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Record Information

Version

5.0

Status

Detected but not Quantified

Creation Date

2013-02-26 19:03:50 UTC

Update Date

2023-02-21 17:29:23 UTC

HMDB ID

HMDB0059779

Secondary Accession Numbers

HMDB59779

Metabolite Identification

Common Name

2,3-Methylene suberic acid

Description

2,3-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. 2,3-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      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      13.598   6.311   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                                                       
CONECT    8    7    9   10                                                  
CONECT    9    8                                                            
CONECT   10    8   11   12                                                  
CONECT   11   10                                                            
CONECT   12   10   13   14                                                  
CONECT   13   12                                                            
CONECT   14   12                                                            
MASTER        0    0    0    0    0    0    0    0   14    0   26    0
END

COMPND    HMDB0059779
HETATM    1  C1  UNL     1       0.017  -2.528  -0.056  1.00  0.00           C  
HETATM    2  C2  UNL     1      -0.822  -1.743  -0.034  1.00  0.00           C  
HETATM    3  C3  UNL     1       0.027  -0.946   1.418  1.00  0.00           C  
HETATM    4  C4  UNL     1       0.348   0.319   0.818  1.00  0.00           C  
HETATM    5  C5  UNL     1       1.272   0.136  -0.433  1.00  0.00           C  
HETATM    6  C6  UNL     1       1.522   1.533  -0.933  1.00  0.00           C  
HETATM    7  C7  UNL     1       2.389   1.574  -2.130  1.00  0.00           C  
HETATM    8  O1  UNL     1       2.812   0.512  -2.654  1.00  0.00           O  
HETATM    9  O2  UNL     1       2.714   2.817  -2.646  1.00  0.00           O  
HETATM   10  C8  UNL     1      -1.872  -0.750   0.013  1.00  0.00           C  
HETATM   11  C9  UNL     1      -2.532  -0.600  -1.205  1.00  0.00           C  
HETATM   12  C10 UNL     1      -2.451   0.052   1.035  1.00  0.00           C  
HETATM   13  O3  UNL     1      -3.463   0.793   0.704  1.00  0.00           O  
HETATM   14  O4  UNL     1      -2.093   0.156   2.340  1.00  0.00           O  
HETATM   15  H1  UNL     1       0.958  -2.832   0.445  1.00  0.00           H  
HETATM   16  H2  UNL     1      -0.078  -3.366  -0.894  1.00  0.00           H  
HETATM   17  H3  UNL     1      -0.728  -1.248   2.043  1.00  0.00           H  
HETATM   18  H4  UNL     1       0.875  -1.605   1.439  1.00  0.00           H  
HETATM   19  H5  UNL     1      -0.395   1.074   0.595  1.00  0.00           H  
HETATM   20  H6  UNL     1       1.072   0.853   1.525  1.00  0.00           H  
HETATM   21  H7  UNL     1       2.163  -0.390  -0.114  1.00  0.00           H  
HETATM   22  H8  UNL     1       0.700  -0.444  -1.177  1.00  0.00           H  
HETATM   23  H9  UNL     1       2.050   2.113  -0.135  1.00  0.00           H  
HETATM   24  H10 UNL     1       0.568   2.016  -1.172  1.00  0.00           H  
HETATM   25  H11 UNL     1       3.197   3.536  -2.121  1.00  0.00           H  
HETATM   26  H12 UNL     1      -3.315   0.101  -1.261  1.00  0.00           H  
HETATM   27  H13 UNL     1      -2.207  -1.168  -2.026  1.00  0.00           H  
HETATM   28  H14 UNL     1      -2.728   0.033   3.132  1.00  0.00           H  
CONECT    1    2    2   15   16
CONECT    2    3   10
CONECT    3    4   17   18
CONECT    4    5   19   20
CONECT    5    6   21   22
CONECT    6    7   23   24
CONECT    7    8    8    9
CONECT    9   25
CONECT   10   11   11   12
CONECT   11   26   27
CONECT   12   13   13   14
CONECT   14   28
END

View in JSmol View Stereo Labels

Synonyms

Value	Source
2,3-Methylene suberate	Generator
2,3-Dimethylideneoctanedioate	Generator

Chemical Formula

C₁₀H₁₄O₄

Average Molecular Weight

198.2158

Monoisotopic Molecular Weight

198.089208936

IUPAC Name

2,3-dimethylideneoctanedioic acid

Traditional Name

2,3-dimethylideneoctanedioic acid

CAS Registry Number

Not Available

SMILES

OC(=O)CCCCC(=C)C(=C)C(O)=O

InChI Identifier

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

InChI Key

CLAQTYSICSOFAV-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: HMDB0059779)

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	1.4 g/L	ALOGPS
logP	1.68	ALOGPS
logP	1.77	ChemAxon
logS	-2.2	ALOGPS
pKa (Strongest Acidic)	4.19	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	50.64 m³·mol⁻¹	ChemAxon
Polarizability	20.53 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]+	145.826	31661259
DarkChem	[M-H]-	143.685	31661259
DeepCCS	[M+H]+	142.715	30932474
DeepCCS	[M-H]-	138.887	30932474
DeepCCS	[M-2H]-	176.612	30932474
DeepCCS	[M+Na]+	152.151	30932474
AllCCS	[M+H]+	147.2	32859911
AllCCS	[M+H-H2O]+	143.4	32859911
AllCCS	[M+NH4]+	150.6	32859911
AllCCS	[M+Na]+	151.6	32859911
AllCCS	[M-H]-	144.4	32859911
AllCCS	[M+Na-2H]-	145.5	32859911
AllCCS	[M+HCOO]-	146.8	32859911

Predicted Kovats Retention Indices

Underivatized

Metabolite	SMILES	Kovats RI Value	Column Type	Reference
2,3-Methylene suberic acid	OC(=O)CCCCC(=C)C(=C)C(O)=O	2662.8	Standard polar	33892256
2,3-Methylene suberic acid	OC(=O)CCCCC(=C)C(=C)C(O)=O	1349.2	Standard non polar	33892256
2,3-Methylene suberic acid	OC(=O)CCCCC(=C)C(=C)C(O)=O	1646.2	Semi standard non polar	33892256

Derivatized

Derivative Name / Structure	SMILES	Kovats RI Value	Column Type	Reference
2,3-Methylene suberic acid,1TMS,isomer #1	C=C(CCCCC(=O)O[Si](C)(C)C)C(=C)C(=O)O	1702.7	Semi standard non polar	33892256
2,3-Methylene suberic acid,1TMS,isomer #2	C=C(CCCCC(=O)O)C(=C)C(=O)O[Si](C)(C)C	1668.6	Semi standard non polar	33892256
2,3-Methylene suberic acid,2TMS,isomer #1	C=C(CCCCC(=O)O[Si](C)(C)C)C(=C)C(=O)O[Si](C)(C)C	1765.8	Semi standard non polar	33892256
2,3-Methylene suberic acid,1TBDMS,isomer #1	C=C(CCCCC(=O)O[Si](C)(C)C(C)(C)C)C(=C)C(=O)O	1935.0	Semi standard non polar	33892256
2,3-Methylene suberic acid,1TBDMS,isomer #2	C=C(CCCCC(=O)O)C(=C)C(=O)O[Si](C)(C)C(C)(C)C	1890.7	Semi standard non polar	33892256
2,3-Methylene suberic acid,2TBDMS,isomer #1	C=C(CCCCC(=O)O[Si](C)(C)C(C)(C)C)C(=C)C(=O)O[Si](C)(C)C(C)(C)C	2195.8	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 - 2,3-Methylene suberic acid GC-MS (Non-derivatized) - 70eV, Positive	splash10-0udm-9800000000-2d4c1ad4164df61d9ef3	2017-09-20	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - 2,3-Methylene suberic acid GC-MS (2 TMS) - 70eV, Positive	splash10-00g0-9451000000-11012b45aeea22c56f71	2017-10-06	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - 2,3-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 - 2,3-Methylene suberic acid 10V, Positive-QTOF	splash10-001i-0900000000-de38d46f28d59b532316	2017-10-06	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 2,3-Methylene suberic acid 20V, Positive-QTOF	splash10-0kcr-3900000000-902ec6be6c70d5a4c440	2017-10-06	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 2,3-Methylene suberic acid 40V, Positive-QTOF	splash10-0ku6-9200000000-e928ec2b6ded2112b64f	2017-10-06	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 2,3-Methylene suberic acid 10V, Negative-QTOF	splash10-0002-0900000000-a9265f8ac626065caac6	2017-10-06	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 2,3-Methylene suberic acid 20V, Negative-QTOF	splash10-0ug1-0900000000-18721b8c5b496eb0d2b9	2017-10-06	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 2,3-Methylene suberic acid 40V, Negative-QTOF	splash10-0a4i-9700000000-30e7f52e298e676ad256	2017-10-06	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 2,3-Methylene suberic acid 10V, Negative-QTOF	splash10-0f6t-0900000000-e67690385126b6883b38	2021-09-23	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 2,3-Methylene suberic acid 20V, Negative-QTOF	splash10-0a4i-1900000000-2887df5835d66e000c5b	2021-09-23	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 2,3-Methylene suberic acid 40V, Negative-QTOF	splash10-0a6r-9600000000-b04b0e313cd839958aa1	2021-09-23	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 2,3-Methylene suberic acid 10V, Positive-QTOF	splash10-001a-2900000000-c7b69f66affb3dda865a	2021-09-24	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 2,3-Methylene suberic acid 20V, Positive-QTOF	splash10-004i-9400000000-a550e96974243d0c04ab	2021-09-24	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 2,3-Methylene suberic acid 40V, Positive-QTOF	splash10-004i-9000000000-46c7fe06c7f2e04a9626	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

Blood
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

Biospecimen	Status	Value	Age	Sex	Condition	Reference	Details
Blood	Expected but not Quantified	Not Quantified	Adult (>18 years old)	Both	Asthma	33739820	details

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

124202116

PDB ID

Not Available

ChEBI ID

89869

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 2,3-Methylene suberic acid (HMDB0059779)

MOL for HMDB0059779 (2,3-Methylene suberic acid)

3D MOL for HMDB0059779 (2,3-Methylene suberic acid)

3D SDF for HMDB0059779 (2,3-Methylene suberic acid)

3D-SDF for HMDB0059779 (2,3-Methylene suberic acid)

PDB for HMDB0059779 (2,3-Methylene suberic acid)

3D PDB for HMDB0059779 (2,3-Methylene suberic acid)

SMILES for HMDB0059779 (2,3-Methylene suberic acid)

INCHI for HMDB0059779 (2,3-Methylene suberic acid)

Structure for HMDB0059779 (2,3-Methylene suberic acid)

3D Structure for HMDB0059779 (2,3-Methylene suberic acid)

Predicted Collision Cross Sections

Predicted Kovats Retention Indices

Underivatized

Derivatized

GC-MS Spectra

MS/MS Spectra

IR Spectra