MiMeDB: Showing metabocard for D-Erythro-3-Methylmalate (MMDBc0030055)

Record Information

Version

1.0

Status

Detected and Quantified

Creation Date

2021-11-17 23:52:14 UTC

Update Date

2022-08-31 17:39:18 UTC

Metabolite ID

MMDBc0030055

Metabolite Identification

Common Name

D-Erythro-3-Methylmalate

Description

D-erythro-3-methylmalate is a member of the chemical class known as Dicarboxylic Acids and Derivatives. These are organic compounds containing exactly two carboxylic acid groups.

Structure

MOL SDF PDB SMILES InChI

HEADER    PROTEIN                                 08-MAR-20   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   08-MAR-20         0                                  
HETATM    1  C   UNK     0       2.874   2.310   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       2.874   0.770   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       1.540   0.000   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       4.207   0.000   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       0.206   0.770   0.000  0.00  0.00           C+0
HETATM    6  O   UNK     0       1.540  -1.540   0.000  0.00  0.00           O+0
HETATM    7  O   UNK     0       5.541   0.770   0.000  0.00  0.00           O+0
HETATM    8  O   UNK     0       4.207  -1.540   0.000  0.00  0.00           O+0
HETATM    9  O   UNK     0      -1.127   0.000   0.000  0.00  0.00           O+0
HETATM   10  O   UNK     0       0.206   2.310   0.000  0.00  0.00           O+0
HETATM   11  H   UNK     0       1.357   1.037   0.000  0.00  0.00           H+0
HETATM   12  H   UNK     0       1.013   1.447   0.000  0.00  0.00           H+0
CONECT    1    2                                                            
CONECT    2    1    3    4   11                                             
CONECT    3    2    5    6   12                                             
CONECT    4    2    7    8                                                  
CONECT    5    3    9   10                                                  
CONECT    6    3                                                            
CONECT    7    4                                                            
CONECT    8    4                                                            
CONECT    9    5                                                            
CONECT   10    5                                                            
CONECT   11    2                                                            
CONECT   12    3                                                            
MASTER        0    0    0    0    0    0    0    0   12    0   22    0
END

Synonyms

Value	Source
(2R,3S)-3-Methylmalate	ChEBI
(2R,3S)-3-Methylmalic acid	Generator
D-Erythro-3-methylmalic acid	Generator

Molecular Formula

C₅H₈O₅

Average Mass

148.114

Monoisotopic Mass

148.037173366

IUPAC Name

(2R,3S)-2-hydroxy-3-methylbutanedioic acid

Traditional Name

D-erythro-3-methylmalate

CAS Registry Number

Not Available

SMILES

[H][C@@](C)(C(O)=O)[C@@]([H])(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)/t2-,3+/m0/s1

InChI Key

NPYQJIHHTGFBLN-STHAYSLISA-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

erythro-3-methylmalic acid (CHEBI:27394 )

Functional Ontology

Not Available

Physical Properties

State

Expected Solid

Predicted Properties

Property	Value	Source
Water Solubility	154 g/L	ALOGPS
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

Spectra

Spectrum Type	Description	Splash Key	Deposition Date	View
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_1_2) - 70eV, Positive	Not Available	2022-08-08	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Positive	splash10-0f8a-3900000000-0757759d8479c38634f0	2015-09-14	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Positive	splash10-0a6r-9200000000-aafee9f80ad3d78f7d1e	2015-09-14	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Positive	splash10-0a6r-9000000000-87d1de119df5d3bfdb12	2015-09-14	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Negative	splash10-0f6t-2900000000-204aa7e58ea1ab8f7640	2015-09-15	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Negative	splash10-0pi9-9500000000-0dca374ca1bbb677091b	2015-09-15	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Negative	splash10-0a4i-9000000000-b2f353c995a6f56458b1	2015-09-15	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 100 MHz, H₂O, predicted)		2022-08-22	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 100 MHz, H₂O, predicted)		2022-08-22	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 1000 MHz, H₂O, predicted)		2022-08-22	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 1000 MHz, H₂O, predicted)		2022-08-22	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 200 MHz, H₂O, predicted)		2022-08-22	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 200 MHz, H₂O, predicted)		2022-08-22	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 300 MHz, H₂O, predicted)		2022-08-22	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 300 MHz, H₂O, predicted)		2022-08-22	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 400 MHz, H₂O, predicted)		2022-08-22	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 400 MHz, H₂O, predicted)		2022-08-22	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 500 MHz, H₂O, predicted)		2022-08-22	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 500 MHz, H₂O, predicted)		2022-08-22	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 600 MHz, H₂O, predicted)		2022-08-22	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 600 MHz, H₂O, predicted)		2022-08-22	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 700 MHz, H₂O, predicted)		2022-08-22	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 700 MHz, H₂O, predicted)		2022-08-22	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 800 MHz, H₂O, predicted)		2022-08-22	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 800 MHz, H₂O, predicted)		2022-08-22	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 900 MHz, H₂O, predicted)		2022-08-22	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 900 MHz, H₂O, predicted)		2022-08-22	View Spectrum

Biological Properties

Cellular Locations

Not Available

Biospecimen Locations

Feces

Tissue Locations

Not Available

Associated OMIM IDs

114500 (Colorectal cancer)
610247 (Eosinophilic esophagitis)

Human Proteins and Enzymes

Protein ID	Protein Name	Protein Type	Uniprot ID	Species

Human Pathways

Pathways

Name	SMPDB/PathBank

Metabolic Reactions

Reaction ID	Precursor	Product	Enzyme	Reaction Type	Data Source	Reference
MMDBr0010958	2-Methylmaleate	D-Erythro-3-Methylmalate	Not Available	3-isopropylmalate/(R)-2-methylmalate dehydratase	VMH	30371894
MMDBr0010959	D-Erythro-3-Methylmalate	2-Ketobutyric acid	Not Available	(2R,3S)-3-methylmalate:NAD+ oxidoreductase	VMH	30371894
MMDBr0015173	D-Erythro-3-Methylmalate	2-oxobutanoic acid	3-isopropylmalate/3-methylmalate dehydrogenase	Dehydrogenation	RHEA	34755880
MMDBr0015854	2-Methylmaleate	D-Erythro-3-Methylmalate	Isopropylmalate/citramalate isomerase large subunit	Isomerization	RHEA	34755880
MMDBr0038870	(2R,3S)-beta-methylmalyl-CoA	D-Erythro-3-Methylmalate	Thioesterase TesA	Hydrolysis	RHEA	34755880

Health Effects and Bioactivity

Health Outcome/Bioactivity	Metabolite Response/Effect	Evidence Type	Host and Biospecimen	Data Source	Reference

Microbial Sources

Superkingdom/Kingdom	Phylum	Total species	Hosts and Body Sites	Microbial Links
Bacteria	Proteobacteria	1	Human ; Human feces; Human feces; pleural fluid plaque; bal; Human stool	Unknown
Bacteria	Bacteroidetes	25	Human feces; Human ; Human stool; Human saliva	Metabolic reconstruction
Archaea/Archaea	Euryarchaeota	1

Exposure Sources

Source Type	Source Sub-type	Species	Data Source	Reference

Host Biospecimen and Location

Host and Biospecimen	Status	Mean	Std	Min	Max	Units	Age	Sex	Health Condition	Data Source	Reference
Human Feces	Detected but not Quantified									HMDB

External Links

HMDB ID

Not Available

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

C06032

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

440892

PDB ID

Not Available

ChEBI ID

27394

Food Biomarker Ontology

Not Available

References

Synthesis Reference

Not Available

General References

Noronha A, Modamio J, Jarosz Y, Guerard E, Sompairac N, Preciat G, Danielsdottir AD, Krecke M, Merten D, Haraldsdottir HS, Heinken A, Heirendt L, Magnusdottir S, Ravcheev DA, Sahoo S, Gawron P, Friscioni L, Garcia B, Prendergast M, Puente A, Rodrigues M, Roy A, Rouquaya M, Wiltgen L, Zagare A, John E, Krueger M, Kuperstein I, Zinovyev A, Schneider R, Fleming RMT, Thiele I: The Virtual Metabolic Human database: integrating human and gut microbiome metabolism with nutrition and disease. Nucleic Acids Res. 2019 Jan 8;47(D1):D614-D624. doi: 10.1093/nar/gky992. [PubMed:30371894 ]
Bansal P, Morgat A, Axelsen KB, Muthukrishnan V, Coudert E, Aimo L, Hyka-Nouspikel N, Gasteiger E, Kerhornou A, Neto TB, Pozzato M, Blatter MC, Ignatchenko A, Redaschi N, Bridge A: Rhea, the reaction knowledgebase in 2022. Nucleic Acids Res. 2022 Jan 7;50(D1):D693-D700. doi: 10.1093/nar/gkab1016. [PubMed:34755880 ]

Showing metabocard for D-Erythro-3-Methylmalate (MMDBc0030055)

MOL for #<Metabolite:0x00007f5a8c00a2d8>

3D MOL for #<Metabolite:0x00007f5a8c00a2d8>

3D SDF for #<Metabolite:0x00007f5a8c00a2d8>

3D-SDF for #<Metabolite:0x00007f5a8c00a2d8>

PDB for #<Metabolite:0x00007f5a8c00a2d8>

3D PDB for #<Metabolite:0x00007f5a8c00a2d8>

SMILES for #<Metabolite:0x00007f5a8c00a2d8>

INCHI for #<Metabolite:0x00007f5a8c00a2d8>

Structure for #<Metabolite:0x00007f5a8c00a2d8>

3D Structure for #<Metabolite:0x00007f5a8c00a2d8>