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Record Information

Version

5.0

Status

Expected but not Quantified

Creation Date

2012-09-11 17:41:35 UTC

Update Date

2022-03-07 02:52:52 UTC

HMDB ID

HMDB0031201

Secondary Accession Numbers

HMDB31201

Metabolite Identification

Common Name

3-Deoxy-D-arabinitol

Description

3-Deoxy-D-arabinitol, also known as 1,2,4,5-pentanetetrol or pentane-1,2,4,5-tetrol, belongs to the class of organic compounds known as secondary alcohols. Secondary alcohols are compounds containing a secondary alcohol functional group, with the general structure HOC(R)(R') (R,R'=alkyl, aryl). Based on a literature review very few articles have been published on 3-Deoxy-D-arabinitol.

Structure

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

View in JSmol View NMR Assignments View Stereo Labels

Synonyms

Value	Source
1,2,4,5-Pentanetetrol	ChEBI
1,2,4,5-Tetrahydroxypentane	ChEBI
Pentane-1,2,4,5-tetrol	ChEBI
D-Threo-form	HMDB

Chemical Formula

C₅H₁₂O₄

Average Molecular Weight

136.1464

Monoisotopic Molecular Weight

136.073558872

IUPAC Name

pentane-1,2,4,5-tetrol

Traditional Name

pentane-1,2,4,5-tetrol

CAS Registry Number

92691-36-6

SMILES

OCC(O)CC(O)CO

InChI Identifier

InChI=1S/C5H12O4/c6-2-4(8)1-5(9)3-7/h4-9H,1-3H2

InChI Key

VHDMXHLHMMROPO-UHFFFAOYSA-N

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as secondary alcohols. Secondary alcohols are compounds containing a secondary alcohol functional group, with the general structure HOC(R)(R') (R,R'=alkyl, aryl).

Kingdom

Organic compounds

Super Class

Organic oxygen compounds

Class

Organooxygen compounds

Sub Class

Alcohols and polyols

Direct Parent

Secondary alcohols

Alternative Parents

Substituents

Secondary alcohol
Polyol
Hydrocarbon derivative
Primary alcohol
Aliphatic acyclic compound

Molecular Framework

Aliphatic acyclic compounds

External Descriptors

Not Available

Ontology

Physiological effect

Not Available

Disposition

Biological location

Cellular substructure

Extracellular (HMDB: HMDB0031201)
Cytoplasm (HMDB: HMDB0031201)

Route of exposure

Enteral

Ingestion (HMDB: HMDB0031201)

Source

Endogenous

Endogenous (HMDB: HMDB0031201)

Plant

Plant (HMDB: HMDB0031201)

Exogenous

Food

Food (HMDB: HMDB0031201)

Herb and spice

Herbs and Spices (FooDB: FOOD00866)

Process

Not Available

Role

Not Available

Physical Properties

State

Solid

Experimental Molecular Properties

Property	Value	Reference
Melting Point	102 °C	Not Available
Boiling Point	Not Available	Not Available
Water Solubility	Not Available	Not Available
LogP	Not Available	Not Available

Experimental Chromatographic Properties

Not Available

Predicted Molecular Properties

Property	Value	Source
Water Solubility	623 g/L	ALOGPS
logP	-2	ALOGPS
logP	-2.4	ChemAxon
logS	0.66	ALOGPS
pKa (Strongest Acidic)	13.91	ChemAxon
pKa (Strongest Basic)	-2.9	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	4	ChemAxon
Hydrogen Donor Count	4	ChemAxon
Polar Surface Area	80.92 Å²	ChemAxon
Rotatable Bond Count	4	ChemAxon
Refractivity	31.34 m³·mol⁻¹	ChemAxon
Polarizability	13.55 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]+	130.383	31661259
DarkChem	[M-H]-	123.964	31661259
DeepCCS	[M+H]+	129.192	30932474
DeepCCS	[M-H]-	126.377	30932474
DeepCCS	[M-2H]-	163.016	30932474
DeepCCS	[M+Na]+	137.85	30932474
AllCCS	[M+H]+	132.2	32859911
AllCCS	[M+H-H2O]+	128.1	32859911
AllCCS	[M+NH4]+	136.0	32859911
AllCCS	[M+Na]+	137.1	32859911
AllCCS	[M-H]-	125.9	32859911
AllCCS	[M+Na-2H]-	128.6	32859911
AllCCS	[M+HCOO]-	131.5	32859911

Predicted Kovats Retention Indices

Underivatized

Metabolite	SMILES	Kovats RI Value	Column Type	Reference
3-Deoxy-D-arabinitol	OCC(O)CC(O)CO	2773.1	Standard polar	33892256
3-Deoxy-D-arabinitol	OCC(O)CC(O)CO	1456.2	Standard non polar	33892256
3-Deoxy-D-arabinitol	OCC(O)CC(O)CO	1362.1	Semi standard non polar	33892256

Derivatized

Derivative Name / Structure	SMILES	Kovats RI Value	Column Type	Reference
3-Deoxy-D-arabinitol,1TMS,isomer #1	C[Si](C)(C)OCC(O)CC(O)CO	1464.4	Semi standard non polar	33892256
3-Deoxy-D-arabinitol,1TMS,isomer #2	C[Si](C)(C)OC(CO)CC(O)CO	1441.3	Semi standard non polar	33892256
3-Deoxy-D-arabinitol,2TMS,isomer #1	C[Si](C)(C)OCC(CC(O)CO)O[Si](C)(C)C	1553.5	Semi standard non polar	33892256
3-Deoxy-D-arabinitol,2TMS,isomer #2	C[Si](C)(C)OCC(O)CC(CO)O[Si](C)(C)C	1537.4	Semi standard non polar	33892256
3-Deoxy-D-arabinitol,2TMS,isomer #3	C[Si](C)(C)OCC(O)CC(O)CO[Si](C)(C)C	1560.1	Semi standard non polar	33892256
3-Deoxy-D-arabinitol,2TMS,isomer #4	C[Si](C)(C)OC(CO)CC(CO)O[Si](C)(C)C	1523.0	Semi standard non polar	33892256
3-Deoxy-D-arabinitol,3TMS,isomer #1	C[Si](C)(C)OCC(CC(CO)O[Si](C)(C)C)O[Si](C)(C)C	1579.6	Semi standard non polar	33892256
3-Deoxy-D-arabinitol,3TMS,isomer #2	C[Si](C)(C)OCC(O)CC(CO[Si](C)(C)C)O[Si](C)(C)C	1607.5	Semi standard non polar	33892256
3-Deoxy-D-arabinitol,4TMS,isomer #1	C[Si](C)(C)OCC(CC(CO[Si](C)(C)C)O[Si](C)(C)C)O[Si](C)(C)C	1571.9	Semi standard non polar	33892256
3-Deoxy-D-arabinitol,1TBDMS,isomer #1	CC(C)(C)[Si](C)(C)OCC(O)CC(O)CO	1685.5	Semi standard non polar	33892256
3-Deoxy-D-arabinitol,1TBDMS,isomer #2	CC(C)(C)[Si](C)(C)OC(CO)CC(O)CO	1683.6	Semi standard non polar	33892256
3-Deoxy-D-arabinitol,2TBDMS,isomer #1	CC(C)(C)[Si](C)(C)OCC(CC(O)CO)O[Si](C)(C)C(C)(C)C	1991.4	Semi standard non polar	33892256
3-Deoxy-D-arabinitol,2TBDMS,isomer #2	CC(C)(C)[Si](C)(C)OCC(O)CC(CO)O[Si](C)(C)C(C)(C)C	1964.9	Semi standard non polar	33892256
3-Deoxy-D-arabinitol,2TBDMS,isomer #3	CC(C)(C)[Si](C)(C)OCC(O)CC(O)CO[Si](C)(C)C(C)(C)C	1968.8	Semi standard non polar	33892256
3-Deoxy-D-arabinitol,2TBDMS,isomer #4	CC(C)(C)[Si](C)(C)OC(CO)CC(CO)O[Si](C)(C)C(C)(C)C	1955.5	Semi standard non polar	33892256
3-Deoxy-D-arabinitol,3TBDMS,isomer #1	CC(C)(C)[Si](C)(C)OCC(CC(CO)O[Si](C)(C)C(C)(C)C)O[Si](C)(C)C(C)(C)C	2200.9	Semi standard non polar	33892256
3-Deoxy-D-arabinitol,3TBDMS,isomer #2	CC(C)(C)[Si](C)(C)OCC(O)CC(CO[Si](C)(C)C(C)(C)C)O[Si](C)(C)C(C)(C)C	2213.5	Semi standard non polar	33892256
3-Deoxy-D-arabinitol,4TBDMS,isomer #1	CC(C)(C)[Si](C)(C)OCC(CC(CO[Si](C)(C)C(C)(C)C)O[Si](C)(C)C(C)(C)C)O[Si](C)(C)C(C)(C)C	2429.1	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 - 3-Deoxy-D-arabinitol GC-MS (Non-derivatized) - 70eV, Positive	splash10-03di-9100000000-928bfa7c5ce9980aebaa	2017-09-01	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - 3-Deoxy-D-arabinitol GC-MS (4 TMS) - 70eV, Positive	splash10-0ab9-9156300000-d764773252e6d8a2bfe9	2017-10-06	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - 3-Deoxy-D-arabinitol GC-MS (Non-derivatized) - 70eV, Positive	Not Available	2021-10-12	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - 3-Deoxy-D-arabinitol 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 - 3-Deoxy-D-arabinitol 10V, Positive-QTOF	splash10-000i-1900000000-a67e7b5d5675757b7157	2015-04-24	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 3-Deoxy-D-arabinitol 20V, Positive-QTOF	splash10-0wp0-7900000000-45d77e13624867d89463	2015-04-24	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 3-Deoxy-D-arabinitol 40V, Positive-QTOF	splash10-0a4i-9200000000-36c46cdb44e02247a93d	2015-04-24	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 3-Deoxy-D-arabinitol 10V, Negative-QTOF	splash10-000i-3900000000-39821d751f8cb7e7ea26	2015-04-25	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 3-Deoxy-D-arabinitol 20V, Negative-QTOF	splash10-0a4r-9500000000-e7458a28cff265dfeae2	2015-04-25	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 3-Deoxy-D-arabinitol 40V, Negative-QTOF	splash10-0a4l-9000000000-919bfcfb099ab021983c	2015-04-25	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 3-Deoxy-D-arabinitol 10V, Negative-QTOF	splash10-0ap1-7900000000-e78140a9f64a9df0e88a	2021-09-22	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 3-Deoxy-D-arabinitol 20V, Negative-QTOF	splash10-0a4l-9000000000-9408e30e7ba0a9ff7df0	2021-09-22	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 3-Deoxy-D-arabinitol 40V, Negative-QTOF	splash10-0a4l-9000000000-e158a7b6b031088ab30d	2021-09-22	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 3-Deoxy-D-arabinitol 10V, Positive-QTOF	splash10-0uy0-1900000000-add5c4e07fa0684cab2d	2021-09-22	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 3-Deoxy-D-arabinitol 20V, Positive-QTOF	splash10-0pdi-9400000000-ea111471a120a8791014	2021-09-22	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 3-Deoxy-D-arabinitol 40V, Positive-QTOF	splash10-0pbd-9200000000-28fbb2b9e6412e47843e	2021-09-22	Wishart Lab	View Spectrum

NMR Spectra

Spectrum Type	Description	Deposition Date	Source	View
Predicted 1D NMR	¹³C NMR Spectrum (1D, 100 MHz, D₂O, predicted)	2021-09-16	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 100 MHz, D₂O, predicted)	2021-09-16	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 200 MHz, D₂O, predicted)	2021-09-16	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 200 MHz, D₂O, predicted)	2021-09-16	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 300 MHz, D₂O, predicted)	2021-09-16	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 300 MHz, D₂O, predicted)	2021-09-16	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 400 MHz, D₂O, predicted)	2021-09-16	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 400 MHz, D₂O, predicted)	2021-09-16	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 500 MHz, D₂O, predicted)	2021-09-16	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 500 MHz, D₂O, predicted)	2021-09-16	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 600 MHz, D₂O, predicted)	2021-09-16	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 600 MHz, D₂O, predicted)	2021-09-16	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 700 MHz, D₂O, predicted)	2021-09-16	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 700 MHz, D₂O, predicted)	2021-09-16	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 800 MHz, D₂O, predicted)	2021-09-16	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 800 MHz, D₂O, predicted)	2021-09-16	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 900 MHz, D₂O, predicted)	2021-09-16	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 900 MHz, D₂O, predicted)	2021-09-16	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 1000 MHz, D₂O, predicted)	2021-09-16	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 1000 MHz, D₂O, predicted)	2021-09-16	Wishart Lab	View Spectrum

Biological Properties

Cellular Locations

Cytoplasm
Extracellular

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

FDB003222

KNApSAcK ID

C00055167

Chemspider ID

10619290

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

14865845

PDB ID

Not Available

ChEBI ID

111506

Food Biomarker Ontology

Not Available

VMH ID

Not Available

MarkerDB ID

Not Available

Good Scents ID

Not Available

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 3-Deoxy-D-arabinitol (HMDB0031201)

MOL for HMDB0031201 (3-Deoxy-D-arabinitol)

3D MOL for HMDB0031201 (3-Deoxy-D-arabinitol)

3D SDF for HMDB0031201 (3-Deoxy-D-arabinitol)

3D-SDF for HMDB0031201 (3-Deoxy-D-arabinitol)

PDB for HMDB0031201 (3-Deoxy-D-arabinitol)

3D PDB for HMDB0031201 (3-Deoxy-D-arabinitol)

SMILES for HMDB0031201 (3-Deoxy-D-arabinitol)

INCHI for HMDB0031201 (3-Deoxy-D-arabinitol)

Structure for HMDB0031201 (3-Deoxy-D-arabinitol)

3D Structure for HMDB0031201 (3-Deoxy-D-arabinitol)

Predicted Collision Cross Sections

Predicted Kovats Retention Indices

Underivatized

Derivatized

GC-MS Spectra

MS/MS Spectra

NMR Spectra