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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

2021-09-11 08:44:42 UTC

Update Date

2021-09-26 23:03:22 UTC

HMDB ID

HMDB0251386

Secondary Accession Numbers

None

Metabolite Identification

Common Name

Dimethyl malonate

Description

This compound has been identified in human blood as reported by (PMID: 31557052 ). Dimethyl malonate is not a naturally occurring metabolite and is only found in those individuals exposed to this compound or its derivatives. Technically Dimethyl malonate is part of the human exposome. The exposome can be defined as the collection of all the exposures of an individual in a lifetime and how those exposures relate to health. An individual's exposure begins before birth and includes insults from environmental and occupational sources.

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 malonic acid	Generator
Methyl malonate	MeSH

Chemical Formula

C₅H₈O₄

Average Molecular Weight

132.1146

Monoisotopic Molecular Weight

132.042258744

IUPAC Name

1,3-dimethyl propanedioate

Traditional Name

dimethyl malonate

CAS Registry Number

Not Available

SMILES

COC(=O)CC(=O)OC

InChI Identifier

InChI=1S/C5H8O4/c1-8-4(6)3-5(7)9-2/h3H2,1-2H3

InChI Key

BEPAFCGSDWSTEL-UHFFFAOYSA-N

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as dicarboxylic acids and derivatives. These are organic compounds containing exactly two carboxylic acid groups.

Kingdom

Organic compounds

Super Class

Organic acids and derivatives

Class

Carboxylic acids and derivatives

Sub Class

Dicarboxylic acids and derivatives

Direct Parent

Dicarboxylic acids and derivatives

Alternative Parents

Substituents

1,3-dicarbonyl compound
Dicarboxylic acid or derivatives
Methyl ester
Carboxylic acid ester
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

Odor

fruity

Disposition

Biological location

Non-excretory biofluid

Biofluid or Excreta

Blood (PMID: 31557052)

Pineapple (FooDB: FOOD00012)

Berry

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

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
logP	0.08	ALOGPS
logP	-0.039	ChemAxon
logS	0.02	ALOGPS
pKa (Strongest Acidic)	12.9	ChemAxon
pKa (Strongest Basic)	-6.8	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	4	ChemAxon
Refractivity	28.53 m³·mol⁻¹	ChemAxon
Polarizability	12.3 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]+	120.657	30932474
DeepCCS	[M-H]-	117.345	30932474
DeepCCS	[M-2H]-	153.877	30932474
DeepCCS	[M+Na]+	129.214	30932474
AllCCS	[M+H]+	131.8	32859911
AllCCS	[M+H-H2O]+	127.7	32859911
AllCCS	[M+NH4]+	135.6	32859911
AllCCS	[M+Na]+	136.7	32859911
AllCCS	[M-H]-	127.5	32859911
AllCCS	[M+Na-2H]-	130.4	32859911
AllCCS	[M+HCOO]-	133.5	32859911

Predicted Kovats Retention Indices

Underivatized

Metabolite	SMILES	Kovats RI Value	Column Type	Reference
Dimethyl malonate	COC(=O)CC(=O)OC	1451.5	Standard polar	33892256
Dimethyl malonate	COC(=O)CC(=O)OC	867.9	Standard non polar	33892256
Dimethyl malonate	COC(=O)CC(=O)OC	1004.9	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 - Dimethyl malonate GC-MS (Non-derivatized) - 70eV, Positive	splash10-0kh9-9700000000-1bb0e3882d36980b644a	2021-09-24	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - Dimethyl malonate 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 malonate 10V, Positive-QTOF	splash10-0f89-0900000000-39aaac7fe5342b35121f	2016-08-03	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Dimethyl malonate 20V, Positive-QTOF	splash10-0f89-1900000000-3d3540d0f8c3efe92c77	2016-08-03	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Dimethyl malonate 40V, Positive-QTOF	splash10-0fk9-9400000000-5e7240ac1297fe0aa29c	2016-08-03	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Dimethyl malonate 10V, Negative-QTOF	splash10-001i-4900000000-b5d2f4416cf152eb1d12	2016-08-03	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Dimethyl malonate 20V, Negative-QTOF	splash10-001j-7900000000-63490232d8de434a6b2e	2016-08-03	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Dimethyl malonate 40V, Negative-QTOF	splash10-014i-9100000000-b2408ef5e6981de720d4	2016-08-03	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Dimethyl malonate 10V, Positive-QTOF	splash10-0f6x-9700000000-52bdbf3ec158dc078f39	2021-10-12	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Dimethyl malonate 20V, Positive-QTOF	splash10-053l-9100000000-0abbced7a0097b09c5b6	2021-10-12	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Dimethyl malonate 40V, Positive-QTOF	splash10-052f-9000000000-65fc30275961c25c9737	2021-10-12	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Dimethyl malonate 10V, Negative-QTOF	splash10-008a-9400000000-4912f28d5a3aa398c03f	2021-10-12	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Dimethyl malonate 20V, Negative-QTOF	splash10-00kg-9000000000-86034907d3258b7847ed	2021-10-12	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Dimethyl malonate 40V, Negative-QTOF	splash10-006x-9000000000-886a09fdc4570cc7531d	2021-10-12	Wishart Lab	View Spectrum

NMR Spectra

Spectrum Type	Description	Deposition Date	Source	View
Predicted 1D NMR	¹H NMR Spectrum (1D, 100 MHz, D₂O, predicted)	2021-10-13	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 100 MHz, D₂O, predicted)	2021-10-13	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 1000 MHz, D₂O, predicted)	2021-10-13	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 1000 MHz, D₂O, predicted)	2021-10-13	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 200 MHz, D₂O, predicted)	2021-10-13	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 200 MHz, D₂O, predicted)	2021-10-13	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 300 MHz, D₂O, predicted)	2021-10-13	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 300 MHz, D₂O, predicted)	2021-10-13	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 400 MHz, D₂O, predicted)	2021-10-13	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 400 MHz, D₂O, predicted)	2021-10-13	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 500 MHz, D₂O, predicted)	2021-10-13	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 500 MHz, D₂O, predicted)	2021-10-13	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 600 MHz, D₂O, predicted)	2021-10-13	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 600 MHz, D₂O, predicted)	2021-10-13	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 700 MHz, D₂O, predicted)	2021-10-13	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 700 MHz, D₂O, predicted)	2021-10-13	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 800 MHz, D₂O, predicted)	2021-10-13	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 800 MHz, D₂O, predicted)	2021-10-13	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 900 MHz, D₂O, predicted)	2021-10-13	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 900 MHz, D₂O, predicted)	2021-10-13	Wishart Lab	View Spectrum

Biological Properties

Cellular Locations

Not Available

Biospecimen Locations

Blood

Tissue Locations

Not Available

Pathways

Not Available

Name	SMPDB/PathBank	KEGG

Normal Concentrations

Biospecimen	Status	Value	Age	Sex	Condition	Reference	Details
Blood	Detected but not Quantified	Not Quantified	Not Specified	Not Specified	Normal	31557052	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

FDB008118

KNApSAcK ID

Not Available

Chemspider ID

Not Available

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Dimethyl malonate

METLIN ID

Not Available

PubChem Compound

7943

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

Barupal DK, Fiehn O: Generating the Blood Exposome Database Using a Comprehensive Text Mining and Database Fusion Approach. Environ Health Perspect. 2019 Sep;127(9):97008. doi: 10.1289/EHP4713. Epub 2019 Sep 26. [PubMed:31557052 ]

Showing metabocard for Dimethyl malonate (HMDB0251386)

MOL for HMDB0251386 (Dimethyl malonate)

3D MOL for HMDB0251386 (Dimethyl malonate)

3D SDF for HMDB0251386 (Dimethyl malonate)

3D-SDF for HMDB0251386 (Dimethyl malonate)

PDB for HMDB0251386 (Dimethyl malonate)

3D PDB for HMDB0251386 (Dimethyl malonate)

SMILES for HMDB0251386 (Dimethyl malonate)

INCHI for HMDB0251386 (Dimethyl malonate)

Structure for HMDB0251386 (Dimethyl malonate)

3D Structure for HMDB0251386 (Dimethyl malonate)

Predicted Collision Cross Sections

Predicted Kovats Retention Indices

Underivatized

GC-MS Spectra

MS/MS Spectra

NMR Spectra