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Record Information

Version

5.0

Status

Detected but not Quantified

Creation Date

2013-02-26 19:02:46 UTC

Update Date

2023-02-21 17:29:21 UTC

HMDB ID

HMDB0059762

Secondary Accession Numbers

HMDB59762

Metabolite Identification

Common Name

2,3-Methylenesuccinic acid

Description

2,3-Methylenesuccinic acid belongs to the class of organic compounds known as branched fatty acids. These are fatty acids containing a branched chain. 2,3-Methylenesuccinic acid is a weakly acidic compound (based on its pKa).

Structure

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

View in JSmol View NMR Assignments View Stereo Labels

Synonyms

Value	Source
2,3-Methylenesuccinate	Generator
Dimethylidenebutanedioate	Generator

Chemical Formula

C₆H₆O₄

Average Molecular Weight

142.1094

Monoisotopic Molecular Weight

142.02660868

IUPAC Name

dimethylidenebutanedioic acid

Traditional Name

dimethylidenebutanedioic acid

CAS Registry Number

Not Available

SMILES

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

InChI Identifier

InChI=1S/C6H6O4/c1-3(5(7)8)4(2)6(9)10/h1-2H2,(H,7,8)(H,9,10)

InChI Key

PQGVRLYVSSROJJ-UHFFFAOYSA-N

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as branched fatty acids. These are fatty acids containing a branched chain.

Kingdom

Organic compounds

Super Class

Lipids and lipid-like molecules

Class

Fatty Acyls

Sub Class

Fatty acids and conjugates

Direct Parent

Branched fatty acids

Alternative Parents

Substituents

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: HMDB0059762)

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	3.2 g/L	ALOGPS
logP	0.66	ALOGPS
logP	0.5	ChemAxon
logS	-1.6	ALOGPS
pKa (Strongest Acidic)	3.7	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	3	ChemAxon
Refractivity	32.29 m³·mol⁻¹	ChemAxon
Polarizability	12.4 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

Predicted Chromatographic Properties

Predicted Collision Cross Sections

Predictor	Adduct Type	CCS Value (Å²)	Reference
DarkChem	[M+H]+	133.303	31661259
DarkChem	[M-H]-	128.896	31661259
DeepCCS	[M+H]+	126.369	30932474
DeepCCS	[M-H]-	122.504	30932474
DeepCCS	[M-2H]-	159.959	30932474
DeepCCS	[M+Na]+	135.387	30932474
AllCCS	[M+H]+	132.7	32859911
AllCCS	[M+H-H2O]+	128.6	32859911
AllCCS	[M+NH4]+	136.5	32859911
AllCCS	[M+Na]+	137.5	32859911
AllCCS	[M-H]-	124.4	32859911
AllCCS	[M+Na-2H]-	126.6	32859911
AllCCS	[M+HCOO]-	129.1	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.	2.61 minutes	32390414
Predicted by Siyang on May 30, 2022	10.3034 minutes	33406817
Predicted by Siyang using ReTip algorithm on June 8, 2022	2.46 minutes	32390414
Fem_Long = Waters ACQUITY UPLC HSS T3 C18 with Water:MeOH and 0.1% Formic Acid	1243.3 seconds	40023050
Fem_Lipids = Ascentis Express C18 with (60:40 water:ACN):(90:10 IPA:ACN) and 10mM NH4COOH + 0.1% Formic Acid	361.4 seconds	40023050
Life_Old = Waters ACQUITY UPLC BEH C18 with Water:(20:80 acetone:ACN) and 0.1% Formic Acid	90.0 seconds	40023050
Life_New = RP Waters ACQUITY UPLC HSS T3 C18 with Water:(30:70 MeOH:ACN) and 0.1% Formic Acid	224.2 seconds	40023050
RIKEN = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid	67.8 seconds	40023050
Eawag_XBridgeC18 = XBridge C18 3.5u 2.1x50 mm with Water:MeOH and 0.1% Formic Acid	269.5 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	402.4 seconds	40023050
HILIC_BDD_2 = Merck SeQuant ZIC-HILIC with ACN(0.1% formic acid):water(16 mM ammonium formate)	233.7 seconds	40023050
UniToyama_Atlantis = RP Waters Atlantis T3 (2.1 x 150 mm, 5 um) with ACN:Water and 0.1% Formic Acid	741.0 seconds	40023050
BDD_C18 = Hypersil Gold 1.9µm C18 with Water:ACN and 0.1% Formic Acid	284.1 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	1024.5 seconds	40023050
SNU_RIKEN_POS = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid	230.5 seconds	40023050
RPMMFDA = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid	312.3 seconds	40023050
MTBLS87 = Merck SeQuant ZIC-pHILIC column with ACN:Water and :ammonium carbonate	645.7 seconds	40023050
KI_GIAR_zic_HILIC_pH2_7 = Merck SeQuant ZIC-HILIC with ACN:Water and 0.1% FA	270.1 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	252.8 seconds	40023050

Predicted Kovats Retention Indices

Underivatized

Metabolite	SMILES	Kovats RI Value	Column Type	Reference
2,3-Methylenesuccinic acid	OC(=O)C(=C)C(=C)C(O)=O	2098.5	Standard polar	33892256
2,3-Methylenesuccinic acid	OC(=O)C(=C)C(=C)C(O)=O	1133.7	Standard non polar	33892256
2,3-Methylenesuccinic acid	OC(=O)C(=C)C(=C)C(O)=O	1262.3	Semi standard non polar	33892256

Derivatized

Derivative Name / Structure	SMILES	Kovats RI Value	Column Type	Reference
2,3-Methylenesuccinic acid,1TMS,isomer #1	C=C(C(=C)C(=O)O[Si](C)(C)C)C(=O)O	1311.4	Semi standard non polar	33892256
2,3-Methylenesuccinic acid,2TMS,isomer #1	C=C(C(=C)C(=O)O[Si](C)(C)C)C(=O)O[Si](C)(C)C	1372.8	Semi standard non polar	33892256
2,3-Methylenesuccinic acid,1TBDMS,isomer #1	C=C(C(=C)C(=O)O[Si](C)(C)C(C)(C)C)C(=O)O	1532.7	Semi standard non polar	33892256
2,3-Methylenesuccinic acid,2TBDMS,isomer #1	C=C(C(=C)C(=O)O[Si](C)(C)C(C)(C)C)C(=O)O[Si](C)(C)C(C)(C)C	1797.5	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-Methylenesuccinic acid GC-MS (Non-derivatized) - 70eV, Positive	splash10-0002-9300000000-8bc6255b213c9c422dde	2017-09-20	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - 2,3-Methylenesuccinic acid GC-MS (2 TMS) - 70eV, Positive	splash10-00di-9330000000-7dd3fecc4df2109e66fb	2017-10-06	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - 2,3-Methylenesuccinic 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-Methylenesuccinic acid 10V, Positive-QTOF	splash10-002f-3900000000-1a68df631f73b6fe89e6	2017-10-06	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 2,3-Methylenesuccinic acid 20V, Positive-QTOF	splash10-0fba-9300000000-84a686f08b30489040c7	2017-10-06	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 2,3-Methylenesuccinic acid 40V, Positive-QTOF	splash10-0ufr-9000000000-eb6590d0bbec05b0387e	2017-10-06	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 2,3-Methylenesuccinic acid 10V, Negative-QTOF	splash10-0006-3900000000-d087ade56bafb1d58e04	2017-10-06	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 2,3-Methylenesuccinic acid 20V, Negative-QTOF	splash10-0007-9500000000-4cbdef9848134c8a0064	2017-10-06	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 2,3-Methylenesuccinic acid 40V, Negative-QTOF	splash10-0udi-9000000000-909b4de89840136f0bd6	2017-10-06	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 2,3-Methylenesuccinic acid 10V, Positive-QTOF	splash10-0059-9200000000-139e79c9cac030ae3662	2021-09-23	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 2,3-Methylenesuccinic acid 20V, Positive-QTOF	splash10-0udi-9000000000-7686dd72c445c54b7344	2021-09-23	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 2,3-Methylenesuccinic acid 40V, Positive-QTOF	splash10-0udi-9000000000-ca3d5386048104e3db73	2021-09-23	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 2,3-Methylenesuccinic acid 10V, Negative-QTOF	splash10-0005-9500000000-1c81c7720e96b396c06b	2021-09-24	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 2,3-Methylenesuccinic acid 20V, Negative-QTOF	splash10-0udj-9000000000-f8eb547ef95f40f19ef9	2021-09-24	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 2,3-Methylenesuccinic acid 40V, Negative-QTOF	splash10-0udi-9000000000-4d245331716417aff6f4	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

284624

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 2,3-Methylenesuccinic acid (HMDB0059762)

MOL for HMDB0059762 (2,3-Methylenesuccinic acid)

3D MOL for HMDB0059762 (2,3-Methylenesuccinic acid)

3D SDF for HMDB0059762 (2,3-Methylenesuccinic acid)

3D-SDF for HMDB0059762 (2,3-Methylenesuccinic acid)

PDB for HMDB0059762 (2,3-Methylenesuccinic acid)

3D PDB for HMDB0059762 (2,3-Methylenesuccinic acid)

SMILES for HMDB0059762 (2,3-Methylenesuccinic acid)

INCHI for HMDB0059762 (2,3-Methylenesuccinic acid)

Structure for HMDB0059762 (2,3-Methylenesuccinic acid)

3D Structure for HMDB0059762 (2,3-Methylenesuccinic 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