MiMeDB: Showing metabocard for D-apionate (MMDBc0055848)

Record Information

Version

2.0

Status

Detected and Quantified

Creation Date

2022-06-17 20:08:39 UTC

Update Date

2025-10-07 16:09:24 UTC

Metabolite ID

MMDBc0055848

Metabolite Identification

Common Name

D-apionate

Description

D-apionate is a metabolite classified within the chemical class of carboxylic acids. Its chemical structure features a propionate backbone with a hydroxymethyl group, which plays a crucial role in various biochemical pathways. D-apionate is involved in enzymatic reactions facilitated by newly identified enzymes such as D-apionate oxidoisomerase, which catalyzes the migration of the hydroxymethyl group. Additionally, it is associated with the activity of 3-oxo-isoapionate-4-phosphate decarboxylase and 3-oxo-isoapionate-4-phosphate transcarboxylase/hydrolase, both of which are classified as RuBisCO-like proteins (RLPs). These enzymes contribute to the metabolic pathways that process D-apionate, highlighting its significance in the broader context of metabolic regulation and energy production (PMID:29867142 ).

Structure

MOL SDF PDB SMILES InChI

HEADER    PROTEIN                                 17-JUN-22   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   17-JUN-22         0                                  
HETATM    1  C   UNK     0       4.207   1.540   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       1.540   0.000   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       3.644  -0.564   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       2.874  -1.897   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       2.874   0.770   0.000  0.00  0.00           C+0
HETATM    6  O   UNK     0       5.541   0.770   0.000  0.00  0.00           O+0
HETATM    7  O   UNK     0       0.206   0.770   0.000  0.00  0.00           O+0
HETATM    8  O   UNK     0       5.184  -0.564   0.000  0.00  0.00           O+0
HETATM    9  O   UNK     0       3.644  -3.231   0.000  0.00  0.00           O+0
HETATM   10  O   UNK     0       1.334  -1.897   0.000  0.00  0.00           O-1
HETATM   11  O   UNK     0       2.104   2.104   0.000  0.00  0.00           O+0
HETATM   12  H   UNK     0       2.104  -0.564   0.000  0.00  0.00           H+0
CONECT    1    5    6                                                       
CONECT    2    5    7                                                       
CONECT    3    4    5    8   12                                             
CONECT    4    3    9   10                                                  
CONECT    5    1    2    3   11                                             
CONECT    6    1                                                            
CONECT    7    2                                                            
CONECT    8    3                                                            
CONECT    9    4                                                            
CONECT   10    4                                                            
CONECT   11    5                                                            
CONECT   12    3                                                            
MASTER        0    0    0    0    0    0    0    0   12    0   22    0
END

Synonyms

Value	Source
D-Apionic acid	Generator

Molecular Formula

C₅H₉O₆

Average Mass

165.122

Monoisotopic Mass

165.04046159

IUPAC Name

(2R)-2,3,4-trihydroxy-3-(hydroxymethyl)butanoate

Traditional Name

(2R)-2,3,4-trihydroxy-3-(hydroxymethyl)butanoate

CAS Registry Number

Not Available

SMILES

[H][C@](O)(C([O-])=O)C(O)(CO)CO

InChI Identifier

InChI=1S/C5H10O6/c6-1-5(11,2-7)3(8)4(9)10/h3,6-8,11H,1-2H2,(H,9,10)/p-1/t3-/m0/s1

InChI Key

WCFGGAKDAXZIAM-VKHMYHEASA-M

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

Short-chain hydroxy acid
Hydroxy fatty acid
Branched fatty acid
Monosaccharide
Tertiary alcohol
Secondary alcohol
Polyol
Monocarboxylic acid or derivatives
Carboxylic acid
Carboxylic acid derivative
Organic oxygen compound
Organic oxide
Hydrocarbon derivative
Primary alcohol
Organooxygen compound
Carbonyl group
Alcohol
Organic anion
Aliphatic acyclic compound

Molecular Framework

Aliphatic acyclic compounds

External Descriptors

Not Available

Functional Ontology

Not Available

Physical Properties

State

Expected Solid

Predicted Properties

Property	Value	Source
logP	-2.9	ChemAxon
pKa (Strongest Acidic)	3.39	ChemAxon
pKa (Strongest Basic)	-3.1	ChemAxon
Physiological Charge	-1	ChemAxon
Hydrogen Acceptor Count	6	ChemAxon
Hydrogen Donor Count	4	ChemAxon
Polar Surface Area	121.05 Å²	ChemAxon
Rotatable Bond Count	4	ChemAxon
Refractivity	43.36 m³·mol⁻¹	ChemAxon
Polarizability	13.79 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	Deposition Date	View
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

Chromatographic Retention Times and Retention Indices

Retention Times

Not Available

Retention Indices

Chromatography Type	Peak Label	SMILES	Stationary Phase	Deposition Date	Retention Index
Gas Chromatography	D-apionate_TMS_1	C[Si](C)(C)O[C@@H](C(=O)[O-])C(O)(CO)CO	standard non polar	2025-10-24	2369.24
Gas Chromatography	D-apionate_TMS_2	C[Si](C)(C)OC(CO)(CO)[C@@H](O)C(=O)[O-]	standard non polar	2025-10-24	1660.21
Gas Chromatography	D-apionate_TMS_3	C[Si](C)(C)OCC(O)(CO)[C@@H](O)C(=O)[O-]	standard non polar	2025-10-24	1936.61
Gas Chromatography	D-apionate_TMS_4	C[Si](C)(C)O[C@@H](C(=O)[O-])C(CO)(CO)O[Si](C)(C)C	standard non polar	2025-10-24	1853.02
Gas Chromatography	D-apionate_TMS_5	C[Si](C)(C)OCC(O)(CO)[C@@H](O[Si](C)(C)C)C(=O)[O-]	standard non polar	2025-10-24	1658.59
Gas Chromatography	D-apionate_TMS_6	C[Si](C)(C)OCC(CO)(O[Si](C)(C)C)[C@@H](O)C(=O)[O-]	standard non polar	2025-10-24	1855.18
Gas Chromatography	D-apionate_TMS_7	C[Si](C)(C)OCC(O)(CO[Si](C)(C)C)[C@@H](O)C(=O)[O-]	standard non polar	2025-10-24	1859.63
Gas Chromatography	D-apionate_TMS_8	C[Si](C)(C)OCC(CO)(O[Si](C)(C)C)[C@@H](O[Si](C)(C)C)C(=O)[O-]	standard non polar	2025-10-24	2653.27
Gas Chromatography	D-apionate_TMS_9	C[Si](C)(C)OCC(O)(CO[Si](C)(C)C)[C@@H](O[Si](C)(C)C)C(=O)[O-]	standard non polar	2025-10-24	1849.24
Gas Chromatography	D-apionate_TMS_10	C[Si](C)(C)OCC(CO[Si](C)(C)C)(O[Si](C)(C)C)[C@@H](O)C(=O)[O-]	standard non polar	2025-10-24	2031.12
Gas Chromatography	D-apionate_TMS_11	C[Si](C)(C)OCC(CO[Si](C)(C)C)(O[Si](C)(C)C)[C@@H](O[Si](C)(C)C)C(=O)[O-]	standard non polar	2025-10-24	1408.94
Gas Chromatography	D-apionate_TMS_1	C[Si](C)(C)O[C@@H](C(=O)[O-])C(O)(CO)CO	standard polar	2025-10-24	2011.79
Gas Chromatography	D-apionate_TMS_2	C[Si](C)(C)OC(CO)(CO)[C@@H](O)C(=O)[O-]	standard polar	2025-10-24	2496.0
Gas Chromatography	D-apionate_TMS_3	C[Si](C)(C)OCC(O)(CO)[C@@H](O)C(=O)[O-]	standard polar	2025-10-24	1977.83
Gas Chromatography	D-apionate_TMS_4	C[Si](C)(C)O[C@@H](C(=O)[O-])C(CO)(CO)O[Si](C)(C)C	standard polar	2025-10-24	2411.58
Gas Chromatography	D-apionate_TMS_5	C[Si](C)(C)OCC(O)(CO)[C@@H](O[Si](C)(C)C)C(=O)[O-]	standard polar	2025-10-24	2358.4
Gas Chromatography	D-apionate_TMS_6	C[Si](C)(C)OCC(CO)(O[Si](C)(C)C)[C@@H](O)C(=O)[O-]	standard polar	2025-10-24	2296.48
Gas Chromatography	D-apionate_TMS_7	C[Si](C)(C)OCC(O)(CO[Si](C)(C)C)[C@@H](O)C(=O)[O-]	standard polar	2025-10-24	2211.09
Gas Chromatography	D-apionate_TMS_8	C[Si](C)(C)OCC(CO)(O[Si](C)(C)C)[C@@H](O[Si](C)(C)C)C(=O)[O-]	standard polar	2025-10-24	2931.52
Gas Chromatography	D-apionate_TMS_9	C[Si](C)(C)OCC(O)(CO[Si](C)(C)C)[C@@H](O[Si](C)(C)C)C(=O)[O-]	standard polar	2025-10-24	1957.59
Gas Chromatography	D-apionate_TMS_10	C[Si](C)(C)OCC(CO[Si](C)(C)C)(O[Si](C)(C)C)[C@@H](O)C(=O)[O-]	standard polar	2025-10-24	1754.06
Gas Chromatography	D-apionate_TMS_11	C[Si](C)(C)OCC(CO[Si](C)(C)C)(O[Si](C)(C)C)[C@@H](O[Si](C)(C)C)C(=O)[O-]	standard polar	2025-10-24	1872.46

Biological Properties

Cellular Locations

Not Available

Biospecimen Locations

Not Available

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

Microbial Pathways

Pathways

Not Available

Metabolic Reactions

Reactions

This table shows at most 20 reactions. For the full list of associated reactions:

See All Associated Reactions

Reaction ID	Precursor	Product	Enzyme	Reaction Type	Data Source	Reference

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/Eubacteria	Proteobacteria	4	Human ; Human feces
Bacteria/Eubacteria	Firmicutes	1	Human feces

Exposure Sources

Other Exposures

Source Type	Data Source	Reference

Host Biospecimen and Location

Host and Biospecimen	Status	Mean	Std	Min	Max	Units	Age	Sex	Health Condition	Data Source	Reference

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

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

134692092

PDB ID

Not Available

ChEBI ID

Not Available

Food Biomarker Ontology

Not Available

CMMC Knowledgebase

Not Available

General References

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-apionate (MMDBc0055848)

MOL for #<Metabolite:0x00007fadd4ffc9e8>

3D MOL for #<Metabolite:0x00007fadd4ffc9e8>

3D SDF for #<Metabolite:0x00007fadd4ffc9e8>

3D-SDF for #<Metabolite:0x00007fadd4ffc9e8>

PDB for #<Metabolite:0x00007fadd4ffc9e8>

3D PDB for #<Metabolite:0x00007fadd4ffc9e8>

SMILES for #<Metabolite:0x00007fadd4ffc9e8>

INCHI for #<Metabolite:0x00007fadd4ffc9e8>

Structure for #<Metabolite:0x00007fadd4ffc9e8>

3D Structure for #<Metabolite:0x00007fadd4ffc9e8>