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Showing metabocard for Xylitol (HMDB0242149)

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Record Information
Version5.0
StatusDetected but not Quantified
Creation Date2021-08-27 05:04:07 UTC
Update Date2022-09-22 18:34:34 UTC
HMDB IDHMDB0242149
Secondary Accession NumbersNone
Metabolite Identification
Common NameXylitol
DescriptionXylitol, also known as xylisorb or meso-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. Xylitol exists in all living species, ranging from bacteria to plants to humans. Xylitol has been detected, but not quantified in, several different foods, such as lemon verbenas (Aloysia triphylla), root vegetables, lowbush blueberries (Vaccinium angustifolium), mangos (Mangifera indica), and rosemaries (Rosmarinus officinalis). This could make xylitol a potential biomarker for the consumption of these foods. Xylitol is a primary metabolite. Primary metabolites are metabolically or physiologically essential metabolites. They are directly involved in an organism’s growth, development or reproduction. Based on a literature review a significant number of articles have been published on Xylitol.
Structure
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MOL3D MOLSDF3D SDFPDB3D PDBSMILESInChI

MOL for HMDB0242149 (Xylitol)

  Mrv1652302102020382D          

 10  9  0  0  1  0            999 V2000
    2.4750   -1.4289    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.1895   -1.8414    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    3.9039   -1.4289    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.6184   -1.8414    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    5.3329   -1.4289    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.0474   -1.8414    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.6184   -2.6664    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.9039   -0.6039    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.1895   -2.6664    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.7605   -1.8414    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  2  1  1  0  0  0  0
  2  3  1  0  0  0  0
  4  3  1  0  0  0  0
  4  5  1  0  0  0  0
  5  6  1  0  0  0  0
  4  7  1  6  0  0  0
  3  8  1  0  0  0  0
  2  9  1  6  0  0  0
  1 10  1  0  0  0  0
M  END
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3D MOL for HMDB0242149 (Xylitol)

HMDB0242149
     RDKit          3D
Xylitol
 22 21  0  0  0  0  0  0  0  0999 V2000
   -2.7150    1.6625   -0.8839 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5940    1.3197   -0.0781 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2193   -0.0899   -0.4867 C   0  0  2  0  0  0  0  0  0  0  0  0
   -2.4394   -0.8110   -0.1975 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1761   -0.7482    0.3495 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2756   -2.1422   -0.0539 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.2603   -0.4588    0.0063 C   0  0  2  0  0  0  0  0  0  0  0  0
    1.9844   -1.4191    0.8009 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.8039    0.8516    0.4328 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.2211    0.8878    0.2457 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5504    2.5045   -1.3699 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9870    1.3558    0.9597 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8248    2.0718   -0.1661 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0148   -0.2021   -1.5401 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3625   -1.7312   -0.5279 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4042   -0.7575    1.4120 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2133   -2.0623   -1.0564 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.4576   -0.7369   -1.0248 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.4825   -2.2607    0.8333 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.3780    1.6483   -0.2489 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.6264    1.1653    1.4485 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.5623   -0.0474    0.2053 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  1  0
  3  4  1  0
  3  5  1  0
  5  6  1  0
  5  7  1  0
  7  8  1  0
  7  9  1  0
  9 10  1  0
  1 11  1  0
  2 12  1  0
  2 13  1  0
  3 14  1  6
  4 15  1  0
  5 16  1  0
  6 17  1  0
  7 18  1  6
  8 19  1  0
  9 20  1  0
  9 21  1  0
 10 22  1  0
M  END
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3D SDF for HMDB0242149 (Xylitol)

  Mrv1652302102020382D          

 10  9  0  0  1  0            999 V2000
    2.4750   -1.4289    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.1895   -1.8414    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    3.9039   -1.4289    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.6184   -1.8414    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    5.3329   -1.4289    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.0474   -1.8414    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.6184   -2.6664    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.9039   -0.6039    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.1895   -2.6664    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.7605   -1.8414    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  2  1  1  0  0  0  0
  2  3  1  0  0  0  0
  4  3  1  0  0  0  0
  4  5  1  0  0  0  0
  5  6  1  0  0  0  0
  4  7  1  6  0  0  0
  3  8  1  0  0  0  0
  2  9  1  6  0  0  0
  1 10  1  0  0  0  0
M  END
> <DATABASE_ID>
HMDB0242149

> <DATABASE_NAME>
hmdb

> <SMILES>
OC[C@H](O)C(O)[C@H](O)CO

> <INCHI_IDENTIFIER>
InChI=1S/C5H12O5/c6-1-3(8)5(10)4(9)2-7/h3-10H,1-2H2/t3-,4+,5?

> <INCHI_KEY>
HEBKCHPVOIAQTA-NGQZWQHPSA-N

> <FORMULA>
C5H12O5

> <MOLECULAR_WEIGHT>
152.1458

> <EXACT_MASS>
152.068473494

> <JCHEM_ACCEPTOR_COUNT>
5

> <JCHEM_ATOM_COUNT>
22

> <JCHEM_AVERAGE_POLARIZABILITY>
14.478298747170115

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
5

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(2R,4S)-pentane-1,2,3,4,5-pentol

> <ALOGPS_LOGP>
-2.53

> <JCHEM_LOGP>
-3.099683906666666

> <ALOGPS_LOGS>
0.64

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
0

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
13.742189661908146

> <JCHEM_PKA_STRONGEST_ACIDIC>
12.760078510562963

> <JCHEM_PKA_STRONGEST_BASIC>
-2.9742034412471314

> <JCHEM_POLAR_SURFACE_AREA>
101.15

> <JCHEM_REFRACTIVITY>
32.4411

> <JCHEM_ROTATABLE_BOND_COUNT>
4

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
6.64e+02 g/l

> <JCHEM_TRADITIONAL_IUPAC>
(2R,4S)-pentane-1,2,3,4,5-pentol

> <JCHEM_VEBER_RULE>
0

$$$$
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3D-SDF for HMDB0242149 (Xylitol)

HMDB0242149
     RDKit          3D
Xylitol
 22 21  0  0  0  0  0  0  0  0999 V2000
   -2.7150    1.6625   -0.8839 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5940    1.3197   -0.0781 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2193   -0.0899   -0.4867 C   0  0  2  0  0  0  0  0  0  0  0  0
   -2.4394   -0.8110   -0.1975 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1761   -0.7482    0.3495 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2756   -2.1422   -0.0539 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.2603   -0.4588    0.0063 C   0  0  2  0  0  0  0  0  0  0  0  0
    1.9844   -1.4191    0.8009 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.8039    0.8516    0.4328 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.2211    0.8878    0.2457 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5504    2.5045   -1.3699 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9870    1.3558    0.9597 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8248    2.0718   -0.1661 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0148   -0.2021   -1.5401 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3625   -1.7312   -0.5279 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4042   -0.7575    1.4120 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2133   -2.0623   -1.0564 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.4576   -0.7369   -1.0248 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.4825   -2.2607    0.8333 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.3780    1.6483   -0.2489 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.6264    1.1653    1.4485 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.5623   -0.0474    0.2053 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  1  0
  3  4  1  0
  3  5  1  0
  5  6  1  0
  5  7  1  0
  7  8  1  0
  7  9  1  0
  9 10  1  0
  1 11  1  0
  2 12  1  0
  2 13  1  0
  3 14  1  6
  4 15  1  0
  5 16  1  0
  6 17  1  0
  7 18  1  6
  8 19  1  0
  9 20  1  0
  9 21  1  0
 10 22  1  0
M  END
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PDB for HMDB0242149 (Xylitol)

HEADER    PROTEIN                                 10-FEB-20   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   10-FEB-20         0                                  
HETATM    1  C   UNK     0       4.620  -2.667   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       5.954  -3.437   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       7.287  -2.667   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       8.621  -3.437   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       9.955  -2.667   0.000  0.00  0.00           C+0
HETATM    6  O   UNK     0      11.288  -3.437   0.000  0.00  0.00           O+0
HETATM    7  O   UNK     0       8.621  -4.977   0.000  0.00  0.00           O+0
HETATM    8  O   UNK     0       7.287  -1.127   0.000  0.00  0.00           O+0
HETATM    9  O   UNK     0       5.954  -4.977   0.000  0.00  0.00           O+0
HETATM   10  O   UNK     0       3.286  -3.437   0.000  0.00  0.00           O+0
CONECT    1    2   10                                                       
CONECT    2    1    3    9                                                  
CONECT    3    2    4    8                                                  
CONECT    4    3    5    7                                                  
CONECT    5    4    6                                                       
CONECT    6    5                                                            
CONECT    7    4                                                            
CONECT    8    3                                                            
CONECT    9    2                                                            
CONECT   10    1                                                            
MASTER        0    0    0    0    0    0    0    0   10    0   18    0
END
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3D PDB for HMDB0242149 (Xylitol)

COMPND    HMDB0242149
HETATM    1  O1  UNL     1      -2.715   1.662  -0.884  1.00  0.00           O  
HETATM    2  C1  UNL     1      -1.594   1.320  -0.078  1.00  0.00           C  
HETATM    3  C2  UNL     1      -1.219  -0.090  -0.487  1.00  0.00           C  
HETATM    4  O2  UNL     1      -2.439  -0.811  -0.197  1.00  0.00           O  
HETATM    5  C3  UNL     1      -0.176  -0.748   0.350  1.00  0.00           C  
HETATM    6  O3  UNL     1      -0.276  -2.142  -0.054  1.00  0.00           O  
HETATM    7  C4  UNL     1       1.260  -0.459   0.006  1.00  0.00           C  
HETATM    8  O4  UNL     1       1.984  -1.419   0.801  1.00  0.00           O  
HETATM    9  C5  UNL     1       1.804   0.852   0.433  1.00  0.00           C  
HETATM   10  O5  UNL     1       3.221   0.888   0.246  1.00  0.00           O  
HETATM   11  H1  UNL     1      -2.550   2.505  -1.370  1.00  0.00           H  
HETATM   12  H2  UNL     1      -1.987   1.356   0.960  1.00  0.00           H  
HETATM   13  H3  UNL     1      -0.825   2.072  -0.166  1.00  0.00           H  
HETATM   14  H4  UNL     1      -1.015  -0.202  -1.540  1.00  0.00           H  
HETATM   15  H5  UNL     1      -2.362  -1.731  -0.528  1.00  0.00           H  
HETATM   16  H6  UNL     1      -0.404  -0.758   1.412  1.00  0.00           H  
HETATM   17  H7  UNL     1      -0.213  -2.062  -1.056  1.00  0.00           H  
HETATM   18  H8  UNL     1       1.458  -0.737  -1.025  1.00  0.00           H  
HETATM   19  H9  UNL     1       1.483  -2.261   0.833  1.00  0.00           H  
HETATM   20  H10 UNL     1       1.378   1.648  -0.249  1.00  0.00           H  
HETATM   21  H11 UNL     1       1.626   1.165   1.448  1.00  0.00           H  
HETATM   22  H12 UNL     1       3.562  -0.047   0.205  1.00  0.00           H  
CONECT    1    2   11
CONECT    2    3   12   13
CONECT    3    4    5   14
CONECT    4   15
CONECT    5    6    7   16
CONECT    6   17
CONECT    7    8    9   18
CONECT    8   19
CONECT    9   10   20   21
CONECT   10   22
END
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SMILES for HMDB0242149 (Xylitol)

OC[C@H](O)C(O)[C@H](O)CO
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INCHI for HMDB0242149 (Xylitol)

InChI=1S/C5H12O5/c6-1-3(8)5(10)4(9)2-7/h3-10H,1-2H2/t3-,4+,5?
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View in JSmolView NMR AssignmentsView Stereo Labels
Synonyms
Chemical FormulaC5H12O5
Average Molecular Weight152.1458
Monoisotopic Molecular Weight152.068473494
IUPAC Name(2R,4S)-pentane-1,2,3,4,5-pentol
Traditional Name(2R,4S)-pentane-1,2,3,4,5-pentol
CAS Registry NumberNot Available
SMILES
OC[C@H](O)C(O)[C@H](O)CO
InChI Identifier
InChI=1S/C5H12O5/c6-1-3(8)5(10)4(9)2-7/h3-10H,1-2H2/t3-,4+,5?
InChI KeyHEBKCHPVOIAQTA-NGQZWQHPSA-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.
KingdomOrganic compounds
Super ClassOrganic oxygen compounds
ClassOrganooxygen compounds
Sub ClassCarbohydrates and carbohydrate conjugates
Direct ParentSugar alcohols
Alternative Parents
Substituents
  • Sugar alcohol
  • Monosaccharide
  • Secondary alcohol
  • Polyol
  • Hydrocarbon derivative
  • Primary alcohol
  • Alcohol
  • Aliphatic acyclic compound
Molecular FrameworkAliphatic acyclic compounds
External DescriptorsNot Available
Ontology
Physiological effect
Organoleptic effect
Disposition
Source
ProcessNot Available
Role
Industrial applicationBiological role
Physical Properties
StateNot Available
Experimental Molecular Properties
PropertyValueReference
Melting PointNot AvailableNot Available
Boiling PointNot AvailableNot Available
Water SolubilityNot AvailableNot Available
LogPNot AvailableNot Available
Experimental Chromatographic Properties

Experimental Collision Cross Sections

Adduct TypeData SourceCCS Value (Å2)Reference
[M-H]-Not Available125.2http://allccs.zhulab.cn/database/detail?ID=AllCCS00000392
Predicted Molecular Properties
Predicted Chromatographic Properties
Spectra
Biological Properties
Cellular LocationsNot Available
Biospecimen Locations
  • Blood
  • Urine
Tissue LocationsNot Available
Pathways
Normal Concentrations
Not Available
Abnormal Concentrations
BiospecimenStatusValueAgeSexConditionReferenceDetails
BloodExpected but not QuantifiedNot QuantifiedNot SpecifiedNot SpecifiedCancer patients undergoing total body irradiation details
UrineDetected but not QuantifiedNot QuantifiedNot SpecifiedNot SpecifiedCancer patients undergoing total body irradiation details
Associated Disorders and Diseases
Disease ReferencesNone
Associated OMIM IDsNone
DrugBank IDNot Available
Phenol Explorer Compound IDNot Available
FooDB IDFDB030801
KNApSAcK IDC00052270
Chemspider ID21391692
KEGG Compound IDC00379
BioCyc IDCPD-496
BiGG ID34810
Wikipedia LinkXylitol
METLIN IDNot Available
PubChem Compound6912
PDB IDNot Available
ChEBI ID1305691
Food Biomarker OntologyNot Available
VMH IDXYLT
MarkerDB IDNot Available
Good Scents IDNot Available
References
Synthesis ReferenceNot Available
Material Safety Data Sheet (MSDS)Not Available
General References
  1. Kong SW, Hernandez-Ferrer C: Assessment of coverage for endogenous metabolites and exogenous chemical compounds using an untargeted metabolomics platform. Pac Symp Biocomput. 2020;25:587-598. [PubMed:31797630 ]

Enzymes

Enzyme Details
1. L-xylulose reductase
General function:
Involved in oxidoreductase activity
Specific function:
Catalyzes the NADPH-dependent reduction of several pentoses, tetroses, trioses, alpha-dicarbonyl compounds and L-xylulose. Participates in the uronate cycle of glucose metabolism. May play a role in the water absorption and cellular osmoregulation in the proximal renal tubules by producing xylitol, an osmolyte, thereby preventing osmolytic stress from occurring in the renal tubules.
Gene Name:
DCXR
Uniprot ID:
Q7Z4W1
Molecular weight:
25742.665
Enzyme Details
2. Sorbitol dehydrogenase
General function:
Involved in zinc ion binding
Specific function:
Converts sorbitol to fructose. Part of the polyol pathway that plays an important role in sperm physiology. May play a role in the sperm motility by providing an energetic source for sperm (By similarity).
Gene Name:
SORD
Uniprot ID:
Q00796
Molecular weight:
38324.25