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Record Information

Version

5.0

Status

Detected but not Quantified

Creation Date

2013-02-26 19:03:08 UTC

Update Date

2023-02-21 17:29:22 UTC

HMDB ID

HMDB0059768

Secondary Accession Numbers

HMDB59768

Metabolite Identification

Common Name

3,4-Methylene suberic acid

Description

3,4-Methylene suberic 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-Methylene suberic 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       4.263   4.001   0.000  0.00  0.00           O+0
HETATM    2  C   UNK     0       5.596   4.771   0.000  0.00  0.00           C+0
HETATM    3  O   UNK     0       5.596   6.311   0.000  0.00  0.00           O+0
HETATM    4  C   UNK     0       6.930   4.001   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       8.264   4.771   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       9.597   4.001   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      10.931   6.311   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0      12.265   4.001   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0      12.265   2.461   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0      13.598   4.771   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0      14.932   4.001   0.000  0.00  0.00           C+0
HETATM   13  O   UNK     0      16.266   4.771   0.000  0.00  0.00           O+0
HETATM   14  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                                                       
CONECT    7    6    8    9                                                  
CONECT    8    7                                                            
CONECT    9    7   10   11                                                  
CONECT   10    9                                                            
CONECT   11    9   12                                                       
CONECT   12   11   13   14                                                  
CONECT   13   12                                                            
CONECT   14   12                                                            
MASTER        0    0    0    0    0    0    0    0   14    0   26    0
END

COMPND    HMDB0059768
HETATM    1  C1  UNL     1      -1.558  -1.366  -0.015  1.00  0.00           C  
HETATM    2  C2  UNL     1      -0.755  -0.321   0.070  1.00  0.00           C  
HETATM    3  C3  UNL     1       0.617  -0.543   0.559  1.00  0.00           C  
HETATM    4  C4  UNL     1       1.684  -0.505  -0.477  1.00  0.00           C  
HETATM    5  C5  UNL     1       3.066  -0.708   0.040  1.00  0.00           C  
HETATM    6  C6  UNL     1       3.334  -1.975   0.704  1.00  0.00           C  
HETATM    7  O1  UNL     1       2.483  -2.883   0.837  1.00  0.00           O  
HETATM    8  O2  UNL     1       4.599  -2.204   1.226  1.00  0.00           O  
HETATM    9  C7  UNL     1      -1.269   0.999  -0.311  1.00  0.00           C  
HETATM   10  C8  UNL     1      -0.515   2.059  -0.216  1.00  0.00           C  
HETATM   11  C9  UNL     1      -2.645   1.050  -0.796  1.00  0.00           C  
HETATM   12  C10 UNL     1      -3.184   2.324  -1.242  1.00  0.00           C  
HETATM   13  O3  UNL     1      -2.673   3.448  -1.305  1.00  0.00           O  
HETATM   14  O4  UNL     1      -4.541   2.265  -1.683  1.00  0.00           O  
HETATM   15  H1  UNL     1      -2.589  -1.268  -0.371  1.00  0.00           H  
HETATM   16  H2  UNL     1      -1.174  -2.341   0.280  1.00  0.00           H  
HETATM   17  H3  UNL     1       0.671  -1.491   1.129  1.00  0.00           H  
HETATM   18  H4  UNL     1       0.813   0.255   1.336  1.00  0.00           H  
HETATM   19  H5  UNL     1       1.647   0.431  -1.048  1.00  0.00           H  
HETATM   20  H6  UNL     1       1.497  -1.298  -1.262  1.00  0.00           H  
HETATM   21  H7  UNL     1       3.348   0.146   0.697  1.00  0.00           H  
HETATM   22  H8  UNL     1       3.757  -0.597  -0.850  1.00  0.00           H  
HETATM   23  H9  UNL     1       4.868  -3.032   1.703  1.00  0.00           H  
HETATM   24  H10 UNL     1       0.522   1.933   0.162  1.00  0.00           H  
HETATM   25  H11 UNL     1      -0.756   3.066  -0.456  1.00  0.00           H  
HETATM   26  H12 UNL     1      -3.356   0.557  -0.058  1.00  0.00           H  
HETATM   27  H13 UNL     1      -2.689   0.334  -1.687  1.00  0.00           H  
HETATM   28  H14 UNL     1      -5.202   1.665  -1.249  1.00  0.00           H  
CONECT    1    2    2   15   16
CONECT    2    3    9
CONECT    3    4   17   18
CONECT    4    5   19   20
CONECT    5    6   21   22
CONECT    6    7    7    8
CONECT    8   23
CONECT    9   10   10   11
CONECT   10   24   25
CONECT   11   12   26   27
CONECT   12   13   13   14
CONECT   14   28
END

View in JSmol View NMR Assignments View Stereo Labels

Synonyms

Value	Source
3,4-Methylene suberate	Generator
3,4-Dimethylideneoctanedioate	Generator

Chemical Formula

C₁₀H₁₄O₄

Average Molecular Weight

198.2158

Monoisotopic Molecular Weight

198.089208936

IUPAC Name

3,4-dimethylideneoctanedioic acid

Traditional Name

3,4-dimethylideneoctanedioic acid

CAS Registry Number

Not Available

SMILES

OC(=O)CCCC(=C)C(=C)CC(O)=O

InChI Identifier

InChI=1S/C10H14O4/c1-7(4-3-5-9(11)12)8(2)6-10(13)14/h1-6H2,(H,11,12)(H,13,14)

InChI Key

LYUINLVGVDIMCT-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: HMDB0059768)

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	2.34 g/L	ALOGPS
logP	1.44	ALOGPS
logP	1.26	ChemAxon
logS	-1.9	ALOGPS
pKa (Strongest Acidic)	4.16	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	7	ChemAxon
Refractivity	50.59 m³·mol⁻¹	ChemAxon
Polarizability	20.23 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]+	147.587	31661259
DarkChem	[M-H]-	141.614	31661259
DeepCCS	[M+H]+	141.712	30932474
DeepCCS	[M-H]-	137.9	30932474
DeepCCS	[M-2H]-	175.653	30932474
DeepCCS	[M+Na]+	151.192	30932474
AllCCS	[M+H]+	147.6	32859911
AllCCS	[M+H-H2O]+	143.9	32859911
AllCCS	[M+NH4]+	151.1	32859911
AllCCS	[M+Na]+	152.1	32859911
AllCCS	[M-H]-	144.2	32859911
AllCCS	[M+Na-2H]-	145.3	32859911
AllCCS	[M+HCOO]-	146.6	32859911

Predicted Kovats Retention Indices

Underivatized

Metabolite	SMILES	Kovats RI Value	Column Type	Reference
3,4-Methylene suberic acid	OC(=O)CCCC(=C)C(=C)CC(O)=O	2647.2	Standard polar	33892256
3,4-Methylene suberic acid	OC(=O)CCCC(=C)C(=C)CC(O)=O	1416.3	Standard non polar	33892256
3,4-Methylene suberic acid	OC(=O)CCCC(=C)C(=C)CC(O)=O	1710.0	Semi standard non polar	33892256

Derivatized

Derivative Name / Structure	SMILES	Kovats RI Value	Column Type	Reference
3,4-Methylene suberic acid,1TMS,isomer #1	C=C(CCCC(=O)O[Si](C)(C)C)C(=C)CC(=O)O	1669.9	Semi standard non polar	33892256
3,4-Methylene suberic acid,1TMS,isomer #2	C=C(CCCC(=O)O)C(=C)CC(=O)O[Si](C)(C)C	1670.3	Semi standard non polar	33892256
3,4-Methylene suberic acid,2TMS,isomer #1	C=C(CCCC(=O)O[Si](C)(C)C)C(=C)CC(=O)O[Si](C)(C)C	1752.2	Semi standard non polar	33892256
3,4-Methylene suberic acid,1TBDMS,isomer #1	C=C(CCCC(=O)O[Si](C)(C)C(C)(C)C)C(=C)CC(=O)O	1898.0	Semi standard non polar	33892256
3,4-Methylene suberic acid,1TBDMS,isomer #2	C=C(CCCC(=O)O)C(=C)CC(=O)O[Si](C)(C)C(C)(C)C	1911.9	Semi standard non polar	33892256
3,4-Methylene suberic acid,2TBDMS,isomer #1	C=C(CCCC(=O)O[Si](C)(C)C(C)(C)C)C(=C)CC(=O)O[Si](C)(C)C(C)(C)C	2191.7	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-Methylene suberic acid GC-MS (Non-derivatized) - 70eV, Positive	splash10-0f9x-4900000000-62ce73b254a50cbcaaaa	2017-09-20	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - 3,4-Methylene suberic acid GC-MS (2 TMS) - 70eV, Positive	splash10-00g0-9271000000-c06071e63be0b3cc8965	2017-10-06	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - 3,4-Methylene suberic 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-Methylene suberic acid 10V, Positive-QTOF	splash10-001i-0900000000-117c2dba7f3185e4ad5d	2017-10-06	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 3,4-Methylene suberic acid 20V, Positive-QTOF	splash10-0zgu-1900000000-0f43099e3b3cd7fbd41f	2017-10-06	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 3,4-Methylene suberic acid 40V, Positive-QTOF	splash10-05ox-9300000000-f71f6a79b86b5178565d	2017-10-06	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 3,4-Methylene suberic acid 10V, Negative-QTOF	splash10-0f92-0900000000-a168633fd44516467661	2017-10-06	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 3,4-Methylene suberic acid 20V, Negative-QTOF	splash10-0fbj-0900000000-0143754a65d272398019	2017-10-06	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 3,4-Methylene suberic acid 40V, Negative-QTOF	splash10-0a4i-9700000000-a286e9316378bdf8c534	2017-10-06	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 3,4-Methylene suberic acid 10V, Positive-QTOF	splash10-0080-2900000000-65c7c8bb69c9f0f40e3b	2021-09-25	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 3,4-Methylene suberic acid 20V, Positive-QTOF	splash10-016u-9200000000-7a1df446c41807c03147	2021-09-25	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 3,4-Methylene suberic acid 40V, Positive-QTOF	splash10-014i-9000000000-5e8aeba5fc2555bcc3f9	2021-09-25	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 3,4-Methylene suberic acid 10V, Negative-QTOF	splash10-0002-0900000000-4d21f441cedcb17c5e3c	2021-09-25	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 3,4-Methylene suberic acid 20V, Negative-QTOF	splash10-0a4i-1900000000-20b9120461ef24aa7feb	2021-09-25	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 3,4-Methylene suberic acid 40V, Negative-QTOF	splash10-0a59-9400000000-7ac09dcb971780d02690	2021-09-25	Wishart Lab	View Spectrum

NMR Spectra

Spectrum Type	Description	Deposition Date	Source	View
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, 100 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, 1000 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, 200 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, 300 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, 400 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, 500 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, 600 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, 700 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, 800 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
Predicted 1D NMR	¹³C 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

124202118

PDB ID

Not Available

ChEBI ID

89887

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-Methylene suberic acid (HMDB0059768)

MOL for HMDB0059768 (3,4-Methylene suberic acid)

3D MOL for HMDB0059768 (3,4-Methylene suberic acid)

3D SDF for HMDB0059768 (3,4-Methylene suberic acid)

3D-SDF for HMDB0059768 (3,4-Methylene suberic acid)

PDB for HMDB0059768 (3,4-Methylene suberic acid)

3D PDB for HMDB0059768 (3,4-Methylene suberic acid)

SMILES for HMDB0059768 (3,4-Methylene suberic acid)

INCHI for HMDB0059768 (3,4-Methylene suberic acid)

Structure for HMDB0059768 (3,4-Methylene suberic acid)

3D Structure for HMDB0059768 (3,4-Methylene suberic acid)

Predicted Collision Cross Sections

Predicted Kovats Retention Indices

Underivatized

Derivatized

GC-MS Spectra

MS/MS Spectra

NMR Spectra

IR Spectra