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Record Information

Version

5.0

Status

Expected but not Quantified

Creation Date

2012-09-11 17:33:41 UTC

Update Date

2022-03-07 02:52:22 UTC

HMDB ID

HMDB0029941

Secondary Accession Numbers

HMDB29941

Metabolite Identification

Common Name

D-Apiose

Description

D-Apiose belongs to the class of organic compounds known as pentoses. These are monosaccharides in which the carbohydrate moiety contains five carbon atoms. D-Apiose has been detected, but not quantified in, parsleys (Petroselinum crispum). This could make D-apiose a potential biomarker for the consumption of these foods. Based on a literature review a significant number of articles have been published on D-Apiose.

Structure

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

View in JSmol View NMR Assignments View Stereo Labels

Synonyms

Value	Source
(R)-Form	HMDB
3-C-Hydroxymethyltetrose	HMDB
Apiose	HMDB
Apiose, 9ci, 8ci	HMDB
b-D-Apiofuranose	Generator
Β-D-apiofuranose	Generator

Chemical Formula

C₅H₁₀O₅

Average Molecular Weight

150.1299

Monoisotopic Molecular Weight

150.05282343

IUPAC Name

4-(hydroxymethyl)oxolane-2,3,4-triol

Traditional Name

4-(hydroxymethyl)oxolane-2,3,4-triol

CAS Registry Number

639-97-4

SMILES

OCC1(O)COC(O)C1O

InChI Identifier

InChI=1S/C5H10O5/c6-1-5(9)2-10-4(8)3(5)7/h3-4,6-9H,1-2H2

InChI Key

ASNHGEVAWNWCRQ-UHFFFAOYSA-N

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as pentoses. These are monosaccharides in which the carbohydrate moiety contains five carbon atoms.

Kingdom

Organic compounds

Super Class

Organic oxygen compounds

Class

Organooxygen compounds

Sub Class

Carbohydrates and carbohydrate conjugates

Direct Parent

Pentoses

Alternative Parents

Substituents

Pentose monosaccharide
Tetrahydrofuran
Tertiary alcohol
Secondary alcohol
Hemiacetal
Oxacycle
Organoheterocyclic compound
Polyol
Hydrocarbon derivative
Primary alcohol
Alcohol
Aliphatic heteromonocyclic compound

Molecular Framework

Aliphatic heteromonocyclic compounds

External Descriptors

a small molecule (CPD-13046 )

Ontology

Not Available

Ingestion (HMDB: HMDB0029941)

Source

Endogenous

Endogenous (HMDB: HMDB0029941)

Plant

Plant (HMDB: HMDB0029941)

Exogenous

Food

Food (HMDB: HMDB0029941)

Herb and spice

Herb

Parsley (FooDB: FOOD00131)

Herbs and Spices (FooDB: FOOD00866)

Vegetable

Leaf vegetable

Green vegetables (FooDB: FOOD00872)

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	1000000 mg/L @ 25 °C (est)	The Good Scents Company Information System
LogP	Not Available	Not Available

Experimental Chromatographic Properties

Not Available

Predicted Molecular Properties

Property	Value	Source
Water Solubility	1290 g/L	ALOGPS
logP	-2.2	ALOGPS
logP	-2.4	ChemAxon
logS	0.94	ALOGPS
pKa (Strongest Acidic)	11.24	ChemAxon
pKa (Strongest Basic)	-3.1	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	5	ChemAxon
Hydrogen Donor Count	4	ChemAxon
Polar Surface Area	90.15 Å²	ChemAxon
Rotatable Bond Count	1	ChemAxon
Refractivity	30.18 m³·mol⁻¹	ChemAxon
Polarizability	13.47 Å³	ChemAxon
Number of Rings	1	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]+	130.047	31661259
DarkChem	[M-H]-	124.926	31661259
DeepCCS	[M+H]+	134.097	30932474
DeepCCS	[M-H]-	131.65	30932474
DeepCCS	[M-2H]-	168.148	30932474
DeepCCS	[M+Na]+	143.174	30932474
AllCCS	[M+H]+	132.3	32859911
AllCCS	[M+H-H2O]+	127.9	32859911
AllCCS	[M+NH4]+	136.5	32859911
AllCCS	[M+Na]+	137.7	32859911
AllCCS	[M-H]-	124.6	32859911
AllCCS	[M+Na-2H]-	126.3	32859911
AllCCS	[M+HCOO]-	128.3	32859911

Predicted Kovats Retention Indices

Underivatized

Metabolite	SMILES	Kovats RI Value	Column Type	Reference
D-Apiose	OCC1(O)COC(O)C1O	3077.5	Standard polar	33892256
D-Apiose	OCC1(O)COC(O)C1O	1439.2	Standard non polar	33892256
D-Apiose	OCC1(O)COC(O)C1O	1490.6	Semi standard non polar	33892256

Derivatized

Derivative Name / Structure	SMILES	Kovats RI Value	Column Type	Reference
D-Apiose,1TMS,isomer #1	C[Si](C)(C)OCC1(O)COC(O)C1O	1509.8	Semi standard non polar	33892256
D-Apiose,1TMS,isomer #2	C[Si](C)(C)OC1(CO)COC(O)C1O	1519.4	Semi standard non polar	33892256
D-Apiose,1TMS,isomer #3	C[Si](C)(C)OC1OCC(O)(CO)C1O	1515.0	Semi standard non polar	33892256
D-Apiose,1TMS,isomer #4	C[Si](C)(C)OC1C(O)OCC1(O)CO	1538.5	Semi standard non polar	33892256
D-Apiose,2TMS,isomer #1	C[Si](C)(C)OCC1(O[Si](C)(C)C)COC(O)C1O	1554.0	Semi standard non polar	33892256
D-Apiose,2TMS,isomer #2	C[Si](C)(C)OCC1(O)COC(O[Si](C)(C)C)C1O	1532.1	Semi standard non polar	33892256
D-Apiose,2TMS,isomer #3	C[Si](C)(C)OCC1(O)COC(O)C1O[Si](C)(C)C	1535.6	Semi standard non polar	33892256
D-Apiose,2TMS,isomer #4	C[Si](C)(C)OC1OCC(CO)(O[Si](C)(C)C)C1O	1540.4	Semi standard non polar	33892256
D-Apiose,2TMS,isomer #5	C[Si](C)(C)OC1C(O)OCC1(CO)O[Si](C)(C)C	1550.2	Semi standard non polar	33892256
D-Apiose,2TMS,isomer #6	C[Si](C)(C)OC1OCC(O)(CO)C1O[Si](C)(C)C	1553.1	Semi standard non polar	33892256
D-Apiose,3TMS,isomer #1	C[Si](C)(C)OCC1(O[Si](C)(C)C)COC(O[Si](C)(C)C)C1O	1569.9	Semi standard non polar	33892256
D-Apiose,3TMS,isomer #2	C[Si](C)(C)OCC1(O[Si](C)(C)C)COC(O)C1O[Si](C)(C)C	1577.5	Semi standard non polar	33892256
D-Apiose,3TMS,isomer #3	C[Si](C)(C)OCC1(O)COC(O[Si](C)(C)C)C1O[Si](C)(C)C	1573.4	Semi standard non polar	33892256
D-Apiose,3TMS,isomer #4	C[Si](C)(C)OC1OCC(CO)(O[Si](C)(C)C)C1O[Si](C)(C)C	1592.2	Semi standard non polar	33892256
D-Apiose,4TMS,isomer #1	C[Si](C)(C)OCC1(O[Si](C)(C)C)COC(O[Si](C)(C)C)C1O[Si](C)(C)C	1574.9	Semi standard non polar	33892256
D-Apiose,1TBDMS,isomer #1	CC(C)(C)[Si](C)(C)OCC1(O)COC(O)C1O	1747.4	Semi standard non polar	33892256
D-Apiose,1TBDMS,isomer #2	CC(C)(C)[Si](C)(C)OC1(CO)COC(O)C1O	1748.3	Semi standard non polar	33892256
D-Apiose,1TBDMS,isomer #3	CC(C)(C)[Si](C)(C)OC1OCC(O)(CO)C1O	1734.7	Semi standard non polar	33892256
D-Apiose,1TBDMS,isomer #4	CC(C)(C)[Si](C)(C)OC1C(O)OCC1(O)CO	1763.2	Semi standard non polar	33892256
D-Apiose,2TBDMS,isomer #1	CC(C)(C)[Si](C)(C)OCC1(O[Si](C)(C)C(C)(C)C)COC(O)C1O	1982.4	Semi standard non polar	33892256
D-Apiose,2TBDMS,isomer #2	CC(C)(C)[Si](C)(C)OCC1(O)COC(O[Si](C)(C)C(C)(C)C)C1O	1973.7	Semi standard non polar	33892256
D-Apiose,2TBDMS,isomer #3	CC(C)(C)[Si](C)(C)OCC1(O)COC(O)C1O[Si](C)(C)C(C)(C)C	1984.0	Semi standard non polar	33892256
D-Apiose,2TBDMS,isomer #4	CC(C)(C)[Si](C)(C)OC1OCC(CO)(O[Si](C)(C)C(C)(C)C)C1O	1977.4	Semi standard non polar	33892256
D-Apiose,2TBDMS,isomer #5	CC(C)(C)[Si](C)(C)OC1C(O)OCC1(CO)O[Si](C)(C)C(C)(C)C	2003.2	Semi standard non polar	33892256
D-Apiose,2TBDMS,isomer #6	CC(C)(C)[Si](C)(C)OC1OCC(O)(CO)C1O[Si](C)(C)C(C)(C)C	2002.4	Semi standard non polar	33892256
D-Apiose,3TBDMS,isomer #1	CC(C)(C)[Si](C)(C)OCC1(O[Si](C)(C)C(C)(C)C)COC(O[Si](C)(C)C(C)(C)C)C1O	2241.6	Semi standard non polar	33892256
D-Apiose,3TBDMS,isomer #2	CC(C)(C)[Si](C)(C)OCC1(O[Si](C)(C)C(C)(C)C)COC(O)C1O[Si](C)(C)C(C)(C)C	2254.9	Semi standard non polar	33892256
D-Apiose,3TBDMS,isomer #3	CC(C)(C)[Si](C)(C)OCC1(O)COC(O[Si](C)(C)C(C)(C)C)C1O[Si](C)(C)C(C)(C)C	2242.3	Semi standard non polar	33892256
D-Apiose,3TBDMS,isomer #4	CC(C)(C)[Si](C)(C)OC1OCC(CO)(O[Si](C)(C)C(C)(C)C)C1O[Si](C)(C)C(C)(C)C	2258.3	Semi standard non polar	33892256
D-Apiose,4TBDMS,isomer #1	CC(C)(C)[Si](C)(C)OCC1(O[Si](C)(C)C(C)(C)C)COC(O[Si](C)(C)C(C)(C)C)C1O[Si](C)(C)C(C)(C)C	2480.2	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 - D-Apiose GC-MS (Non-derivatized) - 70eV, Positive	splash10-05gr-9200000000-41eb36c1f7c732c251ee	2017-09-01	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - D-Apiose GC-MS (4 TMS) - 70eV, Positive	splash10-009i-8249300000-ed63a047f9dacd956894	2017-10-06	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - D-Apiose GC-MS (Non-derivatized) - 70eV, Positive	Not Available	2021-10-12	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - D-Apiose 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 - D-Apiose 10V, Positive-QTOF	splash10-0ue9-2900000000-cbeb1e4ac91264fe7c7f	2015-04-24	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - D-Apiose 20V, Positive-QTOF	splash10-0f89-1900000000-5d26d59066b5ff0320dd	2015-04-24	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - D-Apiose 40V, Positive-QTOF	splash10-03e9-9200000000-e43d22a696a073723b2e	2015-04-24	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - D-Apiose 10V, Negative-QTOF	splash10-00kb-0900000000-4b28d0278fc3c3366550	2015-04-25	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - D-Apiose 20V, Negative-QTOF	splash10-0gb9-1900000000-22ad9e19804a9a602fbb	2015-04-25	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - D-Apiose 40V, Negative-QTOF	splash10-0kpi-9400000000-681635ab1fbf9800d4fd	2015-04-25	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - D-Apiose 10V, Positive-QTOF	splash10-0159-0900000000-d131a5201c3cd939abd1	2021-09-22	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - D-Apiose 20V, Positive-QTOF	splash10-0kwf-9600000000-ad4330076e58bd616459	2021-09-22	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - D-Apiose 40V, Positive-QTOF	splash10-0006-9000000000-432a9982841e4cb65501	2021-09-22	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - D-Apiose 10V, Negative-QTOF	splash10-0002-2900000000-bc8aca53a0671dd20e89	2021-09-23	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - D-Apiose 20V, Negative-QTOF	splash10-05bf-9400000000-b09e5f2d9074bbecb19b	2021-09-23	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - D-Apiose 40V, Negative-QTOF	splash10-052f-9000000000-91c00adbcf1d9e1031c5	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

Not Available

Biospecimen Locations

Not Available

Tissue Locations

Not Available

Pathways

Not Available

Name	SMPDB/PathBank	KEGG

Normal Concentrations

Not Available

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

KNApSAcK ID

Chemspider ID

KEGG Compound ID

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Apiose

METLIN ID

Not Available

PubChem Compound

4479683

PDB ID

Not Available

ChEBI ID

27672

Food Biomarker Ontology

Not Available

VMH ID

APIO_D

MarkerDB ID

Not Available

Good Scents ID

rw1812401

References

Synthesis Reference

Not Available

Material Safety Data Sheet (MSDS)

Not Available

General References

(). Yannai, Shmuel. (2004) Dictionary of food compounds with CD-ROM: Additives, flavors, and ingredients. Boca Raton: Chapman & Hall/CRC.. .

Showing metabocard for D-Apiose (HMDB0029941)

MOL for HMDB0029941 (D-Apiose)

3D MOL for HMDB0029941 (D-Apiose)

3D SDF for HMDB0029941 (D-Apiose)

3D-SDF for HMDB0029941 (D-Apiose)

PDB for HMDB0029941 (D-Apiose)

3D PDB for HMDB0029941 (D-Apiose)

SMILES for HMDB0029941 (D-Apiose)

INCHI for HMDB0029941 (D-Apiose)

Structure for HMDB0029941 (D-Apiose)

3D Structure for HMDB0029941 (D-Apiose)

Predicted Collision Cross Sections

Predicted Kovats Retention Indices

Underivatized

Derivatized

GC-MS Spectra

MS/MS Spectra

NMR Spectra