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Record Information

Version

5.0

Status

Detected but not Quantified

Creation Date

2021-09-10 22:56:52 UTC

Update Date

2021-09-26 22:54:37 UTC

HMDB ID

HMDB0245900

Secondary Accession Numbers

None

Metabolite Identification

Common Name

3-Hydroxymethyl xylitol

Description

3-Hydroxymethyl xylitol belongs to the class of organic compounds known as sugar alcohols. These are hydrogenated forms of carbohydrate in which the carbonyl group (aldehyde or ketone, reducing sugar) has been reduced to a primary or secondary hydroxyl group. Based on a literature review a small amount of articles have been published on 3-Hydroxymethyl xylitol. This compound has been identified in human blood as reported by (PMID: 31557052 ). 3-hydroxymethyl xylitol is not a naturally occurring metabolite and is only found in those individuals exposed to this compound or its derivatives. Technically 3-Hydroxymethyl xylitol is part of the human exposome. The exposome can be defined as the collection of all the exposures of an individual in a lifetime and how those exposures relate to health. An individual's exposure begins before birth and includes insults from environmental and occupational sources.

Structure

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

HEADER    PROTEIN                                 11-SEP-21   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   11-SEP-21         0                                  
HETATM    1  C   UNK     0       1.540   0.000   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       2.310  -1.334   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       3.850  -1.334   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       3.850  -2.874   0.000  0.00  0.00           C+0
HETATM    5  O   UNK     0       5.184  -3.644   0.000  0.00  0.00           O+0
HETATM    6  C   UNK     0       5.390  -1.334   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       6.160  -2.667   0.000  0.00  0.00           C+0
HETATM    8  O   UNK     0       7.700  -2.667   0.000  0.00  0.00           O+0
HETATM    9  O   UNK     0       6.160  -0.000   0.000  0.00  0.00           O+0
HETATM   10  O   UNK     0       3.850   0.206   0.000  0.00  0.00           O+0
HETATM   11  O   UNK     0       1.540  -2.667   0.000  0.00  0.00           O+0
HETATM   12  O   UNK     0       0.000   0.000   0.000  0.00  0.00           O+0
CONECT    1    2   12                                                       
CONECT    2    1    3   11                                                  
CONECT    3    2    4    6   10                                             
CONECT    4    3    5                                                       
CONECT    5    4                                                            
CONECT    6    3    7    9                                                  
CONECT    7    6    8                                                       
CONECT    8    7                                                            
CONECT    9    6                                                            
CONECT   10    3                                                            
CONECT   11    2                                                            
CONECT   12    1                                                            
MASTER        0    0    0    0    0    0    0    0   12    0   22    0
END

View in JSmol View NMR Assignments View Stereo Labels

Synonyms

Not Available

Chemical Formula

C₆H₁₄O₆

Average Molecular Weight

182.172

Monoisotopic Molecular Weight

182.079038171

IUPAC Name

3-(hydroxymethyl)pentane-1,2,3,4,5-pentol

Traditional Name

3-(hydroxymethyl)pentane-1,2,3,4,5-pentol

CAS Registry Number

Not Available

SMILES

OCC(O)C(O)(CO)C(O)CO

InChI Identifier

InChI=1S/C6H14O6/c7-1-4(10)6(12,3-9)5(11)2-8/h4-5,7-12H,1-3H2

InChI Key

VIQLKPMMHCXYIW-UHFFFAOYSA-N

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as sugar alcohols. These are hydrogenated forms of carbohydrate in which the carbonyl group (aldehyde or ketone, reducing sugar) has been reduced to a primary or secondary hydroxyl group.

Kingdom

Organic compounds

Super Class

Organic oxygen compounds

Class

Organooxygen compounds

Sub Class

Carbohydrates and carbohydrate conjugates

Direct Parent

Sugar alcohols

Alternative Parents

Substituents

Sugar alcohol
Tertiary alcohol
Secondary alcohol
1,2-diol
Polyol
Hydrocarbon derivative
Primary alcohol
Alcohol
Aliphatic acyclic compound

Molecular Framework

Aliphatic acyclic compounds

External Descriptors

Not Available

Ontology

Physiological effect

Not Available

Disposition

Biological location

Non-excretory biofluid

Biofluid or Excreta

Blood (PMID: 31557052)

Source

Exogenous

Exogenous (PMID: 31557052)

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	Not Available	Not Available
LogP	Not Available	Not Available

Experimental Chromatographic Properties

Not Available

Predicted Molecular Properties

Property	Value	Source
logP	-2.5	ALOGPS
logP	-3.9	ChemAxon
logS	0.59	ALOGPS
pKa (Strongest Acidic)	11.98	ChemAxon
pKa (Strongest Basic)	-3	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	6	ChemAxon
Hydrogen Donor Count	6	ChemAxon
Polar Surface Area	121.38 Å²	ChemAxon
Rotatable Bond Count	5	ChemAxon
Refractivity	38.62 m³·mol⁻¹	ChemAxon
Polarizability	16.84 Å³	ChemAxon
Number of Rings	0	ChemAxon
Bioavailability	Yes	ChemAxon
Rule of Five	No	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
DeepCCS	[M+H]+	134.057	30932474
DeepCCS	[M-H]-	130.665	30932474
DeepCCS	[M-2H]-	167.924	30932474
DeepCCS	[M+Na]+	143.378	30932474

Predicted Kovats Retention Indices

Underivatized

Metabolite	SMILES	Kovats RI Value	Column Type	Reference
3-Hydroxymethyl xylitol	OCC(O)C(O)(CO)C(O)CO	3217.3	Standard polar	33892256
3-Hydroxymethyl xylitol	OCC(O)C(O)(CO)C(O)CO	2005.1	Standard non polar	33892256
3-Hydroxymethyl xylitol	OCC(O)C(O)(CO)C(O)CO	1761.5	Semi standard non polar	33892256

Derivatized

Derivative Name / Structure	SMILES	Kovats RI Value	Column Type	Reference
3-Hydroxymethyl xylitol,5TBDMS,isomer #1	CC(C)(C)[Si](C)(C)OCC(O[Si](C)(C)C(C)(C)C)C(CO[Si](C)(C)C(C)(C)C)(O[Si](C)(C)C(C)(C)C)C(CO)O[Si](C)(C)C(C)(C)C	2949.2	Semi standard non polar	33892256
3-Hydroxymethyl xylitol,5TBDMS,isomer #1	CC(C)(C)[Si](C)(C)OCC(O[Si](C)(C)C(C)(C)C)C(CO[Si](C)(C)C(C)(C)C)(O[Si](C)(C)C(C)(C)C)C(CO)O[Si](C)(C)C(C)(C)C	2786.8	Standard non polar	33892256
3-Hydroxymethyl xylitol,5TBDMS,isomer #1	CC(C)(C)[Si](C)(C)OCC(O[Si](C)(C)C(C)(C)C)C(CO[Si](C)(C)C(C)(C)C)(O[Si](C)(C)C(C)(C)C)C(CO)O[Si](C)(C)C(C)(C)C	2434.8	Standard polar	33892256

Spectra

GC-MS Spectra

Spectrum Type	Description	Splash Key	Deposition Date	Source	View
Predicted GC-MS	Predicted GC-MS Spectrum - 3-Hydroxymethyl xylitol GC-MS (Non-derivatized) - 70eV, Positive	splash10-0229-6900000000-85ac7b6f79b9f97ceecb	2021-09-24	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - 3-Hydroxymethyl xylitol GC-MS (Non-derivatized) - 70eV, Positive	Not Available	2021-10-12	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - 3-Hydroxymethyl xylitol GC-MS (TMS_1_1) - 70eV, Positive	Not Available	2021-11-03	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - 3-Hydroxymethyl xylitol GC-MS (TMS_1_2) - 70eV, Positive	Not Available	2021-11-03	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - 3-Hydroxymethyl xylitol GC-MS (TMS_1_3) - 70eV, Positive	Not Available	2021-11-03	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - 3-Hydroxymethyl xylitol GC-MS (TMS_1_4) - 70eV, Positive	Not Available	2021-11-03	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - 3-Hydroxymethyl xylitol GC-MS (TMS_2_1) - 70eV, Positive	Not Available	2021-11-03	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - 3-Hydroxymethyl xylitol GC-MS (TMS_2_2) - 70eV, Positive	Not Available	2021-11-03	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - 3-Hydroxymethyl xylitol GC-MS (TMS_2_3) - 70eV, Positive	Not Available	2021-11-03	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - 3-Hydroxymethyl xylitol GC-MS (TMS_2_4) - 70eV, Positive	Not Available	2021-11-03	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - 3-Hydroxymethyl xylitol GC-MS (TMS_2_5) - 70eV, Positive	Not Available	2021-11-03	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - 3-Hydroxymethyl xylitol GC-MS (TMS_2_6) - 70eV, Positive	Not Available	2021-11-03	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - 3-Hydroxymethyl xylitol GC-MS (TMS_2_7) - 70eV, Positive	Not Available	2021-11-03	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - 3-Hydroxymethyl xylitol GC-MS (TMS_2_8) - 70eV, Positive	Not Available	2021-11-03	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - 3-Hydroxymethyl xylitol GC-MS (TMS_2_9) - 70eV, Positive	Not Available	2021-11-03	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - 3-Hydroxymethyl xylitol GC-MS (TMS_3_1) - 70eV, Positive	Not Available	2021-11-03	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - 3-Hydroxymethyl xylitol GC-MS (TMS_3_2) - 70eV, Positive	Not Available	2021-11-03	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - 3-Hydroxymethyl xylitol GC-MS (TMS_3_3) - 70eV, Positive	Not Available	2021-11-03	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - 3-Hydroxymethyl xylitol GC-MS (TMS_3_4) - 70eV, Positive	Not Available	2021-11-03	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - 3-Hydroxymethyl xylitol GC-MS (TMS_3_5) - 70eV, Positive	Not Available	2021-11-03	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - 3-Hydroxymethyl xylitol GC-MS (TMS_3_6) - 70eV, Positive	Not Available	2021-11-03	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - 3-Hydroxymethyl xylitol GC-MS (TMS_3_7) - 70eV, Positive	Not Available	2021-11-03	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - 3-Hydroxymethyl xylitol GC-MS (TMS_3_8) - 70eV, Positive	Not Available	2021-11-03	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - 3-Hydroxymethyl xylitol GC-MS (TMS_3_9) - 70eV, Positive	Not Available	2021-11-03	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - 3-Hydroxymethyl xylitol GC-MS (TMS_3_10) - 70eV, Positive	Not Available	2021-11-03	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-Hydroxymethyl xylitol 10V, Positive-QTOF	splash10-001i-0900000000-b37e00b3a5f272511d4d	2021-10-12	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 3-Hydroxymethyl xylitol 20V, Positive-QTOF	splash10-0ik9-5900000000-bbda291fb9663e3d898c	2021-10-12	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 3-Hydroxymethyl xylitol 40V, Positive-QTOF	splash10-08fu-9300000000-062f2c54c4d3aa51e263	2021-10-12	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 3-Hydroxymethyl xylitol 10V, Negative-QTOF	splash10-001i-2900000000-07ebca3a2011e641bd2e	2021-10-12	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 3-Hydroxymethyl xylitol 20V, Negative-QTOF	splash10-0a4i-9300000000-3d217032de4e243f85f5	2021-10-12	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 3-Hydroxymethyl xylitol 40V, Negative-QTOF	splash10-0a4l-9000000000-3e33278dac00ab6ab2f8	2021-10-12	Wishart Lab	View Spectrum

NMR Spectra

Spectrum Type	Description	Deposition Date	Source	View
Predicted 1D NMR	¹³C NMR Spectrum (1D, 100 MHz, D₂O, predicted)	2021-10-13	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 100 MHz, D₂O, predicted)	2021-10-13	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 1000 MHz, D₂O, predicted)	2021-10-13	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 1000 MHz, D₂O, predicted)	2021-10-13	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 200 MHz, D₂O, predicted)	2021-10-13	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 200 MHz, D₂O, predicted)	2021-10-13	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 300 MHz, D₂O, predicted)	2021-10-13	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 300 MHz, D₂O, predicted)	2021-10-13	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 400 MHz, D₂O, predicted)	2021-10-13	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 400 MHz, D₂O, predicted)	2021-10-13	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 500 MHz, D₂O, predicted)	2021-10-13	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 500 MHz, D₂O, predicted)	2021-10-13	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 600 MHz, D₂O, predicted)	2021-10-13	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 600 MHz, D₂O, predicted)	2021-10-13	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 700 MHz, D₂O, predicted)	2021-10-13	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 700 MHz, D₂O, predicted)	2021-10-13	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 800 MHz, D₂O, predicted)	2021-10-13	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 800 MHz, D₂O, predicted)	2021-10-13	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 900 MHz, D₂O, predicted)	2021-10-13	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 900 MHz, D₂O, predicted)	2021-10-13	Wishart Lab	View Spectrum

Biological Properties

Cellular Locations

Not Available

Biospecimen Locations

Blood

Tissue Locations

Not Available

Pathways

Not Available

Name	SMPDB/PathBank	KEGG

Normal Concentrations

Biospecimen	Status	Value	Age	Sex	Condition	Reference	Details
Blood	Detected but not Quantified	Not Quantified	Not Specified	Not Specified	Normal	31557052	details

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

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

25014560

PDB ID

Not Available

ChEBI ID

Not Available

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

Barupal DK, Fiehn O: Generating the Blood Exposome Database Using a Comprehensive Text Mining and Database Fusion Approach. Environ Health Perspect. 2019 Sep;127(9):97008. doi: 10.1289/EHP4713. Epub 2019 Sep 26. [PubMed:31557052 ]

Showing metabocard for 3-Hydroxymethyl xylitol (HMDB0245900)

MOL for HMDB0245900 (3-Hydroxymethyl xylitol)

3D MOL for HMDB0245900 (3-Hydroxymethyl xylitol)

3D SDF for HMDB0245900 (3-Hydroxymethyl xylitol)

3D-SDF for HMDB0245900 (3-Hydroxymethyl xylitol)

PDB for HMDB0245900 (3-Hydroxymethyl xylitol)

3D PDB for HMDB0245900 (3-Hydroxymethyl xylitol)

SMILES for HMDB0245900 (3-Hydroxymethyl xylitol)

INCHI for HMDB0245900 (3-Hydroxymethyl xylitol)

Structure for HMDB0245900 (3-Hydroxymethyl xylitol)

3D Structure for HMDB0245900 (3-Hydroxymethyl xylitol)

Predicted Collision Cross Sections

Predicted Kovats Retention Indices

Underivatized

Derivatized

GC-MS Spectra

MS/MS Spectra

NMR Spectra