      13.598   4.771   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0      14.932   4.001   0.000  0.00  0.00           C+0
HETATM   11  O   UNK     0      16.266   4.771   0.000  0.00  0.00           O+0
HETATM   12  O   UNK     0      14.932   2.461   0.000  0.00  0.00           O+0
CONECT    1    2                                                            
CONECT    2    1    3    4                                                  
CONECT    3    2                                                            
CONECT    4    2    5                                                       
CONECT    5    4    6    7                                                  
CONECT    6    5                                                            
CONECT    7    5    8                                                       
CONECT    8    7    9                                                       
CONECT    9    8   10                                                       
CONECT   10    9   11   12                                                  
CONECT   11   10                                                            
CONECT   12   10                                                            
MASTER        0    0    0    0    0    0    0    0   12    0   22    0
END

View in JSmol View NMR Assignments View Stereo Labels

Synonyms

Value	Source
3-Methylpimelate	Generator
3-Methylheptanedioate	Generator

Chemical Formula

C₈H₁₄O₄

Average Molecular Weight

174.1944

Monoisotopic Molecular Weight

174.089208936

IUPAC Name

3-methylheptanedioic acid

Traditional Name

3-methylheptanedioic acid

CAS Registry Number

10200-31-4

SMILES

CC(CCCC(O)=O)CC(O)=O

InChI Identifier

InChI=1S/C8H14O4/c1-6(5-8(11)12)3-2-4-7(9)10/h6H,2-5H2,1H3,(H,9,10)(H,11,12)

InChI Key

NXDCNRPLRGMKHU-UHFFFAOYSA-N

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as medium-chain fatty acids. These are fatty acids with an aliphatic tail that contains between 4 and 12 carbon atoms.

Kingdom

Organic compounds

Super Class

Lipids and lipid-like molecules

Class

Fatty Acyls

Sub Class

Fatty acids and conjugates

Direct Parent

Medium-chain fatty acids

Alternative Parents

Substituents

Medium-chain fatty acid
Methyl-branched fatty acid
Branched fatty acid
Dicarboxylic acid or derivatives
Carboxylic acid
Carboxylic acid derivative
Organic oxygen compound
Organic oxide
Hydrocarbon derivative
Organooxygen compound
Carbonyl group
Aliphatic acyclic compound

Molecular Framework

Aliphatic acyclic compounds

External Descriptors

Not Available

Ontology

Not Available

Urine (PMID: 2338430)

Source

Exogenous

Exogenous (HMDB: HMDB0059757)

Process

Not Available

Role

Not Available

Physical Properties

State

Not Available

Experimental Molecular Properties

Property	Value	Reference
Melting Point	Not Available	Not Available
Boiling Point	Not Available	Not Available
Water Solubility	Not Available	Not Available
LogP	Not Available	Not Available

Experimental Chromatographic Properties

Not Available

Predicted Molecular Properties

Property	Value	Source
Water Solubility	6.07 g/L	ALOGPS
logP	0.89	ALOGPS
logP	1.22	ChemAxon
logS	-1.5	ALOGPS
pKa (Strongest Acidic)	4.15	ChemAxon
Physiological Charge	-2	ChemAxon
Hydrogen Acceptor Count	4	ChemAxon
Hydrogen Donor Count	2	ChemAxon
Polar Surface Area	74.6 Å²	ChemAxon
Rotatable Bond Count	6	ChemAxon
Refractivity	41.89 m³·mol⁻¹	ChemAxon
Polarizability	17.95 Å³	ChemAxon
Number of Rings	0	ChemAxon
Bioavailability	Yes	ChemAxon
Rule of Five	Yes	ChemAxon
Ghose Filter	Yes	ChemAxon
Veber's Rule	No	ChemAxon
MDDR-like Rule	No	ChemAxon

Predicted Chromatographic Properties

Predicted Collision Cross Sections

Predictor	Adduct Type	CCS Value (Å²)	Reference
DarkChem	[M+H]+	140.303	31661259
DarkChem	[M-H]-	135.469	31661259
DeepCCS	[M+H]+	133.344	30932474
DeepCCS	[M-H]-	129.512	30932474
DeepCCS	[M-2H]-	166.728	30932474
DeepCCS	[M+Na]+	142.117	30932474
AllCCS	[M+H]+	140.8	32859911
AllCCS	[M+H-H2O]+	137.0	32859911
AllCCS	[M+NH4]+	144.4	32859911
AllCCS	[M+Na]+	145.4	32859911
AllCCS	[M-H]-	139.4	32859911
AllCCS	[M+Na-2H]-	141.0	32859911
AllCCS	[M+HCOO]-	142.9	32859911

Predicted Kovats Retention Indices

Underivatized

Metabolite	SMILES	Kovats RI Value	Column Type	Reference
3-Methylpimelic acid	CC(CCCC(O)=O)CC(O)=O	2436.7	Standard polar	33892256
3-Methylpimelic acid	CC(CCCC(O)=O)CC(O)=O	1248.0	Standard non polar	33892256
3-Methylpimelic acid	CC(CCCC(O)=O)CC(O)=O	1505.8	Semi standard non polar	33892256

Derivatized

Derivative Name / Structure	SMILES	Kovats RI Value	Column Type	Reference
3-Methylpimelic acid,1TMS,isomer #1	CC(CCCC(=O)O[Si](C)(C)C)CC(=O)O	1541.4	Semi standard non polar	33892256
3-Methylpimelic acid,1TMS,isomer #2	CC(CCCC(=O)O)CC(=O)O[Si](C)(C)C	1540.8	Semi standard non polar	33892256
3-Methylpimelic acid,2TMS,isomer #1	CC(CCCC(=O)O[Si](C)(C)C)CC(=O)O[Si](C)(C)C	1629.4	Semi standard non polar	33892256
3-Methylpimelic acid,1TBDMS,isomer #1	CC(CCCC(=O)O[Si](C)(C)C(C)(C)C)CC(=O)O	1783.6	Semi standard non polar	33892256
3-Methylpimelic acid,1TBDMS,isomer #2	CC(CCCC(=O)O)CC(=O)O[Si](C)(C)C(C)(C)C	1784.9	Semi standard non polar	33892256
3-Methylpimelic acid,2TBDMS,isomer #1	CC(CCCC(=O)O[Si](C)(C)C(C)(C)C)CC(=O)O[Si](C)(C)C(C)(C)C	2077.2	Semi standard non polar	33892256

Spectra

GC-MS Spectra

Spectrum Type	Description	Splash Key	Deposition Date	Source	View
Predicted GC-MS	Predicted GC-MS Spectrum - 3-Methylpimelic acid GC-MS (Non-derivatized) - 70eV, Positive	splash10-02bf-9800000000-848b0992d7c8e32d78b1	2017-09-20	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - 3-Methylpimelic acid GC-MS (2 TMS) - 70eV, Positive	splash10-0079-9331000000-306b42766798d5497f0e	2017-10-06	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - 3-Methylpimelic acid GC-MS (Non-derivatized) - 70eV, Positive	Not Available	2021-10-12	Wishart Lab	View Spectrum

MS/MS Spectra

Spectrum Type	Description	Splash Key	Deposition Date	Source	View
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 3-Methylpimelic acid 10V, Positive-QTOF	splash10-0a4i-0900000000-df18c01c6fb1893f682c	2017-10-06	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 3-Methylpimelic acid 20V, Positive-QTOF	splash10-0691-6900000000-2a24bb693567948ed771	2017-10-06	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 3-Methylpimelic acid 40V, Positive-QTOF	splash10-014i-9000000000-d88d3fc86ff2fcfbd88a	2017-10-06	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 3-Methylpimelic acid 10V, Negative-QTOF	splash10-05i0-0900000000-c89e08dcb101966b611b	2017-10-06	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 3-Methylpimelic acid 20V, Negative-QTOF	splash10-0adi-1900000000-8e6c87f4a1d7ad6c89b3	2017-10-06	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 3-Methylpimelic acid 40V, Negative-QTOF	splash10-0a4i-9500000000-d7012b2fd187ef59da74	2017-10-06	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 3-Methylpimelic acid 10V, Negative-QTOF	splash10-024i-0900000000-eadd6b91fe3648187b7f	2021-09-23	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 3-Methylpimelic acid 20V, Negative-QTOF	splash10-0a6r-5900000000-7325d07601c0ddfb8853	2021-09-23	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 3-Methylpimelic acid 40V, Negative-QTOF	splash10-0a4l-9100000000-268318fd7fc1150c897d	2021-09-23	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 3-Methylpimelic acid 10V, Positive-QTOF	splash10-014i-7900000000-a1fe9a32f919a2521b03	2021-09-24	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 3-Methylpimelic acid 20V, Positive-QTOF	splash10-00lr-9200000000-681fa1dc90e8b4f3a854	2021-09-24	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 3-Methylpimelic acid 40V, Positive-QTOF	splash10-00kf-9000000000-527c018476f3935938e1	2021-09-24	Wishart Lab	View Spectrum

NMR Spectra

Spectrum Type	Description	Deposition Date	Source	View
Predicted 1D NMR	¹³C NMR Spectrum (1D, 100 MHz, D₂O, predicted)	2021-09-24	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 100 MHz, D₂O, predicted)	2021-09-24	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 1000 MHz, D₂O, predicted)	2021-09-24	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 1000 MHz, D₂O, predicted)	2021-09-24	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 200 MHz, D₂O, predicted)	2021-09-24	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 200 MHz, D₂O, predicted)	2021-09-24	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 300 MHz, D₂O, predicted)	2021-09-24	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 300 MHz, D₂O, predicted)	2021-09-24	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 400 MHz, D₂O, predicted)	2021-09-24	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 400 MHz, D₂O, predicted)	2021-09-24	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 500 MHz, D₂O, predicted)	2021-09-24	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 500 MHz, D₂O, predicted)	2021-09-24	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 600 MHz, D₂O, predicted)	2021-09-24	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 600 MHz, D₂O, predicted)	2021-09-24	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 700 MHz, D₂O, predicted)	2021-09-24	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 700 MHz, D₂O, predicted)	2021-09-24	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 800 MHz, D₂O, predicted)	2021-09-24	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 800 MHz, D₂O, predicted)	2021-09-24	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 900 MHz, D₂O, predicted)	2021-09-24	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 900 MHz, D₂O, predicted)	2021-09-24	Wishart Lab	View Spectrum

IR Spectra

Spectrum Type	Description	Deposition Date	Source	View
Predicted IR Spectrum	IR Ion Spectrum (Predicted IRIS Spectrum, Adduct: [M-H]-)	2023-02-04	FELIX lab	View Spectrum
Predicted IR Spectrum	IR Ion Spectrum (Predicted IRIS Spectrum, Adduct: [M+H]+)	2023-02-04	FELIX lab	View Spectrum
Predicted IR Spectrum	IR Ion Spectrum (Predicted IRIS Spectrum, Adduct: [M+Na]+)	2023-02-04	FELIX lab	View Spectrum

Biological Properties

Cellular Locations

Not Available

Biospecimen Locations

Urine

Tissue Locations

Not Available

Pathways

Not Available

Name	SMPDB/PathBank	KEGG

Normal Concentrations

Biospecimen	Status	Value	Age	Sex	Condition	Reference	Details
Urine	Detected but not Quantified	Not Quantified	Not Specified	Not Specified	Normal	2338430	details

Abnormal Concentrations

Not Available

Associated Disorders and Diseases

Disease References

None

Associated OMIM IDs

None

External Links

DrugBank ID

Not Available

Phenol Explorer Compound ID

Not Available

FooDB ID

Not Available

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

21510350

PDB ID

Not Available

ChEBI ID

Not Available

Food Biomarker Ontology

Not Available

VMH ID

Not Available

MarkerDB ID

Not Available

Good Scents ID

Not Available

References

Synthesis Reference

Not Available

Material Safety Data Sheet (MSDS)

Not Available

General References

Simons K, Toomre D: Lipid rafts and signal transduction. Nat Rev Mol Cell Biol. 2000 Oct;1(1):31-9. [PubMed:11413487 ]
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. Epub 2006 Aug 10. [PubMed:16902246 ]
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. 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 ]
Gunstone, Frank D., John L. Harwood, and Albert J. Dijkstra (2007). The lipid handbook with CD-ROM. CRC Press.

Showing metabocard for 3-Methylpimelic acid (HMDB0059757)

MOL for HMDB0059757 (3-Methylpimelic acid)

3D MOL for HMDB0059757 (3-Methylpimelic acid)

3D SDF for HMDB0059757 (3-Methylpimelic acid)

3D-SDF for HMDB0059757 (3-Methylpimelic acid)

PDB for HMDB0059757 (3-Methylpimelic acid)

3D PDB for HMDB0059757 (3-Methylpimelic acid)

SMILES for HMDB0059757 (3-Methylpimelic acid)

INCHI for HMDB0059757 (3-Methylpimelic acid)

Structure for HMDB0059757 (3-Methylpimelic acid)

3D Structure for HMDB0059757 (3-Methylpimelic acid)

Predicted Collision Cross Sections

Predicted Kovats Retention Indices

Underivatized

Derivatized

GC-MS Spectra

MS/MS Spectra

NMR Spectra

IR Spectra