MiMeDB: Showing metabocard for Aldehydo-D-apiose (MMDBc0057106)

Record Information

Version

2.0

Status

Detected and Quantified

Creation Date

2022-10-17 17:52:37 UTC

Update Date

2025-10-07 16:09:49 UTC

Metabolite ID

MMDBc0057106

Metabolite Identification

Common Name

Aldehydo-D-apiose

Description

Aldehydo-D-apiose is a carbohydrate belonging to the class of aldoses. There is limited literature available on this metabolite, indicating that further research may be needed to fully understand its biological significance and potential applications.

Structure

MOL SDF PDB SMILES InChI

Synonyms

Value	Source
3-C-Hydroxymethyltetrose	ChEBI
Apiose	ChEBI
D-Api	ChEBI

Molecular Formula

C₅H₁₀O₅

Average Mass

150.13

Monoisotopic Mass

150.052823422

IUPAC Name

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

Traditional Name

D-api

CAS Registry Number

Not Available

SMILES

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

InChI Identifier

InChI=1S/C5H10O5/c6-1-4(9)5(10,2-7)3-8/h1,4,7-10H,2-3H2/t4-/m0/s1

InChI Key

AVGPOAXYRRIZMM-BYPYZUCNSA-N

Chemical Taxonomy

Description

This compound belongs to the class of organic compounds known as monosaccharides. These are compounds containing one carbohydrate unit not glycosidically linked to another such unit, and no set of two or more glycosidically linked carbohydrate units. Monosaccharides have the general formula CnH2nOn.

Kingdom

Organic compounds

Super Class

Organooxygen compounds

Class

Carbohydrates and carbohydrate conjugates

Sub Class

Monosaccharides

Direct Parent

Monosaccharides

Alternative Parents

Substituents

Monosaccharide
Beta-hydroxy aldehyde
Alpha-hydroxyaldehyde
Tertiary alcohol
Secondary alcohol
1,2-diol
Polyol
Organic oxide
Hydrocarbon derivative
Short-chain aldehyde
Primary alcohol
Carbonyl group
Aldehyde
Alcohol
Aliphatic acyclic compound

Molecular Framework

Aliphatic acyclic compounds

External Descriptors

tetrose (CHEBI:16689 )

Functional Ontology

Not Available

Physical Properties

State

Not Available

Predicted Properties

Property	Value	Source
Water Solubility	539 g/L	ALOGPS
logP	-2.1	ALOGPS
logP	-3.1	ChemAxon
logS	0.56	ALOGPS
pKa (Strongest Acidic)	11.89	ChemAxon
pKa (Strongest Basic)	-3.1	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	5	ChemAxon
Hydrogen Donor Count	4	ChemAxon
Polar Surface Area	97.99 Å²	ChemAxon
Rotatable Bond Count	4	ChemAxon
Refractivity	31.6 m³·mol⁻¹	ChemAxon
Polarizability	13.33 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

Not Available

Chromatographic Retention Times and Retention Indices

Retention Times

Chromatography Type	Technique	Column	Deposition Date	Retention Time (s)
Liquid Chromatography	HILIC	Waters Acquity UPLC-BEH Amide column (eluted)	2025-10-24	432.8
Liquid Chromatography	HILIC	Accucore 150 Amide HILIC (eluted)	2025-10-24	325.7
Liquid Chromatography	Reversed-phase	Hypersil Gold 1.9 µm C18 (void)	2025-10-24	43.4
Liquid Chromatography	Reversed-phase	Agilent Zorbax Eclipse Plus C18 (2.1 mm x 150 mm, 3.5 um) (eluted)	2025-10-24	228.2
Liquid Chromatography	Reversed-phase	XBridge C18 3.5u 2.1x50 mm (eluted)	2025-10-24	278.8
Liquid Chromatography	Reversed-phase	Ascentis Express C18 (void)	2025-10-24	320.9
Liquid Chromatography	Reversed-phase	Waters ACQUITY UPLC HSS T3 C18 (void)	2025-10-24	528.1
Liquid Chromatography	HILIC	Merck SeQuant ZIC-HILIC (eluted)	2025-10-24	592.7
Liquid Chromatography	HILIC	Merck SeQuant ZIC-pHILIC (eluted)	2025-10-24	813.2
Liquid Chromatography	Reversed-phase	Waters ACQUITY UPLC HSS T3 C18 (eluted)	2025-10-24	179.3
Liquid Chromatography	HILIC	Merck SeQuant ZIC-HILIC (eluted)	2025-10-24	304.4
Liquid Chromatography	Reversed-phase	Waters ACQUITY UPLC HSS T3 C18 (eluted)	2025-10-24	193.4
Liquid Chromatography	Reversed-phase	Waters ACQUITY UPLC BEH C18 (eluted)	2025-10-24	37.2
Liquid Chromatography	HILIC	Merck SeQuant ZIC-pHILIC column (eluted)	2025-10-24	357.5
Liquid Chromatography	HILIC	Merck SeQuant ZIC-pHILIC column (eluted)	2025-10-24	619.9
Liquid Chromatography	Reversed-phase	Waters ACQUITY UPLC BEH C18 (void)	2025-10-24	71.0
Liquid Chromatography	Reversed-phase	Waters ACQUITY UPLC BEH C18 (eluted)	2025-10-24	291.3
Liquid Chromatography	Reversed-phase	Kinetex Core-Shell C18 2.6 um, 3.0 x 100 mm, Phenomenex (eluted)	2025-10-24	765.2
Liquid Chromatography	Reversed-phase	Waters Atlantis T3 (2.1 x 150 mm, 5 um) (eluted)	2025-10-24	586.0

Retention Indices

Chromatography Type	Peak Label	SMILES	Stationary Phase	Deposition Date	Retention Index
Gas Chromatography	Aldehydo-D-apiose_TMS_1	C[Si](C)(C)OCC(O)(CO)[C@@H](O)C=O	standard non polar	2025-10-24	1603.7
Gas Chromatography	Aldehydo-D-apiose_TMS_2	C[Si](C)(C)OC(CO)(CO)[C@@H](O)C=O	standard non polar	2025-10-24	1799.47
Gas Chromatography	Aldehydo-D-apiose_TMS_3	C[Si](C)(C)O[C@@H](C=O)C(O)(CO)CO	standard non polar	2025-10-24	1896.34
Gas Chromatography	Aldehydo-D-apiose_TMS_4	C[Si](C)(C)OC=C(O)C(O)(CO)CO	standard non polar	2025-10-24	1871.87
Gas Chromatography	Aldehydo-D-apiose_TMS_5	C[Si](C)(C)OCC(CO)(O[Si](C)(C)C)[C@@H](O)C=O	standard non polar	2025-10-24	2029.01
Gas Chromatography	Aldehydo-D-apiose_TMS_6	C[Si](C)(C)OCC(O)(CO[Si](C)(C)C)[C@@H](O)C=O	standard non polar	2025-10-24	1817.28
Gas Chromatography	Aldehydo-D-apiose_TMS_7	C[Si](C)(C)OCC(O)(CO)[C@H](C=O)O[Si](C)(C)C	standard non polar	2025-10-24	1749.19
Gas Chromatography	Aldehydo-D-apiose_TMS_8	C[Si](C)(C)OC=C(O)C(O)(CO)CO[Si](C)(C)C	standard non polar	2025-10-24	2294.37
Gas Chromatography	Aldehydo-D-apiose_TMS_9	C[Si](C)(C)O[C@@H](C=O)C(CO)(CO)O[Si](C)(C)C	standard non polar	2025-10-24	1949.62
Gas Chromatography	Aldehydo-D-apiose_TMS_10	C[Si](C)(C)OC=C(O)C(CO)(CO)O[Si](C)(C)C	standard non polar	2025-10-24	2111.07
Gas Chromatography	Aldehydo-D-apiose_TMS_11	C[Si](C)(C)OC=C(O[Si](C)(C)C)C(O)(CO)CO	standard non polar	2025-10-24	1859.15
Gas Chromatography	Aldehydo-D-apiose_TMS_12	C[Si](C)(C)OCC(CO[Si](C)(C)C)(O[Si](C)(C)C)[C@@H](O)C=O	standard non polar	2025-10-24	1909.37
Gas Chromatography	Aldehydo-D-apiose_TMS_13	C[Si](C)(C)OCC(CO)(O[Si](C)(C)C)[C@H](C=O)O[Si](C)(C)C	standard non polar	2025-10-24	2096.35
Gas Chromatography	Aldehydo-D-apiose_TMS_14	C[Si](C)(C)OC=C(O)C(CO)(CO[Si](C)(C)C)O[Si](C)(C)C	standard non polar	2025-10-24	2282.23
Gas Chromatography	Aldehydo-D-apiose_TMS_15	C[Si](C)(C)OCC(O)(CO[Si](C)(C)C)[C@H](C=O)O[Si](C)(C)C	standard non polar	2025-10-24	1872.94
Gas Chromatography	Aldehydo-D-apiose_TMS_16	C[Si](C)(C)OC=C(O)C(O)(CO[Si](C)(C)C)CO[Si](C)(C)C	standard non polar	2025-10-24	1756.52
Gas Chromatography	Aldehydo-D-apiose_TMS_17	C[Si](C)(C)OC=C(O[Si](C)(C)C)C(O)(CO)CO[Si](C)(C)C	standard non polar	2025-10-24	1791.52
Gas Chromatography	Aldehydo-D-apiose_TMS_18	C[Si](C)(C)OC=C(O[Si](C)(C)C)C(CO)(CO)O[Si](C)(C)C	standard non polar	2025-10-24	2156.68
Gas Chromatography	Aldehydo-D-apiose_TMS_19	C[Si](C)(C)OCC(CO[Si](C)(C)C)(O[Si](C)(C)C)[C@H](C=O)O[Si](C)(C)C	standard non polar	2025-10-24	1323.71
Gas Chromatography	Aldehydo-D-apiose_TMS_20	C[Si](C)(C)OC=C(O)C(CO[Si](C)(C)C)(CO[Si](C)(C)C)O[Si](C)(C)C	standard non polar	2025-10-24	2456.61
Gas Chromatography	Aldehydo-D-apiose_TMS_21	C[Si](C)(C)OC=C(O[Si](C)(C)C)C(CO)(CO[Si](C)(C)C)O[Si](C)(C)C	standard non polar	2025-10-24	2391.47
Gas Chromatography	Aldehydo-D-apiose_TMS_22	C[Si](C)(C)OC=C(O[Si](C)(C)C)C(O)(CO[Si](C)(C)C)CO[Si](C)(C)C	standard non polar	2025-10-24	2656.95
Gas Chromatography	Aldehydo-D-apiose_TMS_23	C[Si](C)(C)OC=C(O[Si](C)(C)C)C(CO[Si](C)(C)C)(CO[Si](C)(C)C)O[Si](C)(C)C	standard non polar	2025-10-24	2363.39
Gas Chromatography	Aldehydo-D-apiose_TMS_1	C[Si](C)(C)OCC(O)(CO)[C@@H](O)C=O	standard polar	2025-10-24	2198.86
Gas Chromatography	Aldehydo-D-apiose_TMS_2	C[Si](C)(C)OC(CO)(CO)[C@@H](O)C=O	standard polar	2025-10-24	2336.33
Gas Chromatography	Aldehydo-D-apiose_TMS_3	C[Si](C)(C)O[C@@H](C=O)C(O)(CO)CO	standard polar	2025-10-24	2011.95
Gas Chromatography	Aldehydo-D-apiose_TMS_4	C[Si](C)(C)OC=C(O)C(O)(CO)CO	standard polar	2025-10-24	2020.02
Gas Chromatography	Aldehydo-D-apiose_TMS_5	C[Si](C)(C)OCC(CO)(O[Si](C)(C)C)[C@@H](O)C=O	standard polar	2025-10-24	2155.9
Gas Chromatography	Aldehydo-D-apiose_TMS_6	C[Si](C)(C)OCC(O)(CO[Si](C)(C)C)[C@@H](O)C=O	standard polar	2025-10-24	2232.58
Gas Chromatography	Aldehydo-D-apiose_TMS_7	C[Si](C)(C)OCC(O)(CO)[C@H](C=O)O[Si](C)(C)C	standard polar	2025-10-24	1750.71
Gas Chromatography	Aldehydo-D-apiose_TMS_8	C[Si](C)(C)OC=C(O)C(O)(CO)CO[Si](C)(C)C	standard polar	2025-10-24	1552.43
Gas Chromatography	Aldehydo-D-apiose_TMS_9	C[Si](C)(C)O[C@@H](C=O)C(CO)(CO)O[Si](C)(C)C	standard polar	2025-10-24	2338.9
Gas Chromatography	Aldehydo-D-apiose_TMS_10	C[Si](C)(C)OC=C(O)C(CO)(CO)O[Si](C)(C)C	standard polar	2025-10-24	2000.45
Gas Chromatography	Aldehydo-D-apiose_TMS_11	C[Si](C)(C)OC=C(O[Si](C)(C)C)C(O)(CO)CO	standard polar	2025-10-24	1740.75
Gas Chromatography	Aldehydo-D-apiose_TMS_12	C[Si](C)(C)OCC(CO[Si](C)(C)C)(O[Si](C)(C)C)[C@@H](O)C=O	standard polar	2025-10-24	1972.95
Gas Chromatography	Aldehydo-D-apiose_TMS_13	C[Si](C)(C)OCC(CO)(O[Si](C)(C)C)[C@H](C=O)O[Si](C)(C)C	standard polar	2025-10-24	2348.57
Gas Chromatography	Aldehydo-D-apiose_TMS_14	C[Si](C)(C)OC=C(O)C(CO)(CO[Si](C)(C)C)O[Si](C)(C)C	standard polar	2025-10-24	1926.03
Gas Chromatography	Aldehydo-D-apiose_TMS_15	C[Si](C)(C)OCC(O)(CO[Si](C)(C)C)[C@H](C=O)O[Si](C)(C)C	standard polar	2025-10-24	2076.93
Gas Chromatography	Aldehydo-D-apiose_TMS_16	C[Si](C)(C)OC=C(O)C(O)(CO[Si](C)(C)C)CO[Si](C)(C)C	standard polar	2025-10-24	2452.39
Gas Chromatography	Aldehydo-D-apiose_TMS_17	C[Si](C)(C)OC=C(O[Si](C)(C)C)C(O)(CO)CO[Si](C)(C)C	standard polar	2025-10-24	2090.75
Gas Chromatography	Aldehydo-D-apiose_TMS_18	C[Si](C)(C)OC=C(O[Si](C)(C)C)C(CO)(CO)O[Si](C)(C)C	standard polar	2025-10-24	2137.05
Gas Chromatography	Aldehydo-D-apiose_TMS_19	C[Si](C)(C)OCC(CO[Si](C)(C)C)(O[Si](C)(C)C)[C@H](C=O)O[Si](C)(C)C	standard polar	2025-10-24	2896.61
Gas Chromatography	Aldehydo-D-apiose_TMS_20	C[Si](C)(C)OC=C(O)C(CO[Si](C)(C)C)(CO[Si](C)(C)C)O[Si](C)(C)C	standard polar	2025-10-24	2001.46
Gas Chromatography	Aldehydo-D-apiose_TMS_21	C[Si](C)(C)OC=C(O[Si](C)(C)C)C(CO)(CO[Si](C)(C)C)O[Si](C)(C)C	standard polar	2025-10-24	2131.75
Gas Chromatography	Aldehydo-D-apiose_TMS_22	C[Si](C)(C)OC=C(O[Si](C)(C)C)C(O)(CO[Si](C)(C)C)CO[Si](C)(C)C	standard polar	2025-10-24	1488.12
Gas Chromatography	Aldehydo-D-apiose_TMS_23	C[Si](C)(C)OC=C(O[Si](C)(C)C)C(CO[Si](C)(C)C)(CO[Si](C)(C)C)O[Si](C)(C)C	standard polar	2025-10-24	1851.63

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
MMDBr0025635	Aldehydo-D-apiose	apulose	D-apiose isomerase	Isomerization	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

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

4573800

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

5460157

PDB ID

Not Available

ChEBI ID

16689

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 Aldehydo-D-apiose (MMDBc0057106)

MOL for #<Metabolite:0x0000564322f39a88>

3D MOL for #<Metabolite:0x0000564322f39a88>

3D SDF for #<Metabolite:0x0000564322f39a88>

3D-SDF for #<Metabolite:0x0000564322f39a88>

PDB for #<Metabolite:0x0000564322f39a88>

3D PDB for #<Metabolite:0x0000564322f39a88>

SMILES for #<Metabolite:0x0000564322f39a88>

INCHI for #<Metabolite:0x0000564322f39a88>

Structure for #<Metabolite:0x0000564322f39a88>

3D Structure for #<Metabolite:0x0000564322f39a88>