Jump To Section:

Identification Taxonomy Ontology Physical properties Spectra Biological properties Concentrations Links References XML

Record Information

Version

5.0

Status

Detected but not Quantified

Creation Date

2021-09-11 07:55:01 UTC

Update Date

2021-09-26 23:02:28 UTC

HMDB ID

HMDB0250808

Secondary Accession Numbers

None

Metabolite Identification

Common Name

D-Xylose, 4-O-beta-D-xylopyranosyl-

Description

2,3,5-trihydroxy-4-[(3,4,5-trihydroxyoxan-2-yl)oxy]pentanal belongs to the class of organic compounds known as o-glycosyl compounds. These are glycoside in which a sugar group is bonded through one carbon to another group via a O-glycosidic bond. Based on a literature review very few articles have been published on 2,3,5-trihydroxy-4-[(3,4,5-trihydroxyoxan-2-yl)oxy]pentanal. This compound has been identified in human blood as reported by (PMID: 31557052 ). D-xylose, 4-o-beta-d-xylopyranosyl- is not a naturally occurring metabolite and is only found in those individuals exposed to this compound or its derivatives. Technically D-Xylose, 4-O-beta-D-xylopyranosyl- 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

HMDB0250808
     RDKit          3D
D-Xylose, 4-O-beta-D-xylopyranosyl-
 37 37  0  0  0  0  0  0  0  0999 V2000
    3.6172    2.0186    2.6419 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.2012    0.8899    2.5239 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.1056    0.6608    1.5148 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.8008    1.8550    0.9136 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.5719   -0.3881    0.5039 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.7368    0.1009   -0.1097 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.4759   -0.5239   -0.5202 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.9963   -1.5489   -1.5497 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.2547   -2.7127   -0.8143 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.3707   -0.9993    0.0511 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8089   -0.3526   -0.0587 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2501   -0.0108    1.2093 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1045    1.0590    1.1751 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8068    1.1777   -0.1351 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.0476    1.8065    0.1113 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.1069   -0.1365   -0.7949 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.2669   -0.6926   -0.2525 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9307   -1.0957   -0.7136 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6603   -1.5344   -1.9860 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.6269    0.1109    3.1368 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.2428    0.3176    2.1113 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.6070    2.2902    0.5754 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.7257   -1.3304    1.0340 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.4860    0.7199   -0.8234 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.4124    0.4417   -1.0500 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.2645   -1.7039   -2.3520 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.9589   -1.2112   -1.9711 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.7424   -3.3898   -1.3423 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6619    0.5794   -0.6415 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7891    1.0223    2.0465 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4799    1.9847    1.3005 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2880    1.8368   -0.8619 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.8309    2.5593    0.7202 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.3651    0.1002   -1.8676 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.8251   -1.1050   -0.9591 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2555   -1.9590   -0.0901 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7192   -0.8366   -2.6758 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  2  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
  8  9  1  0
  7 10  1  0
 10 11  1  0
 11 12  1  0
 12 13  1  0
 13 14  1  0
 14 15  1  0
 14 16  1  0
 16 17  1  0
 16 18  1  0
 18 19  1  0
 18 11  1  0
  2 20  1  0
  3 21  1  0
  4 22  1  0
  5 23  1  0
  6 24  1  0
  7 25  1  0
  8 26  1  0
  8 27  1  0
  9 28  1  0
 11 29  1  0
 13 30  1  0
 13 31  1  0
 14 32  1  0
 15 33  1  0
 16 34  1  0
 17 35  1  0
 18 36  1  0
 19 37  1  0
M  END

  Mrv1533004191520322D          

 19 19  0  0  0  0            999 V2000
    2.1434    0.4125    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289   -0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289   -0.8250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145   -1.2375    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000   -0.8250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7145   -1.2375    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4289   -0.8250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4289   -0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1434    0.4125    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7145    0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7145    1.2375    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000   -0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145    0.4125    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.1434   -1.2375    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.1434   -2.0625    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.8579   -0.8250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8579   -0.0000    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.5724   -1.2375    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.2868   -0.8250    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  2  3  1  0  0  0  0
  3  4  1  0  0  0  0
  4  5  1  0  0  0  0
  5  6  1  0  0  0  0
  6  7  1  0  0  0  0
  7  8  1  0  0  0  0
  8  9  1  0  0  0  0
  8 10  1  0  0  0  0
 10 11  1  0  0  0  0
 10 12  1  0  0  0  0
  5 12  1  0  0  0  0
 12 13  1  0  0  0  0
  3 14  1  0  0  0  0
 14 15  1  0  0  0  0
 14 16  1  0  0  0  0
 16 17  1  0  0  0  0
 16 18  1  0  0  0  0
 18 19  2  0  0  0  0
M  END
> <DATABASE_ID>
HMDB0250808

> <DATABASE_NAME>
hmdb

> <SMILES>
OCC(OC1OCC(O)C(O)C1O)C(O)C(O)C=O

> <INCHI_IDENTIFIER>
InChI=1S/C10H18O9/c11-1-4(13)7(15)6(2-12)19-10-9(17)8(16)5(14)3-18-10/h1,4-10,12-17H,2-3H2

> <INCHI_KEY>
SQNRKWHRVIAKLP-UHFFFAOYSA-N

> <FORMULA>
C10H18O9

> <MOLECULAR_WEIGHT>
282.245

> <EXACT_MASS>
282.09508216

> <JCHEM_ACCEPTOR_COUNT>
9

> <JCHEM_ATOM_COUNT>
37

> <JCHEM_AVERAGE_POLARIZABILITY>
25.59984823215196

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
6

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
2,3,5-trihydroxy-4-[(3,4,5-trihydroxyoxan-2-yl)oxy]pentanal

> <ALOGPS_LOGP>
-2.51

> <JCHEM_LOGP>
-4.078526324666667

> <ALOGPS_LOGS>
0.06

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
1

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
12.566055798897612

> <JCHEM_PKA_STRONGEST_ACIDIC>
12.003270336517579

> <JCHEM_PKA_STRONGEST_BASIC>
-2.9813638837163197

> <JCHEM_POLAR_SURFACE_AREA>
156.91

> <JCHEM_REFRACTIVITY>
57.83389999999999

> <JCHEM_ROTATABLE_BOND_COUNT>
6

> <JCHEM_RULE_OF_FIVE>
0

> <ALOGPS_SOLUBILITY>
3.27e+02 g/l

> <JCHEM_TRADITIONAL_IUPAC>
2,3,5-trihydroxy-4-[(3,4,5-trihydroxyoxan-2-yl)oxy]pentanal

> <JCHEM_VEBER_RULE>
0

$$$$

HMDB0250808
     RDKit          3D
D-Xylose, 4-O-beta-D-xylopyranosyl-
 37 37  0  0  0  0  0  0  0  0999 V2000
    3.6172    2.0186    2.6419 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.2012    0.8899    2.5239 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.1056    0.6608    1.5148 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.8008    1.8550    0.9136 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.5719   -0.3881    0.5039 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.7368    0.1009   -0.1097 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.4759   -0.5239   -0.5202 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.9963   -1.5489   -1.5497 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.2547   -2.7127   -0.8143 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.3707   -0.9993    0.0511 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8089   -0.3526   -0.0587 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2501   -0.0108    1.2093 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1045    1.0590    1.1751 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8068    1.1777   -0.1351 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.0476    1.8065    0.1113 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.1069   -0.1365   -0.7949 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.2669   -0.6926   -0.2525 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9307   -1.0957   -0.7136 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6603   -1.5344   -1.9860 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.6269    0.1109    3.1368 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.2428    0.3176    2.1113 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.6070    2.2902    0.5754 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.7257   -1.3304    1.0340 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.4860    0.7199   -0.8234 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.4124    0.4417   -1.0500 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.2645   -1.7039   -2.3520 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.9589   -1.2112   -1.9711 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.7424   -3.3898   -1.3423 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6619    0.5794   -0.6415 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7891    1.0223    2.0465 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4799    1.9847    1.3005 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2880    1.8368   -0.8619 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.8309    2.5593    0.7202 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.3651    0.1002   -1.8676 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.8251   -1.1050   -0.9591 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2555   -1.9590   -0.0901 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7192   -0.8366   -2.6758 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  2  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
  8  9  1  0
  7 10  1  0
 10 11  1  0
 11 12  1  0
 12 13  1  0
 13 14  1  0
 14 15  1  0
 14 16  1  0
 16 17  1  0
 16 18  1  0
 18 19  1  0
 18 11  1  0
  2 20  1  0
  3 21  1  0
  4 22  1  0
  5 23  1  0
  6 24  1  0
  7 25  1  0
  8 26  1  0
  8 27  1  0
  9 28  1  0
 11 29  1  0
 13 30  1  0
 13 31  1  0
 14 32  1  0
 15 33  1  0
 16 34  1  0
 17 35  1  0
 18 36  1  0
 19 37  1  0
M  END

HEADER    PROTEIN                                 19-APR-15   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   19-APR-15         0                                  
HETATM    1  O   UNK     0       4.001   0.770   0.000  0.00  0.00           O+0
HETATM    2  C   UNK     0       2.667  -0.000   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       2.667  -1.540   0.000  0.00  0.00           C+0
HETATM    4  O   UNK     0       1.334  -2.310   0.000  0.00  0.00           O+0
HETATM    5  C   UNK     0       0.000  -1.540   0.000  0.00  0.00           C+0
HETATM    6  O   UNK     0      -1.334  -2.310   0.000  0.00  0.00           O+0
HETATM    7  C   UNK     0      -2.667  -1.540   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0      -2.667  -0.000   0.000  0.00  0.00           C+0
HETATM    9  O   UNK     0      -4.001   0.770   0.000  0.00  0.00           O+0
HETATM   10  C   UNK     0      -1.334   0.770   0.000  0.00  0.00           C+0
HETATM   11  O   UNK     0      -1.334   2.310   0.000  0.00  0.00           O+0
HETATM   12  C   UNK     0       0.000  -0.000   0.000  0.00  0.00           C+0
HETATM   13  O   UNK     0       1.334   0.770   0.000  0.00  0.00           O+0
HETATM   14  C   UNK     0       4.001  -2.310   0.000  0.00  0.00           C+0
HETATM   15  O   UNK     0       4.001  -3.850   0.000  0.00  0.00           O+0
HETATM   16  C   UNK     0       5.335  -1.540   0.000  0.00  0.00           C+0
HETATM   17  O   UNK     0       5.335  -0.000   0.000  0.00  0.00           O+0
HETATM   18  C   UNK     0       6.668  -2.310   0.000  0.00  0.00           C+0
HETATM   19  O   UNK     0       8.002  -1.540   0.000  0.00  0.00           O+0
CONECT    1    2                                                            
CONECT    2    1    3                                                       
CONECT    3    2    4   14                                                  
CONECT    4    3    5                                                       
CONECT    5    4    6   12                                                  
CONECT    6    5    7                                                       
CONECT    7    6    8                                                       
CONECT    8    7    9   10                                                  
CONECT    9    8                                                            
CONECT   10    8   11   12                                                  
CONECT   11   10                                                            
CONECT   12   10    5   13                                                  
CONECT   13   12                                                            
CONECT   14    3   15   16                                                  
CONECT   15   14                                                            
CONECT   16   14   17   18                                                  
CONECT   17   16                                                            
CONECT   18   16   19                                                       
CONECT   19   18                                                            
MASTER        0    0    0    0    0    0    0    0   19    0   38    0
END

COMPND    HMDB0250808
HETATM    1  O1  UNL     1       3.617   2.019   2.642  1.00  0.00           O  
HETATM    2  C1  UNL     1       3.201   0.890   2.524  1.00  0.00           C  
HETATM    3  C2  UNL     1       2.106   0.661   1.515  1.00  0.00           C  
HETATM    4  O2  UNL     1       1.801   1.855   0.914  1.00  0.00           O  
HETATM    5  C3  UNL     1       2.572  -0.388   0.504  1.00  0.00           C  
HETATM    6  O3  UNL     1       3.737   0.101  -0.110  1.00  0.00           O  
HETATM    7  C4  UNL     1       1.476  -0.524  -0.520  1.00  0.00           C  
HETATM    8  C5  UNL     1       1.996  -1.549  -1.550  1.00  0.00           C  
HETATM    9  O4  UNL     1       2.255  -2.713  -0.814  1.00  0.00           O  
HETATM   10  O5  UNL     1       0.371  -0.999   0.051  1.00  0.00           O  
HETATM   11  C6  UNL     1      -0.809  -0.353  -0.059  1.00  0.00           C  
HETATM   12  O6  UNL     1      -1.250  -0.011   1.209  1.00  0.00           O  
HETATM   13  C7  UNL     1      -2.105   1.059   1.175  1.00  0.00           C  
HETATM   14  C8  UNL     1      -2.807   1.178  -0.135  1.00  0.00           C  
HETATM   15  O7  UNL     1      -4.048   1.807   0.111  1.00  0.00           O  
HETATM   16  C9  UNL     1      -3.107  -0.136  -0.795  1.00  0.00           C  
HETATM   17  O8  UNL     1      -4.267  -0.693  -0.252  1.00  0.00           O  
HETATM   18  C10 UNL     1      -1.931  -1.096  -0.714  1.00  0.00           C  
HETATM   19  O9  UNL     1      -1.660  -1.534  -1.986  1.00  0.00           O  
HETATM   20  H1  UNL     1       3.627   0.111   3.137  1.00  0.00           H  
HETATM   21  H2  UNL     1       1.243   0.318   2.111  1.00  0.00           H  
HETATM   22  H3  UNL     1       2.607   2.290   0.575  1.00  0.00           H  
HETATM   23  H4  UNL     1       2.726  -1.330   1.034  1.00  0.00           H  
HETATM   24  H5  UNL     1       3.486   0.720  -0.823  1.00  0.00           H  
HETATM   25  H6  UNL     1       1.412   0.442  -1.050  1.00  0.00           H  
HETATM   26  H7  UNL     1       1.264  -1.704  -2.352  1.00  0.00           H  
HETATM   27  H8  UNL     1       2.959  -1.211  -1.971  1.00  0.00           H  
HETATM   28  H9  UNL     1       2.742  -3.390  -1.342  1.00  0.00           H  
HETATM   29  H10 UNL     1      -0.662   0.579  -0.641  1.00  0.00           H  
HETATM   30  H11 UNL     1      -2.789   1.022   2.047  1.00  0.00           H  
HETATM   31  H12 UNL     1      -1.480   1.985   1.300  1.00  0.00           H  
HETATM   32  H13 UNL     1      -2.288   1.837  -0.862  1.00  0.00           H  
HETATM   33  H14 UNL     1      -3.831   2.559   0.720  1.00  0.00           H  
HETATM   34  H15 UNL     1      -3.365   0.100  -1.868  1.00  0.00           H  
HETATM   35  H16 UNL     1      -4.825  -1.105  -0.959  1.00  0.00           H  
HETATM   36  H17 UNL     1      -2.255  -1.959  -0.090  1.00  0.00           H  
HETATM   37  H18 UNL     1      -1.719  -0.837  -2.676  1.00  0.00           H  
CONECT    1    2    2
CONECT    2    3   20
CONECT    3    4    5   21
CONECT    4   22
CONECT    5    6    7   23
CONECT    6   24
CONECT    7    8   10   25
CONECT    8    9   26   27
CONECT    9   28
CONECT   10   11
CONECT   11   12   18   29
CONECT   12   13
CONECT   13   14   30   31
CONECT   14   15   16   32
CONECT   15   33
CONECT   16   17   18   34
CONECT   17   35
CONECT   18   19   36
CONECT   19   37
END

HMDB0250808
     RDKit          3D
D-Xylose, 4-O-beta-D-xylopyranosyl-
 37 37  0  0  0  0  0  0  0  0999 V2000
    3.6172    2.0186    2.6419 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.2012    0.8899    2.5239 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.1056    0.6608    1.5148 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.8008    1.8550    0.9136 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.5719   -0.3881    0.5039 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.7368    0.1009   -0.1097 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.4759   -0.5239   -0.5202 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.9963   -1.5489   -1.5497 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.2547   -2.7127   -0.8143 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.3707   -0.9993    0.0511 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8089   -0.3526   -0.0587 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2501   -0.0108    1.2093 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1045    1.0590    1.1751 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8068    1.1777   -0.1351 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.0476    1.8065    0.1113 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.1069   -0.1365   -0.7949 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.2669   -0.6926   -0.2525 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9307   -1.0957   -0.7136 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6603   -1.5344   -1.9860 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.6269    0.1109    3.1368 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.2428    0.3176    2.1113 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.6070    2.2902    0.5754 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.7257   -1.3304    1.0340 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.4860    0.7199   -0.8234 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.4124    0.4417   -1.0500 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.2645   -1.7039   -2.3520 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.9589   -1.2112   -1.9711 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.7424   -3.3898   -1.3423 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6619    0.5794   -0.6415 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7891    1.0223    2.0465 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4799    1.9847    1.3005 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2880    1.8368   -0.8619 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.8309    2.5593    0.7202 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.3651    0.1002   -1.8676 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.8251   -1.1050   -0.9591 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2555   -1.9590   -0.0901 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7192   -0.8366   -2.6758 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  2  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
  8  9  1  0
  7 10  1  0
 10 11  1  0
 11 12  1  0
 12 13  1  0
 13 14  1  0
 14 15  1  0
 14 16  1  0
 16 17  1  0
 16 18  1  0
 18 19  1  0
 18 11  1  0
  2 20  1  0
  3 21  1  0
  4 22  1  0
  5 23  1  0
  6 24  1  0
  7 25  1  0
  8 26  1  0
  8 27  1  0
  9 28  1  0
 11 29  1  0
 13 30  1  0
 13 31  1  0
 14 32  1  0
 15 33  1  0
 16 34  1  0
 17 35  1  0
 18 36  1  0
 19 37  1  0
M  END

View in JSmol View Stereo Labels

Synonyms

Not Available

Chemical Formula

C₁₀H₁₈O₉

Average Molecular Weight

282.245

Monoisotopic Molecular Weight

282.09508216

IUPAC Name

2,3,5-trihydroxy-4-[(3,4,5-trihydroxyoxan-2-yl)oxy]pentanal

Traditional Name

2,3,5-trihydroxy-4-[(3,4,5-trihydroxyoxan-2-yl)oxy]pentanal

CAS Registry Number

Not Available

SMILES

OCC(OC1OCC(O)C(O)C1O)C(O)C(O)C=O

InChI Identifier

InChI=1S/C10H18O9/c11-1-4(13)7(15)6(2-12)19-10-9(17)8(16)5(14)3-18-10/h1,4-10,12-17H,2-3H2

InChI Key

SQNRKWHRVIAKLP-UHFFFAOYSA-N

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as o-glycosyl compounds. These are glycoside in which a sugar group is bonded through one carbon to another group via a O-glycosidic bond.

Kingdom

Organic compounds

Super Class

Organic oxygen compounds

Class

Organooxygen compounds

Sub Class

Carbohydrates and carbohydrate conjugates

Direct Parent

O-glycosyl compounds

Alternative Parents

Substituents

Disaccharide
O-glycosyl compound
Beta-hydroxy aldehyde
Oxane
Alpha-hydroxyaldehyde
Secondary alcohol
Polyol
Acetal
Organoheterocyclic compound
Oxacycle
Primary alcohol
Alcohol
Hydrocarbon derivative
Organic oxide
Carbonyl group
Aldehyde
Aliphatic heteromonocyclic compound

Molecular Framework

Aliphatic heteromonocyclic 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	-4.1	ChemAxon
logS	0.06	ALOGPS
pKa (Strongest Acidic)	12	ChemAxon
pKa (Strongest Basic)	-3	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	9	ChemAxon
Hydrogen Donor Count	6	ChemAxon
Polar Surface Area	156.91 Å²	ChemAxon
Rotatable Bond Count	6	ChemAxon
Refractivity	57.83 m³·mol⁻¹	ChemAxon
Polarizability	25.6 Å³	ChemAxon
Number of Rings	1	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]+	159.009	30932474
DeepCCS	[M-H]-	156.651	30932474
DeepCCS	[M-2H]-	189.537	30932474
DeepCCS	[M+Na]+	165.102	30932474
AllCCS	[M+H]+	162.6	32859911
AllCCS	[M+H-H2O]+	159.4	32859911
AllCCS	[M+NH4]+	165.5	32859911
AllCCS	[M+Na]+	166.4	32859911
AllCCS	[M-H]-	160.4	32859911
AllCCS	[M+Na-2H]-	160.3	32859911
AllCCS	[M+HCOO]-	160.4	32859911

Predicted Kovats Retention Indices

Underivatized

Metabolite	SMILES	Kovats RI Value	Column Type	Reference
D-Xylose, 4-O-beta-D-xylopyranosyl-	OCC(OC1OCC(O)C(O)C1O)C(O)C(O)C=O	3657.9	Standard polar	33892256
D-Xylose, 4-O-beta-D-xylopyranosyl-	OCC(OC1OCC(O)C(O)C1O)C(O)C(O)C=O	2604.4	Standard non polar	33892256
D-Xylose, 4-O-beta-D-xylopyranosyl-	OCC(OC1OCC(O)C(O)C1O)C(O)C(O)C=O	2316.6	Semi standard non polar	33892256

Derivatized

Derivative Name / Structure	SMILES	Kovats RI Value	Column Type	Reference
D-Xylose, 4-O-beta-D-xylopyranosyl-,7TMS,isomer #1	C[Si](C)(C)OC=C(O[Si](C)(C)C)C(O[Si](C)(C)C)C(CO[Si](C)(C)C)OC1OCC(O[Si](C)(C)C)C(O[Si](C)(C)C)C1O[Si](C)(C)C	2395.5	Semi standard non polar	33892256
D-Xylose, 4-O-beta-D-xylopyranosyl-,7TMS,isomer #1	C[Si](C)(C)OC=C(O[Si](C)(C)C)C(O[Si](C)(C)C)C(CO[Si](C)(C)C)OC1OCC(O[Si](C)(C)C)C(O[Si](C)(C)C)C1O[Si](C)(C)C	2549.4	Standard non polar	33892256
D-Xylose, 4-O-beta-D-xylopyranosyl-,7TMS,isomer #1	C[Si](C)(C)OC=C(O[Si](C)(C)C)C(O[Si](C)(C)C)C(CO[Si](C)(C)C)OC1OCC(O[Si](C)(C)C)C(O[Si](C)(C)C)C1O[Si](C)(C)C	2638.7	Standard polar	33892256

Spectra

GC-MS Spectra

Spectrum Type	Description	Splash Key	Deposition Date	Source	View
Predicted GC-MS	Predicted GC-MS Spectrum - D-Xylose, 4-O-beta-D-xylopyranosyl- GC-MS (Non-derivatized) - 70eV, Positive	splash10-0ha0-6590000000-6282f1a453c778497003	2021-09-24	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - D-Xylose, 4-O-beta-D-xylopyranosyl- GC-MS (Non-derivatized) - 70eV, Positive	Not Available	2021-10-12	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - D-Xylose, 4-O-beta-D-xylopyranosyl- GC-MS (TMS_1_1) - 70eV, Positive	Not Available	2021-11-03	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - D-Xylose, 4-O-beta-D-xylopyranosyl- GC-MS (TMS_1_2) - 70eV, Positive	Not Available	2021-11-03	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - D-Xylose, 4-O-beta-D-xylopyranosyl- GC-MS (TMS_1_3) - 70eV, Positive	Not Available	2021-11-03	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - D-Xylose, 4-O-beta-D-xylopyranosyl- GC-MS (TMS_1_4) - 70eV, Positive	Not Available	2021-11-03	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - D-Xylose, 4-O-beta-D-xylopyranosyl- GC-MS (TMS_1_5) - 70eV, Positive	Not Available	2021-11-03	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - D-Xylose, 4-O-beta-D-xylopyranosyl- GC-MS (TMS_1_6) - 70eV, Positive	Not Available	2021-11-03	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - D-Xylose, 4-O-beta-D-xylopyranosyl- GC-MS (TMS_1_7) - 70eV, Positive	Not Available	2021-11-03	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - D-Xylose, 4-O-beta-D-xylopyranosyl- GC-MS (TMS_2_1) - 70eV, Positive	Not Available	2021-11-03	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - D-Xylose, 4-O-beta-D-xylopyranosyl- GC-MS (TMS_2_2) - 70eV, Positive	Not Available	2021-11-03	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - D-Xylose, 4-O-beta-D-xylopyranosyl- GC-MS (TMS_2_3) - 70eV, Positive	Not Available	2021-11-03	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - D-Xylose, 4-O-beta-D-xylopyranosyl- GC-MS (TMS_2_4) - 70eV, Positive	Not Available	2021-11-03	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - D-Xylose, 4-O-beta-D-xylopyranosyl- GC-MS (TMS_2_5) - 70eV, Positive	Not Available	2021-11-03	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - D-Xylose, 4-O-beta-D-xylopyranosyl- GC-MS (TMS_2_6) - 70eV, Positive	Not Available	2021-11-03	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - D-Xylose, 4-O-beta-D-xylopyranosyl- GC-MS (TMS_2_7) - 70eV, Positive	Not Available	2021-11-03	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - D-Xylose, 4-O-beta-D-xylopyranosyl- GC-MS (TMS_2_8) - 70eV, Positive	Not Available	2021-11-03	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - D-Xylose, 4-O-beta-D-xylopyranosyl- GC-MS (TMS_2_9) - 70eV, Positive	Not Available	2021-11-03	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - D-Xylose, 4-O-beta-D-xylopyranosyl- GC-MS (TMS_2_10) - 70eV, Positive	Not Available	2021-11-03	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - D-Xylose, 4-O-beta-D-xylopyranosyl- GC-MS (TMS_2_11) - 70eV, Positive	Not Available	2021-11-03	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - D-Xylose, 4-O-beta-D-xylopyranosyl- GC-MS (TMS_2_12) - 70eV, Positive	Not Available	2021-11-03	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - D-Xylose, 4-O-beta-D-xylopyranosyl- GC-MS (TMS_2_13) - 70eV, Positive	Not Available	2021-11-03	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - D-Xylose, 4-O-beta-D-xylopyranosyl- GC-MS (TMS_2_14) - 70eV, Positive	Not Available	2021-11-03	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - D-Xylose, 4-O-beta-D-xylopyranosyl- GC-MS (TMS_2_15) - 70eV, Positive	Not Available	2021-11-03	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - D-Xylose, 4-O-beta-D-xylopyranosyl- GC-MS (TMS_2_16) - 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 - D-Xylose, 4-O-beta-D-xylopyranosyl- 10V, Positive-QTOF	splash10-00lr-0690000000-f57963adf1ee42f1c23c	2021-10-12	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - D-Xylose, 4-O-beta-D-xylopyranosyl- 20V, Positive-QTOF	splash10-03di-9400000000-11c3ca270c3fd559cd86	2021-10-12	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - D-Xylose, 4-O-beta-D-xylopyranosyl- 40V, Positive-QTOF	splash10-02t9-9800000000-e680d7375d9f0e3656bc	2021-10-12	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - D-Xylose, 4-O-beta-D-xylopyranosyl- 10V, Negative-QTOF	splash10-001l-7690000000-cb6e7dd3c73c00e1b495	2021-10-12	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - D-Xylose, 4-O-beta-D-xylopyranosyl- 20V, Negative-QTOF	splash10-0a4l-9100000000-b7464c1944f94207d7b5	2021-10-12	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - D-Xylose, 4-O-beta-D-xylopyranosyl- 40V, Negative-QTOF	splash10-0006-9000000000-1900b66a3ac5fc7960bf	2021-10-12	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

4283006

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

5107731

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 D-Xylose, 4-O-beta-D-xylopyranosyl- (HMDB0250808)

MOL for HMDB0250808 (D-Xylose, 4-O-beta-D-xylopyranosyl-)

3D MOL for HMDB0250808 (D-Xylose, 4-O-beta-D-xylopyranosyl-)

3D SDF for HMDB0250808 (D-Xylose, 4-O-beta-D-xylopyranosyl-)

3D-SDF for HMDB0250808 (D-Xylose, 4-O-beta-D-xylopyranosyl-)

PDB for HMDB0250808 (D-Xylose, 4-O-beta-D-xylopyranosyl-)

3D PDB for HMDB0250808 (D-Xylose, 4-O-beta-D-xylopyranosyl-)

SMILES for HMDB0250808 (D-Xylose, 4-O-beta-D-xylopyranosyl-)

INCHI for HMDB0250808 (D-Xylose, 4-O-beta-D-xylopyranosyl-)

Structure for HMDB0250808 (D-Xylose, 4-O-beta-D-xylopyranosyl-)

3D Structure for HMDB0250808 (D-Xylose, 4-O-beta-D-xylopyranosyl-)

Predicted Collision Cross Sections

Predicted Kovats Retention Indices

Underivatized

Derivatized

GC-MS Spectra

MS/MS Spectra