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Record Information

Version

5.0

Status

Expected but not Quantified

Creation Date

2017-03-23 05:57:50 UTC

Update Date

2022-03-07 03:17:59 UTC

HMDB ID

HMDB0062739

Secondary Accession Numbers

HMDB62739

Metabolite Identification

Common Name

3-methylmalate(2-)

Description

3-methylmalate(2-), also known as beta-methylmalate or b-methylmalic acid, belongs to the class of organic compounds known as hydroxy fatty acids. These are fatty acids in which the chain bears a hydroxyl group. 3-methylmalate(2-) is an extremely weak basic (essentially neutral) 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-Hydroxy-3-methylsuccinic acid	ChEBI
beta-Methylmalate	ChEBI
2-Hydroxy-3-methylsuccinate	Generator
b-Methylmalate	Generator
b-Methylmalic acid	Generator
beta-Methylmalic acid	Generator
Β-methylmalate	Generator
Β-methylmalic acid	Generator
3-Methylmalic acid(2-)	Generator
3-Methylmalate	HMDB

Chemical Formula

C₅H₈O₅

Average Molecular Weight

148.114

Monoisotopic Molecular Weight

148.037173366

IUPAC Name

2-hydroxy-3-methylbutanedioic acid

Traditional Name

3-methylmalic acid

CAS Registry Number

Not Available

SMILES

CC(C(O)C(O)=O)C(O)=O

InChI Identifier

InChI=1S/C5H8O5/c1-2(4(7)8)3(6)5(9)10/h2-3,6H,1H3,(H,7,8)(H,9,10)

InChI Key

NPYQJIHHTGFBLN-UHFFFAOYSA-N

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as hydroxy fatty acids. These are fatty acids in which the chain bears a hydroxyl group.

Kingdom

Organic compounds

Super Class

Lipids and lipid-like molecules

Class

Fatty Acyls

Sub Class

Fatty acids and conjugates

Direct Parent

Hydroxy fatty acids

Alternative Parents

Substituents

Beta-hydroxy acid
Branched fatty acid
Hydroxy fatty acid
Short-chain hydroxy acid
Methyl-branched fatty acid
Alpha-hydroxy acid
Hydroxy acid
Dicarboxylic acid or derivatives
Secondary alcohol
Carboxylic acid
Carboxylic acid derivative
Organooxygen compound
Carbonyl group
Alcohol
Hydrocarbon derivative
Organic oxide
Organic oxygen compound
Aliphatic acyclic compound

Molecular Framework

Aliphatic acyclic compounds

External Descriptors

dicarboxylic acid (CHEBI:25312 )

Ontology

Not Available

Exogenous (HMDB: HMDB0062739)

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	560 g/l	ALOGPS
LogP	-0.78	ALOGPS

Experimental Chromatographic Properties

Not Available

Predicted Molecular Properties

Property	Value	Source
logP	-0.33	ALOGPS
logP	-0.57	ChemAxon
logS	0.02	ALOGPS
pKa (Strongest Acidic)	3.39	ChemAxon
pKa (Strongest Basic)	-4	ChemAxon
Physiological Charge	-2	ChemAxon
Hydrogen Acceptor Count	5	ChemAxon
Hydrogen Donor Count	3	ChemAxon
Polar Surface Area	94.83 Å²	ChemAxon
Rotatable Bond Count	3	ChemAxon
Refractivity	29.45 m³·mol⁻¹	ChemAxon
Polarizability	12.74 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
DeepCCS	[M+H]+	125.032	30932474
DeepCCS	[M-H]-	121.468	30932474
DeepCCS	[M-2H]-	158.791	30932474
DeepCCS	[M+Na]+	133.835	30932474
AllCCS	[M+H]+	134.5	32859911
AllCCS	[M+H-H2O]+	130.5	32859911
AllCCS	[M+NH4]+	138.2	32859911
AllCCS	[M+Na]+	139.3	32859911
AllCCS	[M-H]-	126.5	32859911
AllCCS	[M+Na-2H]-	128.7	32859911
AllCCS	[M+HCOO]-	131.3	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 × 2.1 mm; 1.7 μmparticle diameter)). Predicted by Afia on May 17, 2022.	1.32 minutes	32390414
Predicted by Siyang on May 30, 2022	9.9933 minutes	33406817
Fem_Long = Waters ACQUITY UPLC HSS T3 C18 with Water:MeOH and 0.1% Formic Acid	739.6 seconds	40023050
Fem_Lipids = Ascentis Express C18 with (60:40 water:ACN):(90:10 IPA:ACN) and 10mM NH4COOH + 0.1% Formic Acid	361.9 seconds	40023050
Life_Old = Waters ACQUITY UPLC BEH C18 with Water:(20:80 acetone:ACN) and 0.1% Formic Acid	44.3 seconds	40023050
Life_New = RP Waters ACQUITY UPLC HSS T3 C18 with Water:(30:70 MeOH:ACN) and 0.1% Formic Acid	213.1 seconds	40023050
RIKEN = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid	77.6 seconds	40023050
Eawag_XBridgeC18 = XBridge C18 3.5u 2.1x50 mm with Water:MeOH and 0.1% Formic Acid	291.3 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	251.3 seconds	40023050
HILIC_BDD_2 = Merck SeQuant ZIC-HILIC with ACN(0.1% formic acid):water(16 mM ammonium formate)	564.3 seconds	40023050
UniToyama_Atlantis = RP Waters Atlantis T3 (2.1 x 150 mm, 5 um) with ACN:Water and 0.1% Formic Acid	631.1 seconds	40023050
BDD_C18 = Hypersil Gold 1.9µm C18 with Water:ACN and 0.1% Formic Acid	65.1 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	795.5 seconds	40023050
SNU_RIKEN_POS = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid	210.3 seconds	40023050
RPMMFDA = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid	280.8 seconds	40023050
MTBLS87 = Merck SeQuant ZIC-pHILIC column with ACN:Water and :ammonium carbonate	670.3 seconds	40023050
KI_GIAR_zic_HILIC_pH2_7 = Merck SeQuant ZIC-HILIC with ACN:Water and 0.1% FA	325.9 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	391.2 seconds	40023050

Predicted Kovats Retention Indices

Underivatized

Metabolite	SMILES	Kovats RI Value	Column Type	Reference
3-methylmalate(2-)	CC(C(O)C(O)=O)C(O)=O	2374.8	Standard polar	33892256
3-methylmalate(2-)	CC(C(O)C(O)=O)C(O)=O	1097.0	Standard non polar	33892256
3-methylmalate(2-)	CC(C(O)C(O)=O)C(O)=O	1329.1	Semi standard non polar	33892256

Derivatized

Derivative Name / Structure	SMILES	Kovats RI Value	Column Type	Reference
3-methylmalate(2-),1TMS,isomer #1	CC(C(=O)O)C(O[Si](C)(C)C)C(=O)O	1367.5	Semi standard non polar	33892256
3-methylmalate(2-),1TMS,isomer #2	CC(C(=O)O)C(O)C(=O)O[Si](C)(C)C	1341.5	Semi standard non polar	33892256
3-methylmalate(2-),1TMS,isomer #3	CC(C(=O)O[Si](C)(C)C)C(O)C(=O)O	1344.3	Semi standard non polar	33892256
3-methylmalate(2-),2TMS,isomer #1	CC(C(=O)O[Si](C)(C)C)C(O[Si](C)(C)C)C(=O)O	1437.7	Semi standard non polar	33892256
3-methylmalate(2-),2TMS,isomer #2	CC(C(=O)O)C(O[Si](C)(C)C)C(=O)O[Si](C)(C)C	1443.0	Semi standard non polar	33892256
3-methylmalate(2-),2TMS,isomer #3	CC(C(=O)O[Si](C)(C)C)C(O)C(=O)O[Si](C)(C)C	1416.3	Semi standard non polar	33892256
3-methylmalate(2-),3TMS,isomer #1	CC(C(=O)O[Si](C)(C)C)C(O[Si](C)(C)C)C(=O)O[Si](C)(C)C	1518.2	Semi standard non polar	33892256
3-methylmalate(2-),1TBDMS,isomer #1	CC(C(=O)O)C(O[Si](C)(C)C(C)(C)C)C(=O)O	1618.0	Semi standard non polar	33892256
3-methylmalate(2-),1TBDMS,isomer #2	CC(C(=O)O)C(O)C(=O)O[Si](C)(C)C(C)(C)C	1593.0	Semi standard non polar	33892256
3-methylmalate(2-),1TBDMS,isomer #3	CC(C(=O)O[Si](C)(C)C(C)(C)C)C(O)C(=O)O	1604.6	Semi standard non polar	33892256
3-methylmalate(2-),2TBDMS,isomer #1	CC(C(=O)O[Si](C)(C)C(C)(C)C)C(O[Si](C)(C)C(C)(C)C)C(=O)O	1877.7	Semi standard non polar	33892256
3-methylmalate(2-),2TBDMS,isomer #2	CC(C(=O)O)C(O[Si](C)(C)C(C)(C)C)C(=O)O[Si](C)(C)C(C)(C)C	1868.3	Semi standard non polar	33892256
3-methylmalate(2-),2TBDMS,isomer #3	CC(C(=O)O[Si](C)(C)C(C)(C)C)C(O)C(=O)O[Si](C)(C)C(C)(C)C	1856.7	Semi standard non polar	33892256
3-methylmalate(2-),3TBDMS,isomer #1	CC(C(=O)O[Si](C)(C)C(C)(C)C)C(O[Si](C)(C)C(C)(C)C)C(=O)O[Si](C)(C)C(C)(C)C	2124.1	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-Methylmalic acid GC-MS (Non-derivatized) - 70eV, Positive	splash10-0006-9200000000-8fdf1b491605c0d141de	2017-09-20	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - 3-Methylmalic acid GC-MS (Non-derivatized) - 70eV, Positive	Not Available	2021-10-12	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - 3-Methylmalic 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-methylmalate(2-) 10V, Positive-QTOF	splash10-0f8a-2900000000-d2cfe20ac3adff0b88d3	2017-10-06	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 3-methylmalate(2-) 20V, Positive-QTOF	splash10-0a4i-9200000000-d397d5ceef658e89c458	2017-10-06	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 3-methylmalate(2-) 40V, Positive-QTOF	splash10-0a6r-9000000000-49fcb646de0d01716f47	2017-10-06	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 3-methylmalate(2-) 10V, Negative-QTOF	splash10-0f6t-1900000000-e09bd704939576307b08	2017-10-06	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 3-methylmalate(2-) 20V, Negative-QTOF	splash10-0pb9-9700000000-92423d1a1308b7a8a70d	2017-10-06	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 3-methylmalate(2-) 40V, Negative-QTOF	splash10-0a4i-9000000000-2494bf9553975b844eae	2017-10-06	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 3-methylmalate(2-) 10V, Positive-QTOF	splash10-01qi-3900000000-9c6820c234915ebef73a	2021-09-24	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 3-methylmalate(2-) 20V, Positive-QTOF	splash10-052r-9100000000-a5bdf5415b6953f89120	2021-09-24	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 3-methylmalate(2-) 40V, Positive-QTOF	splash10-0a4i-9000000000-0f8220f404a16d16dde9	2021-09-24	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 3-methylmalate(2-) 10V, Negative-QTOF	splash10-0f6t-1900000000-7c9a1f38efebfc554e0a	2021-09-24	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 3-methylmalate(2-) 20V, Negative-QTOF	splash10-0k9i-9200000000-88adb83c269938bf62c2	2021-09-24	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 3-methylmalate(2-) 40V, Negative-QTOF	splash10-0a4i-9000000000-c82ca4bf61497061eceb	2021-09-24	Wishart Lab	View Spectrum

NMR Spectra

Spectrum Type	Description	Deposition Date	Source	View
Predicted 1D NMR	¹H NMR Spectrum (1D, 100 MHz, D₂O, predicted)	2021-09-25	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 100 MHz, D₂O, predicted)	2021-09-25	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 1000 MHz, D₂O, predicted)	2021-09-25	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 1000 MHz, D₂O, predicted)	2021-09-25	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 200 MHz, D₂O, predicted)	2021-09-25	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 200 MHz, D₂O, predicted)	2021-09-25	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 300 MHz, D₂O, predicted)	2021-09-25	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 300 MHz, D₂O, predicted)	2021-09-25	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 400 MHz, D₂O, predicted)	2021-09-25	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 400 MHz, D₂O, predicted)	2021-09-25	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 500 MHz, D₂O, predicted)	2021-09-25	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 500 MHz, D₂O, predicted)	2021-09-25	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 600 MHz, D₂O, predicted)	2021-09-25	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 600 MHz, D₂O, predicted)	2021-09-25	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 700 MHz, D₂O, predicted)	2021-09-25	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 700 MHz, D₂O, predicted)	2021-09-25	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 800 MHz, D₂O, predicted)	2021-09-25	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 800 MHz, D₂O, predicted)	2021-09-25	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 900 MHz, D₂O, predicted)	2021-09-25	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 900 MHz, D₂O, predicted)	2021-09-25	Wishart Lab	View Spectrum

Biological Properties

Cellular Locations

Not Available

Biospecimen Locations

Not Available

Tissue Locations

Not Available

Pathways

Not Available

Name	SMPDB/PathBank	KEGG

Normal Concentrations

Not Available

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

558882

PDB ID

Not Available

ChEBI ID

25312

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-methylmalate(2-) (HMDB0062739)

MOL for HMDB0062739 (3-methylmalate(2-))

3D MOL for HMDB0062739 (3-methylmalate(2-))

3D SDF for HMDB0062739 (3-methylmalate(2-))

3D-SDF for HMDB0062739 (3-methylmalate(2-))

PDB for HMDB0062739 (3-methylmalate(2-))

3D PDB for HMDB0062739 (3-methylmalate(2-))

SMILES for HMDB0062739 (3-methylmalate(2-))

INCHI for HMDB0062739 (3-methylmalate(2-))

Structure for HMDB0062739 (3-methylmalate(2-))

3D Structure for HMDB0062739 (3-methylmalate(2-))

Predicted Collision Cross Sections

Predicted Retention Times

Underivatized

Predicted Kovats Retention Indices

Underivatized

Derivatized

GC-MS Spectra

MS/MS Spectra

NMR Spectra