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Record Information

Version

5.0

Status

Detected but not Quantified

Creation Date

2013-02-26 19:00:48 UTC

Update Date

2023-02-21 17:29:17 UTC

HMDB ID

HMDB0059730

Secondary Accession Numbers

HMDB59730

Metabolite Identification

Common Name

3,4-Methylenepimelic acid

Description

3,4-Methylenepimelic acid 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. 3,4-Methylenepimelic 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      10.931   4.771   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0      10.931   6.311   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      12.265   2.461   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0      13.598   4.771   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0      14.932   4.001   0.000  0.00  0.00           C+0
HETATM   12  O   UNK     0      16.266   4.771   0.000  0.00  0.00           O+0
HETATM   13  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                                                       
CONECT    6    5    7    8                                                  
CONECT    7    6                                                            
CONECT    8    6    9   10                                                  
CONECT    9    8                                                            
CONECT   10    8   11                                                       
CONECT   11   10   12   13                                                  
CONECT   12   11                                                            
CONECT   13   11                                                            
MASTER        0    0    0    0    0    0    0    0   13    0   24    0
END

View in JSmol View NMR Assignments View Stereo Labels

Synonyms

Value	Source
3,4-Methylenepimelate	Generator
3,4-Dimethylideneheptanedioate	Generator

Chemical Formula

C₉H₁₂O₄

Average Molecular Weight

184.1892

Monoisotopic Molecular Weight

184.073558872

IUPAC Name

3,4-dimethylideneheptanedioic acid

Traditional Name

3,4-dimethylideneheptanedioic acid

CAS Registry Number

Not Available

SMILES

OC(=O)CCC(=C)C(=C)CC(O)=O

InChI Identifier

InChI=1S/C9H12O4/c1-6(3-4-8(10)11)7(2)5-9(12)13/h1-5H2,(H,10,11)(H,12,13)

InChI Key

CSNVGEOLHZRUFI-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
Branched fatty acid
Unsaturated 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: HMDB0059730)

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	4.41 g/L	ALOGPS
logP	1.12	ALOGPS
logP	0.81	ChemAxon
logS	-1.6	ALOGPS
pKa (Strongest Acidic)	4.08	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	45.99 m³·mol⁻¹	ChemAxon
Polarizability	18.07 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]+	143.458	31661259
DarkChem	[M-H]-	137.353	31661259
DeepCCS	[M+H]+	137.094	30932474
DeepCCS	[M-H]-	133.265	30932474
DeepCCS	[M-2H]-	170.765	30932474
DeepCCS	[M+Na]+	146.304	30932474
AllCCS	[M+H]+	143.3	32859911
AllCCS	[M+H-H2O]+	139.5	32859911
AllCCS	[M+NH4]+	146.9	32859911
AllCCS	[M+Na]+	147.9	32859911
AllCCS	[M-H]-	139.0	32859911
AllCCS	[M+Na-2H]-	140.3	32859911
AllCCS	[M+HCOO]-	141.8	32859911

Predicted Retention Times

Underivatized

Chromatographic Method	Retention Time	Reference
Measured using a Waters Acquity ultraperformance liquid chromatography (UPLC) ethylene-bridged hybrid (BEH) C18 column (100 mm √ó 2.1 mm; 1.7 Œºmparticle diameter). Predicted by Afia on May 17, 2022.	3.96 minutes	32390414
Predicted by Siyang on May 30, 2022	10.7578 minutes	33406817
Predicted by Siyang using ReTip algorithm on June 8, 2022	2.2 minutes	32390414
Fem_Long = Waters ACQUITY UPLC HSS T3 C18 with Water:MeOH and 0.1% Formic Acid	1405.4 seconds	40023050
Fem_Lipids = Ascentis Express C18 with (60:40 water:ACN):(90:10 IPA:ACN) and 10mM NH4COOH + 0.1% Formic Acid	314.2 seconds	40023050
Life_Old = Waters ACQUITY UPLC BEH C18 with Water:(20:80 acetone:ACN) and 0.1% Formic Acid	113.3 seconds	40023050
Life_New = RP Waters ACQUITY UPLC HSS T3 C18 with Water:(30:70 MeOH:ACN) and 0.1% Formic Acid	188.0 seconds	40023050
RIKEN = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid	83.6 seconds	40023050
Eawag_XBridgeC18 = XBridge C18 3.5u 2.1x50 mm with Water:MeOH and 0.1% Formic Acid	297.5 seconds	40023050
BfG_NTS_RP1 =Agilent Zorbax Eclipse Plus C18 (2.1 mm x 150 mm, 3.5 um) with Water:ACN and 0.1% Formic Acid	424.2 seconds	40023050
HILIC_BDD_2 = Merck SeQuant ZIC-HILIC with ACN(0.1% formic acid):water(16 mM ammonium formate)	94.9 seconds	40023050
UniToyama_Atlantis = RP Waters Atlantis T3 (2.1 x 150 mm, 5 um) with ACN:Water and 0.1% Formic Acid	812.9 seconds	40023050
BDD_C18 = Hypersil Gold 1.9µm C18 with Water:ACN and 0.1% Formic Acid	330.4 seconds	40023050
UFZ_Phenomenex = Kinetex Core-Shell C18 2.6 um, 3.0 x 100 mm, Phenomenex with Water:MeOH and 0.1% Formic Acid	1109.7 seconds	40023050
SNU_RIKEN_POS = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid	248.9 seconds	40023050
RPMMFDA = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid	294.8 seconds	40023050
MTBLS87 = Merck SeQuant ZIC-pHILIC column with ACN:Water and :ammonium carbonate	471.8 seconds	40023050
KI_GIAR_zic_HILIC_pH2_7 = Merck SeQuant ZIC-HILIC with ACN:Water and 0.1% FA	213.1 seconds	40023050
Meister zic-pHILIC pH9.3 = Merck SeQuant ZIC-pHILIC column with ACN:Water 5mM NH4Ac pH9.3 and 5mM ammonium acetate in water	126.9 seconds	40023050

Predicted Kovats Retention Indices

Underivatized

Metabolite	SMILES	Kovats RI Value	Column Type	Reference
3,4-Methylenepimelic acid	OC(=O)CCC(=C)C(=C)CC(O)=O	2521.4	Standard polar	33892256
3,4-Methylenepimelic acid	OC(=O)CCC(=C)C(=C)CC(O)=O	1307.3	Standard non polar	33892256
3,4-Methylenepimelic acid	OC(=O)CCC(=C)C(=C)CC(O)=O	1613.7	Semi standard non polar	33892256

Derivatized

Derivative Name / Structure	SMILES	Kovats RI Value	Column Type	Reference
3,4-Methylenepimelic acid,1TMS,isomer #1	C=C(CCC(=O)O[Si](C)(C)C)C(=C)CC(=O)O	1582.5	Semi standard non polar	33892256
3,4-Methylenepimelic acid,1TMS,isomer #2	C=C(CCC(=O)O)C(=C)CC(=O)O[Si](C)(C)C	1571.5	Semi standard non polar	33892256
3,4-Methylenepimelic acid,2TMS,isomer #1	C=C(CCC(=O)O[Si](C)(C)C)C(=C)CC(=O)O[Si](C)(C)C	1640.0	Semi standard non polar	33892256
3,4-Methylenepimelic acid,1TBDMS,isomer #1	C=C(CCC(=O)O[Si](C)(C)C(C)(C)C)C(=C)CC(=O)O	1804.0	Semi standard non polar	33892256
3,4-Methylenepimelic acid,1TBDMS,isomer #2	C=C(CCC(=O)O)C(=C)CC(=O)O[Si](C)(C)C(C)(C)C	1801.3	Semi standard non polar	33892256
3,4-Methylenepimelic acid,2TBDMS,isomer #1	C=C(CCC(=O)O[Si](C)(C)C(C)(C)C)C(=C)CC(=O)O[Si](C)(C)C(C)(C)C	2072.2	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 - 3,4-Methylenepimelic acid GC-MS (Non-derivatized) - 70eV, Positive	splash10-029f-6900000000-97ed6b3714d2b97d2912	2017-09-20	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - 3,4-Methylenepimelic acid GC-MS (2 TMS) - 70eV, Positive	splash10-01w0-9331000000-6432b66d29ae1a4664cc	2017-10-06	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - 3,4-Methylenepimelic 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 - 3,4-Methylenepimelic acid 10V, Positive-QTOF	splash10-014i-0900000000-5371b689c8d203316562	2017-10-06	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 3,4-Methylenepimelic acid 20V, Positive-QTOF	splash10-00rj-3900000000-d0c34a147a86dc8f69cc	2017-10-06	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 3,4-Methylenepimelic acid 40V, Positive-QTOF	splash10-0fvl-9100000000-ebafc8a21a636df92e5a	2017-10-06	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 3,4-Methylenepimelic acid 10V, Negative-QTOF	splash10-00m0-0900000000-7932c7e57ef515d4e02a	2017-10-06	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 3,4-Methylenepimelic acid 20V, Negative-QTOF	splash10-01c9-1900000000-2db33fb825970a4af0a0	2017-10-06	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 3,4-Methylenepimelic acid 40V, Negative-QTOF	splash10-0avl-7900000000-ae0e9a11c7af6d7bdd51	2017-10-06	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 3,4-Methylenepimelic acid 10V, Negative-QTOF	splash10-001i-0900000000-4ba4afd9556aea976b4a	2021-09-23	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 3,4-Methylenepimelic acid 20V, Negative-QTOF	splash10-000i-5900000000-01854d31bc56cb708bca	2021-09-23	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 3,4-Methylenepimelic acid 40V, Negative-QTOF	splash10-006x-9300000000-bd3310934e9450ea925b	2021-09-23	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 3,4-Methylenepimelic acid 10V, Positive-QTOF	splash10-004i-9700000000-5cf832b8a92431970175	2021-09-25	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 3,4-Methylenepimelic acid 20V, Positive-QTOF	splash10-016u-9100000000-fa6c93e7da5dfafed085	2021-09-25	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 3,4-Methylenepimelic acid 40V, Positive-QTOF	splash10-0fb9-9000000000-6e5e70251af8b2c59f13	2021-09-25	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

124202121

PDB ID

Not Available

ChEBI ID

89913

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 3,4-Methylenepimelic acid (HMDB0059730)

MOL for HMDB0059730 (3,4-Methylenepimelic acid)

3D MOL for HMDB0059730 (3,4-Methylenepimelic acid)

3D SDF for HMDB0059730 (3,4-Methylenepimelic acid)

3D-SDF for HMDB0059730 (3,4-Methylenepimelic acid)

PDB for HMDB0059730 (3,4-Methylenepimelic acid)

3D PDB for HMDB0059730 (3,4-Methylenepimelic acid)

SMILES for HMDB0059730 (3,4-Methylenepimelic acid)

INCHI for HMDB0059730 (3,4-Methylenepimelic acid)

Structure for HMDB0059730 (3,4-Methylenepimelic acid)

3D Structure for HMDB0059730 (3,4-Methylenepimelic acid)

Predicted Collision Cross Sections

Predicted Retention Times

Underivatized

Predicted Kovats Retention Indices

Underivatized

Derivatized

GC-MS Spectra

MS/MS Spectra

NMR Spectra

IR Spectra