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Identification Taxonomy Ontology Physical properties Spectra Biological properties Concentrations Links References XML

Record Information

Version

5.0

Status

Detected but not Quantified

Creation Date

2012-09-11 18:36:40 UTC

Update Date

2023-02-21 17:23:40 UTC

HMDB ID

HMDB0033837

Secondary Accession Numbers

HMDB33837

Metabolite Identification

Common Name

Dimethyl succinate

Description

Dimethyl succinate belongs to the class of organic compounds known as fatty acid methyl esters. Fatty acid methyl esters are compounds containing a fatty acid that is esterified with a methyl group. They have the general structure RC(=O)OR', where R=fatty aliphatic tail or organyl group and R'=methyl group. Based on a literature review a small amount of articles have been published on Dimethyl succinate.

Structure

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

View in JSmol View NMR Assignments View Stereo Labels

Synonyms

Value	Source
Dimethyl succinic acid	Generator
Succinic acid, dimethyl ester	MeSH
Butanedioic acid, 1,4-dimethyl ester	HMDB
Butanedioic acid, dimethyl ester	HMDB
CH3OC(O)CH2CH2C(O)OCH3	HMDB
DBE-4	HMDB
DBE-4 dibasic ester	HMDB
Dimethyl ester OF succinic acid	HMDB
Dimethylsuccinate	HMDB
FEMA 2396	HMDB
Methyl butanedioate	HMDB
Methyl succinate	HMDB
Succinic acid dimethyl ester	HMDB
1,4-Dimethyl butanedioic acid	Generator
Dimethyl succinate	MeSH

Chemical Formula

C₆H₁₀O₄

Average Molecular Weight

146.1412

Monoisotopic Molecular Weight

146.057908808

IUPAC Name

1,4-dimethyl butanedioate

Traditional Name

dimethyl succinate

CAS Registry Number

106-65-0

SMILES

COC(=O)CCC(=O)OC

InChI Identifier

InChI=1S/C6H10O4/c1-9-5(7)3-4-6(8)10-2/h3-4H2,1-2H3

InChI Key

MUXOBHXGJLMRAB-UHFFFAOYSA-N

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as fatty acid methyl esters. Fatty acid methyl esters are compounds containing a fatty acid that is esterified with a methyl group. They have the general structure RC(=O)OR', where R=fatty aliphatic tail or organyl group and R'=methyl group.

Kingdom

Organic compounds

Super Class

Lipids and lipid-like molecules

Class

Fatty Acyls

Sub Class

Fatty acid esters

Direct Parent

Fatty acid methyl esters

Alternative Parents

Substituents

Fatty acid methyl ester
Dicarboxylic acid or derivatives
Methyl ester
Carboxylic acid ester
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

Physiological effect

Organoleptic effect

Taste

Sweet

Feces (PMID: 25985090)
Urine (HMDB: HMDB0033837)

Cellular substructure

Route of exposure

Enteral

Ingestion (HMDB: HMDB0033837)

Source

Endogenous

Endogenous (HMDB: HMDB0033837)

Plant

Plant (HMDB: HMDB0033837)

Animal

Animal (HMDB: HMDB0033837)

Exogenous

Food

Food (HMDB: HMDB0033837)

Nut

Nuts (FooDB: FOOD00869)

Fruit

Berry

Evergreen blackberry (FooDB: FOOD00901)
Blackberry (FooDB: FOOD00906)

Exogenous (HMDB: HMDB0033837)

Process

Naturally occurring process

Biological process

Chemical reaction

Lipid Peroxidation (HMDB: HMDB0033837)

Biochemical pathway

Metabolic pathway

Fatty Acid Metabolism (HMDB: HMDB0033837)

Lipid metabolism pathway (HMDB: HMDB0033837)

Biochemical process

Lipid transport (HMDB: HMDB0033837)

Role

Biological role

Energy source (HMDB: HMDB0033837)

Industrial application

Food and nutrition

Food additive

Flavoring agent

Flavoring Agent (HMDB: HMDB0033837)

Physical Properties

State

Liquid

Experimental Molecular Properties

Property	Value	Reference
Melting Point	19 °C	Not Available
Boiling Point	195.00 to 197.00 °C. @ 760.00 mm Hg	The Good Scents Company Information System
Water Solubility	25000 mg/L @ 20 °C (exp)	The Good Scents Company Information System
LogP	0.35	Not Available

Experimental Chromatographic Properties

Not Available

Predicted Molecular Properties

Property	Value	Source
Water Solubility	67 g/L	ALOGPS
logP	0.2	ALOGPS
logP	-0.11	ChemAxon
logS	-0.34	ALOGPS
pKa (Strongest Basic)	-6.7	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	2	ChemAxon
Hydrogen Donor Count	0	ChemAxon
Polar Surface Area	52.6 Å²	ChemAxon
Rotatable Bond Count	5	ChemAxon
Refractivity	33.08 m³·mol⁻¹	ChemAxon
Polarizability	14.27 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]+	133.148	31661259
DarkChem	[M-H]-	129.403	31661259
DeepCCS	[M+H]+	119.152	30932474
DeepCCS	[M-H]-	115.321	30932474
DeepCCS	[M-2H]-	152.077	30932474
DeepCCS	[M+Na]+	127.707	30932474
AllCCS	[M+H]+	134.7	32859911
AllCCS	[M+H-H2O]+	130.7	32859911
AllCCS	[M+NH4]+	138.4	32859911
AllCCS	[M+Na]+	139.5	32859911
AllCCS	[M-H]-	131.6	32859911
AllCCS	[M+Na-2H]-	134.0	32859911
AllCCS	[M+HCOO]-	136.6	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. Predicted by Afia on May 17, 2022.	3.46 minutes	32390414
Predicted by Siyang on May 30, 2022	10.4227 minutes	33406817
Predicted by Siyang using ReTip algorithm on June 8, 2022	1.17 minutes	32390414
AjsUoB = Accucore 150 Amide HILIC with 10mM Ammonium Formate, 0.1% Formic Acid	27.1 seconds	40023050
Fem_Long = Waters ACQUITY UPLC HSS T3 C18 with Water:MeOH and 0.1% Formic Acid	1590.4 seconds	40023050
Fem_Lipids = Ascentis Express C18 with (60:40 water:ACN):(90:10 IPA:ACN) and 10mM NH4COOH + 0.1% Formic Acid	333.1 seconds	40023050
Life_Old = Waters ACQUITY UPLC BEH C18 with Water:(20:80 acetone:ACN) and 0.1% Formic Acid	125.0 seconds	40023050
Life_New = RP Waters ACQUITY UPLC HSS T3 C18 with Water:(30:70 MeOH:ACN) and 0.1% Formic Acid	207.3 seconds	40023050
RIKEN = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid	61.0 seconds	40023050
Eawag_XBridgeC18 = XBridge C18 3.5u 2.1x50 mm with Water:MeOH and 0.1% Formic Acid	305.1 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	414.7 seconds	40023050
HILIC_BDD_2 = Merck SeQuant ZIC-HILIC with ACN(0.1% formic acid):water(16 mM ammonium formate)	88.0 seconds	40023050
UniToyama_Atlantis = RP Waters Atlantis T3 (2.1 x 150 mm, 5 um) with ACN:Water and 0.1% Formic Acid	833.7 seconds	40023050
BDD_C18 = Hypersil Gold 1.9µm C18 with Water:ACN and 0.1% Formic Acid	314.5 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	977.8 seconds	40023050
SNU_RIKEN_POS = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid	224.6 seconds	40023050
RPMMFDA = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid	274.6 seconds	40023050
MTBLS87 = Merck SeQuant ZIC-pHILIC column with ACN:Water and :ammonium carbonate	486.4 seconds	40023050
KI_GIAR_zic_HILIC_pH2_7 = Merck SeQuant ZIC-HILIC with ACN:Water and 0.1% FA	288.1 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	161.4 seconds	40023050

Predicted Kovats Retention Indices

Underivatized

Metabolite	SMILES	Kovats RI Value	Column Type	Reference
Dimethyl succinate	COC(=O)CCC(=O)OC	1647.0	Standard polar	33892256
Dimethyl succinate	COC(=O)CCC(=O)OC	965.0	Standard non polar	33892256
Dimethyl succinate	COC(=O)CCC(=O)OC	1101.5	Semi standard non polar	33892256

Spectra

GC-MS Spectra

Spectrum Type	Description	Splash Key	Deposition Date	Source	View
Experimental GC-MS	GC-MS Spectrum - Dimethyl succinate EI-B (Non-derivatized)	splash10-066r-9700000000-a5816c939f45d0df9f23	2017-09-12	HMDB team, MONA, MassBank	View Spectrum
Experimental GC-MS	GC-MS Spectrum - Dimethyl succinate EI-B (Non-derivatized)	splash10-066r-9500000000-c195fe7b6f9368cc8661	2017-09-12	HMDB team, MONA, MassBank	View Spectrum
Experimental GC-MS	GC-MS Spectrum - Dimethyl succinate EI-B (Non-derivatized)	splash10-014i-5900000000-3fa4f2e4fd1516958b42	2017-09-12	HMDB team, MONA, MassBank	View Spectrum
Experimental GC-MS	GC-MS Spectrum - Dimethyl succinate CI-B (Non-derivatized)	splash10-014i-0900000000-0e64cb9a284ec8ab9250	2017-09-12	HMDB team, MONA, MassBank	View Spectrum
Experimental GC-MS	GC-MS Spectrum - Dimethyl succinate EI-B (Non-derivatized)	splash10-066r-9400000000-cb3f9b045e51f533a8e0	2017-09-12	HMDB team, MONA, MassBank	View Spectrum
Experimental GC-MS	GC-MS Spectrum - Dimethyl succinate EI-B (Non-derivatized)	splash10-066r-8900000000-cbb2443772e2180e08e1	2017-09-12	HMDB team, MONA, MassBank	View Spectrum
Experimental GC-MS	GC-MS Spectrum - Dimethyl succinate EI-B (Non-derivatized)	splash10-066r-9700000000-a5816c939f45d0df9f23	2018-05-18	HMDB team, MONA, MassBank	View Spectrum
Experimental GC-MS	GC-MS Spectrum - Dimethyl succinate EI-B (Non-derivatized)	splash10-066r-9500000000-c195fe7b6f9368cc8661	2018-05-18	HMDB team, MONA, MassBank	View Spectrum
Experimental GC-MS	GC-MS Spectrum - Dimethyl succinate EI-B (Non-derivatized)	splash10-014i-5900000000-3fa4f2e4fd1516958b42	2018-05-18	HMDB team, MONA, MassBank	View Spectrum
Experimental GC-MS	GC-MS Spectrum - Dimethyl succinate CI-B (Non-derivatized)	splash10-014i-0900000000-0e64cb9a284ec8ab9250	2018-05-18	HMDB team, MONA, MassBank	View Spectrum
Experimental GC-MS	GC-MS Spectrum - Dimethyl succinate EI-B (Non-derivatized)	splash10-066r-9400000000-cb3f9b045e51f533a8e0	2018-05-18	HMDB team, MONA, MassBank	View Spectrum
Experimental GC-MS	GC-MS Spectrum - Dimethyl succinate EI-B (Non-derivatized)	splash10-066r-8900000000-cbb2443772e2180e08e1	2018-05-18	HMDB team, MONA, MassBank	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - Dimethyl succinate GC-MS (Non-derivatized) - 70eV, Positive	splash10-000i-9300000000-f53fb6e02e43fe5e819a	2017-09-01	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - Dimethyl succinate 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 - Dimethyl succinate 10V, Positive-QTOF	splash10-00kb-1900000000-35f2f0323633fed535ae	2016-08-01	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Dimethyl succinate 20V, Positive-QTOF	splash10-00kk-4900000000-304552701b084e11ba48	2016-08-01	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Dimethyl succinate 40V, Positive-QTOF	splash10-0a4i-9000000000-9b9869b242d9b647654c	2016-08-01	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Dimethyl succinate 10V, Negative-QTOF	splash10-0002-0900000000-cd5f13b968db727393af	2016-08-03	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Dimethyl succinate 20V, Negative-QTOF	splash10-01ot-3900000000-548aaf5315b41f088aca	2016-08-03	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Dimethyl succinate 40V, Negative-QTOF	splash10-001i-9100000000-5d4f47f6c139c1367035	2016-08-03	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Dimethyl succinate 10V, Negative-QTOF	splash10-03dl-7900000000-7433202c380f718fe5aa	2021-09-22	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Dimethyl succinate 20V, Negative-QTOF	splash10-06rx-9100000000-8035f50986337bf2c5f2	2021-09-22	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Dimethyl succinate 40V, Negative-QTOF	splash10-0a4l-9100000000-73065d3106fcf78ddc63	2021-09-22	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Dimethyl succinate 10V, Positive-QTOF	splash10-00ku-9500000000-a8267125513f2c41a43a	2021-09-22	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Dimethyl succinate 20V, Positive-QTOF	splash10-0a4i-9100000000-7c2cea53e4e4479aa92e	2021-09-22	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Dimethyl succinate 40V, Positive-QTOF	splash10-0a4i-9000000000-f60a38451d88bbd4eaed	2021-09-22	Wishart Lab	View Spectrum

NMR Spectra

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

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+Na]+)	2023-02-04	FELIX lab	View Spectrum

Biological Properties

Cellular Locations

Cytoplasm
Extracellular

Biospecimen Locations

Feces

Tissue Locations

Not Available

Pathways

Not Available

Name	SMPDB/PathBank	KEGG

Normal Concentrations

Biospecimen	Status	Value	Age	Sex	Condition	Reference	Details
Feces	Detected but not Quantified	Not Quantified	Adult (>18 years old)	Not Specified	Normal	25985090	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

FDB012011

KNApSAcK ID

Not Available

Chemspider ID

13848341

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

7820

PDB ID

Not Available

ChEBI ID

Not Available

Food Biomarker Ontology

Not Available

VMH ID

Not Available

MarkerDB ID

Not Available

Good Scents ID

rw1021021

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 ]
(). Yannai, Shmuel. (2004) Dictionary of food compounds with CD-ROM: Additives, flavors, and ingredients. Boca Raton: Chapman & Hall/CRC.. .
Gunstone, Frank D., John L. Harwood, and Albert J. Dijkstra (2007). The lipid handbook with CD-ROM. CRC Press.

Showing metabocard for Dimethyl succinate (HMDB0033837)

MOL for HMDB0033837 (Dimethyl succinate)

3D MOL for HMDB0033837 (Dimethyl succinate)

3D SDF for HMDB0033837 (Dimethyl succinate)

3D-SDF for HMDB0033837 (Dimethyl succinate)

PDB for HMDB0033837 (Dimethyl succinate)

3D PDB for HMDB0033837 (Dimethyl succinate)

SMILES for HMDB0033837 (Dimethyl succinate)

INCHI for HMDB0033837 (Dimethyl succinate)

Structure for HMDB0033837 (Dimethyl succinate)

3D Structure for HMDB0033837 (Dimethyl succinate)

Predicted Collision Cross Sections

Predicted Retention Times

Underivatized

Predicted Kovats Retention Indices

Underivatized

GC-MS Spectra

MS/MS Spectra

NMR Spectra

IR Spectra