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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 17:43:47 UTC

Update Date

2022-03-07 02:53:00 UTC

HMDB ID

HMDB0031518

Secondary Accession Numbers

HMDB31518

Metabolite Identification

Common Name

D-Malic acid

Description

D-Malic acid, also known as D-malate, belongs to the class of organic compounds known as beta hydroxy acids and derivatives. Beta hydroxy acids and derivatives are compounds containing a carboxylic acid substituted with a hydroxyl group on the C3 carbon atom. D-Malic acid exists in all living organisms, ranging from bacteria to humans. D-Malic acid is a primary metabolite. Primary metabolites are metabolically or physiologically essential metabolites. They are directly involved in an organism’s growth, development or reproduction. Based on a literature review a significant number of articles have been published on D-Malic acid.

Structure

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

View in JSmol View NMR Assignments View Stereo Labels

Synonyms

Value	Source
(+)-D-Malic acid	ChEBI
(R)-2-Hydroxybutanedioic acid	ChEBI
2-HYDROXY-succinIC ACID	ChEBI
D-Malate	Kegg
(+)-D-Malate	Generator
(R)-2-Hydroxybutanedioate	Generator
2-HYDROXY-succinate	Generator
(R)-Malate	HMDB
(R)-Hydroxybutanedioic acid	HMDB
D-(+)-Malic acid	HMDB
D-Hydroxybutanedioic acid	HMDB
Hydroxy-(R)-butanedioic acid	HMDB
R-Malic acid	HMDB
D-Malic acid	ChEBI

Chemical Formula

C₄H₆O₅

Average Molecular Weight

134.0874

Monoisotopic Molecular Weight

134.021523302

IUPAC Name

(2R)-2-hydroxybutanedioic acid

Traditional Name

.+-.-malic acid

CAS Registry Number

636-61-3

SMILES

O[C@H](CC(O)=O)C(O)=O

InChI Identifier

InChI=1S/C4H6O5/c5-2(4(8)9)1-3(6)7/h2,5H,1H2,(H,6,7)(H,8,9)/t2-/m1/s1

InChI Key

BJEPYKJPYRNKOW-UWTATZPHSA-N

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as beta hydroxy acids and derivatives. Beta hydroxy acids and derivatives are compounds containing a carboxylic acid substituted with a hydroxyl group on the C3 carbon atom.

Kingdom

Organic compounds

Super Class

Organic acids and derivatives

Class

Hydroxy acids and derivatives

Sub Class

Beta hydroxy acids and derivatives

Direct Parent

Beta hydroxy acids and derivatives

Alternative Parents

Substituents

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

Molecular Framework

Aliphatic acyclic compounds

External Descriptors

malic acid (CHEBI:30796 )

Ontology

Not Available

Feces (PMID: 18085514)
Urine (HMDB: HMDB0031518)

Cellular substructure

Organelle

Adiposome (HMDB: HMDB0031518)

Route of exposure

Enteral

Ingestion (HMDB: HMDB0031518)

Source

Exogenous

Exogenous (HMDB: HMDB0031518)

Food

Food (HMDB: HMDB0031518)

Herb and spice

Herbs and Spices (FooDB: FOOD00866)

Endogenous

Endogenous (HMDB: HMDB0031518)

Plant

Plant (HMDB: HMDB0031518)

Process

Naturally occurring process

Biological process

Chemical reaction

Lipid Peroxidation (HMDB: HMDB0031518)

Biochemical pathway

Metabolic pathway

Fatty Acid Metabolism (HMDB: HMDB0031518)

Lipid metabolism pathway (HMDB: HMDB0031518)

Biochemical process

Lipid transport (HMDB: HMDB0031518)

Role

Biological role

Energy source (HMDB: HMDB0031518)

Industrial application

Pharmaceutical industry

Pharmaceutical (HMDB: HMDB0031518)

Physical Properties

State

Solid

Experimental Molecular Properties

Property	Value	Reference
Melting Point	101 °C	Not Available
Boiling Point	306.00 to 307.00 °C. @ 760.00 mm Hg (est)	The Good Scents Company Information System
Water Solubility	364 mg/mL at 20 °C	Not Available
LogP	-1.26	Not Available

Experimental Chromatographic Properties

Experimental Collision Cross Sections

Adduct Type	Data Source	CCS Value (Å²)	Reference
[M-H]-	Baker	120.679	30932474
[M-H]-	Not Available	120.679	http://allccs.zhulab.cn/database/detail?ID=AllCCS00001764

Predicted Molecular Properties

Property	Value	Source
Water Solubility	218 g/L	ALOGPS
logP	-0.87	ALOGPS
logP	-1.1	ChemAxon
logS	0.21	ALOGPS
pKa (Strongest Acidic)	3.2	ChemAxon
pKa (Strongest Basic)	-3.9	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	24.88 m³·mol⁻¹	ChemAxon
Polarizability	10.93 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]+	128.017	31661259
DarkChem	[M-H]-	121.648	31661259
DeepCCS	[M+H]+	122.154	30932474
DeepCCS	[M-H]-	118.56	30932474
DeepCCS	[M-2H]-	155.829	30932474
DeepCCS	[M+Na]+	130.861	30932474
AllCCS	[M+H]+	131.9	32859911
AllCCS	[M+H-H2O]+	127.8	32859911
AllCCS	[M+NH4]+	135.7	32859911
AllCCS	[M+Na]+	136.8	32859911
AllCCS	[M-H]-	122.7	32859911
AllCCS	[M+Na-2H]-	125.3	32859911
AllCCS	[M+HCOO]-	128.2	32859911

Predicted Kovats Retention Indices

Underivatized

Metabolite	SMILES	Kovats RI Value	Column Type	Reference
D-Malic acid	O[C@H](CC(O)=O)C(O)=O	2199.2	Standard polar	33892256
D-Malic acid	O[C@H](CC(O)=O)C(O)=O	1008.0	Standard non polar	33892256
D-Malic acid	O[C@H](CC(O)=O)C(O)=O	1328.4	Semi standard non polar	33892256

Derivatized

Derivative Name / Structure	SMILES	Kovats RI Value	Column Type	Reference
D-Malic acid,1TMS,isomer #1	C[Si](C)(C)O[C@H](CC(=O)O)C(=O)O	1317.5	Semi standard non polar	33892256
D-Malic acid,1TMS,isomer #2	C[Si](C)(C)OC(=O)C[C@@H](O)C(=O)O	1311.4	Semi standard non polar	33892256
D-Malic acid,1TMS,isomer #3	C[Si](C)(C)OC(=O)[C@H](O)CC(=O)O	1279.0	Semi standard non polar	33892256
D-Malic acid,2TMS,isomer #1	C[Si](C)(C)OC(=O)C[C@@H](O[Si](C)(C)C)C(=O)O	1404.0	Semi standard non polar	33892256
D-Malic acid,2TMS,isomer #2	C[Si](C)(C)OC(=O)[C@@H](CC(=O)O)O[Si](C)(C)C	1376.6	Semi standard non polar	33892256
D-Malic acid,2TMS,isomer #3	C[Si](C)(C)OC(=O)C[C@@H](O)C(=O)O[Si](C)(C)C	1382.5	Semi standard non polar	33892256
D-Malic acid,3TMS,isomer #1	C[Si](C)(C)OC(=O)C[C@@H](O[Si](C)(C)C)C(=O)O[Si](C)(C)C	1498.5	Semi standard non polar	33892256
D-Malic acid,1TBDMS,isomer #1	CC(C)(C)[Si](C)(C)O[C@H](CC(=O)O)C(=O)O	1572.3	Semi standard non polar	33892256
D-Malic acid,1TBDMS,isomer #2	CC(C)(C)[Si](C)(C)OC(=O)C[C@@H](O)C(=O)O	1571.3	Semi standard non polar	33892256
D-Malic acid,1TBDMS,isomer #3	CC(C)(C)[Si](C)(C)OC(=O)[C@H](O)CC(=O)O	1555.1	Semi standard non polar	33892256
D-Malic acid,2TBDMS,isomer #1	CC(C)(C)[Si](C)(C)OC(=O)C[C@@H](O[Si](C)(C)C(C)(C)C)C(=O)O	1851.7	Semi standard non polar	33892256
D-Malic acid,2TBDMS,isomer #2	CC(C)(C)[Si](C)(C)OC(=O)[C@@H](CC(=O)O)O[Si](C)(C)C(C)(C)C	1836.9	Semi standard non polar	33892256
D-Malic acid,2TBDMS,isomer #3	CC(C)(C)[Si](C)(C)OC(=O)C[C@@H](O)C(=O)O[Si](C)(C)C(C)(C)C	1825.4	Semi standard non polar	33892256
D-Malic acid,3TBDMS,isomer #1	CC(C)(C)[Si](C)(C)OC(=O)C[C@@H](O[Si](C)(C)C(C)(C)C)C(=O)O[Si](C)(C)C(C)(C)C	2116.5	Semi standard non polar	33892256

Spectra

GC-MS Spectra

Spectrum Type	Description	Splash Key	Deposition Date	Source	View
Experimental GC-MS	GC-MS Spectrum - D-Malic acid GC-EI-TOF (Non-derivatized)	splash10-0002-0930000000-53a536e3bc82b8e91612	2017-09-12	HMDB team, MONA, MassBank	View Spectrum
Experimental GC-MS	GC-MS Spectrum - D-Malic acid GC-EI-TOF (Non-derivatized)	splash10-00di-9610000000-883e07f52319a029b9f9	2017-09-12	HMDB team, MONA, MassBank	View Spectrum
Experimental GC-MS	GC-MS Spectrum - D-Malic acid GC-EI-TOF (Non-derivatized)	splash10-0002-0930000000-53a536e3bc82b8e91612	2018-05-18	HMDB team, MONA, MassBank	View Spectrum
Experimental GC-MS	GC-MS Spectrum - D-Malic acid GC-EI-TOF (Non-derivatized)	splash10-00di-9610000000-883e07f52319a029b9f9	2018-05-18	HMDB team, MONA, MassBank	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - D-Malic acid GC-MS (Non-derivatized) - 70eV, Positive	splash10-0006-9100000000-add08efe51cfe6d9243c	2017-09-01	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - D-Malic acid GC-MS (3 TMS) - 70eV, Positive	splash10-02j9-7191000000-b78c78194b39deee0ca4	2017-10-06	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - D-Malic 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
Experimental LC-MS/MS	LC-MS/MS Spectrum - D-Malic acid LC-ESI-QTOF , negative-QTOF	splash10-0159-3900000000-b601107a03ca7060bc56	2017-09-14	HMDB team, MONA	View Spectrum
Experimental LC-MS/MS	LC-MS/MS Spectrum - D-Malic acid 10V, Negative-QTOF	splash10-01b9-7900000000-7e16d13cd13953520b72	2021-09-20	HMDB team, MONA	View Spectrum
Experimental LC-MS/MS	LC-MS/MS Spectrum - D-Malic acid 20V, Negative-QTOF	splash10-00di-9000000000-ed4a8a4776b51e62327c	2021-09-20	HMDB team, MONA	View Spectrum
Experimental LC-MS/MS	LC-MS/MS Spectrum - D-Malic acid 40V, Negative-QTOF	splash10-0006-9000000000-22c9ebc50090b4cd6671	2021-09-20	HMDB team, MONA	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - D-Malic acid 10V, Positive-QTOF	splash10-014i-6900000000-3b7d14a7ed7bb42627e4	2015-09-15	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - D-Malic acid 20V, Positive-QTOF	splash10-01bj-9300000000-20f68e610aeba32d1947	2015-09-15	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - D-Malic acid 40V, Positive-QTOF	splash10-00dl-9000000000-044292489a383c81ae1d	2015-09-15	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - D-Malic acid 10V, Negative-QTOF	splash10-00m0-8900000000-9da4062d3c439ed2f7eb	2015-09-15	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - D-Malic acid 20V, Negative-QTOF	splash10-00ri-9200000000-c4d019ab4961e5b1a1ae	2015-09-15	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - D-Malic acid 40V, Negative-QTOF	splash10-05fu-9000000000-bc073c2d0e1a2f8a82e3	2015-09-15	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - D-Malic acid 10V, Negative-QTOF	splash10-00y0-9400000000-b346287170f4b47937d9	2021-09-22	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - D-Malic acid 20V, Negative-QTOF	splash10-00du-9000000000-94fcc5032bed94eae77e	2021-09-22	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - D-Malic acid 40V, Negative-QTOF	splash10-052f-9000000000-43c40f8a7715a996c55b	2021-09-22	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - D-Malic acid 10V, Positive-QTOF	splash10-00ri-9400000000-a20ca040dba0bb25ae2b	2021-09-23	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - D-Malic acid 20V, Positive-QTOF	splash10-0095-9000000000-90064952bc6def150ecc	2021-09-23	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - D-Malic acid 40V, Positive-QTOF	splash10-0006-9000000000-4dd1a07ea5d3aab2c6ea	2021-09-23	Wishart Lab	View Spectrum

NMR Spectra

Spectrum Type	Description	Deposition Date	Source	View
Predicted 1D NMR	¹³C NMR Spectrum (1D, 100 MHz, D₂O, predicted)	2021-09-30	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 100 MHz, D₂O, predicted)	2021-09-30	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 1000 MHz, D₂O, predicted)	2021-09-30	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 1000 MHz, D₂O, predicted)	2021-09-30	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 200 MHz, D₂O, predicted)	2021-09-30	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 200 MHz, D₂O, predicted)	2021-09-30	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 300 MHz, D₂O, predicted)	2021-09-30	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 300 MHz, D₂O, predicted)	2021-09-30	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 400 MHz, D₂O, predicted)	2021-09-30	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 400 MHz, D₂O, predicted)	2021-09-30	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 500 MHz, D₂O, predicted)	2021-09-30	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 500 MHz, D₂O, predicted)	2021-09-30	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 600 MHz, D₂O, predicted)	2021-09-30	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 600 MHz, D₂O, predicted)	2021-09-30	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 700 MHz, D₂O, predicted)	2021-09-30	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 700 MHz, D₂O, predicted)	2021-09-30	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 800 MHz, D₂O, predicted)	2021-09-30	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 800 MHz, D₂O, predicted)	2021-09-30	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 900 MHz, D₂O, predicted)	2021-09-30	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 900 MHz, D₂O, predicted)	2021-09-30	Wishart 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)	Both	Normal	27543620	details
Feces	Detected but not Quantified	Not Quantified	Adult (>18 years old)	Both	Normal	25037050	details
Feces	Detected but not Quantified	Not Quantified	Adult (>18 years old)	Both	Normal	18085514	details
Feces	Detected but not Quantified	Not Quantified	Adult (>18 years old)	Both	Normal	29808030	details

Abnormal Concentrations

Biospecimen	Status	Value	Age	Sex	Condition	Reference	Details
Feces	Detected but not Quantified	Not Quantified	Adult (>18 years old)	Both	Colorectal cancer	27015276	details
Feces	Detected but not Quantified	Not Quantified	Adult (>18 years old)	Both	Colorectal cancer	25037050	details

Associated Disorders and Diseases

Disease References

Colorectal cancer

Sinha R, Ahn J, Sampson JN, Shi J, Yu G, Xiong X, Hayes RB, Goedert JJ: Fecal Microbiota, Fecal Metabolome, and Colorectal Cancer Interrelations. PLoS One. 2016 Mar 25;11(3):e0152126. doi: 10.1371/journal.pone.0152126. eCollection 2016. [PubMed:27015276 ]
Goedert JJ, Sampson JN, Moore SC, Xiao Q, Xiong X, Hayes RB, Ahn J, Shi J, Sinha R: Fecal metabolomics: assay performance and association with colorectal cancer. Carcinogenesis. 2014 Sep;35(9):2089-96. doi: 10.1093/carcin/bgu131. Epub 2014 Jul 18. [PubMed:25037050 ]

Associated OMIM IDs

114500 (Colorectal cancer)

External Links

DrugBank ID

DB03499

Phenol Explorer Compound ID

Not Available

FooDB ID

FDB008115

KNApSAcK ID

Not Available

Chemspider ID

83793

KEGG Compound ID

C00497

BioCyc ID

CPD-660

BiGG ID

Not Available

Wikipedia Link

Malic_acid

METLIN ID

Not Available

PubChem Compound

92824

PDB ID

DMR

ChEBI ID

30796

Food Biomarker Ontology

Not Available

VMH ID

MAL_D

MarkerDB ID

Not Available

Good Scents ID

rw1107901

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 D-Malic acid (HMDB0031518)

MOL for HMDB0031518 (D-Malic acid)

3D MOL for HMDB0031518 (D-Malic acid)

3D SDF for HMDB0031518 (D-Malic acid)

3D-SDF for HMDB0031518 (D-Malic acid)

PDB for HMDB0031518 (D-Malic acid)

3D PDB for HMDB0031518 (D-Malic acid)

SMILES for HMDB0031518 (D-Malic acid)

INCHI for HMDB0031518 (D-Malic acid)

Structure for HMDB0031518 (D-Malic acid)

3D Structure for HMDB0031518 (D-Malic acid)

Experimental Collision Cross Sections

Predicted Collision Cross Sections

Predicted Kovats Retention Indices

Underivatized

Derivatized

GC-MS Spectra

MS/MS Spectra

NMR Spectra