Showing metabocard for D-Xylose (MMDBc0000026)

Record Information
Version1.0
StatusDetected and Quantified
Creation Date2020-10-27 23:27:40 UTC
Update Date2022-08-30 23:10:49 UTC
Metabolite IDMMDBc0000026
Metabolite Identification
Common NameD-Xylose
DescriptionXylose or wood sugar is an aldopentose - a monosaccharide containing five carbon atoms and an aldehyde functional group. It has chemical formula C5H10O5 and is 40% as sweet as sucrose. Xylose is found in the embryos of most edible plants. The polysaccharide xylan, which is closely associated with cellulose, consists practically entirely of d-xylose. Corncobs, cottonseed hulls, pecan shells, and straw contain considerable amounts of this sugar. Xylose is also found in mucopolysaccharides of connective tissue and sometimes in the urine. Xylose is the first sugar added to serine or threonine residues during proteoglycan type O-glycosylation. Therefore xylose is involved in the biosythetic pathways of most anionic polysaccharides such as heparan sulphate and chondroitin sulphate. In medicine, xylose is used to test for malabsorption by administering a xylose solution to the patient after fasting. If xylose is detected in the blood and/or urine within the next few hours, it has been absorbed by the intestines. Xylose is said to be one of eight sugars which are essential for human nutrition, the others being galactose, glucose, mannose, N-acetylglucosamine, N-acetylgalactosamine, fucose, and sialic acid. (Wikipedia ). Xylose in the urine is a biomarker for the consumption of apples and other fruits.
Structure
MOL3D MOLSDF3D SDFPDB3D PDBSMILESInChI

MOL for #<Metabolite:0x00007f1240cbc9e8>


  Mrv1652305271900082D          

 10 10  0  0  1  0            999 V2000
   12.6685  -10.4077    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   10.5250   -9.1702    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   11.9540   -8.3452    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   10.5250  -10.8202    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   13.3829   -9.1702    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   11.2395   -9.5827    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   11.9540   -9.1702    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   11.2395  -10.4077    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   12.6685   -9.5827    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   11.9540  -10.8202    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
  1  9  1  0  0  0  0
  1 10  1  0  0  0  0
  6  2  1  6  0  0  0
  7  3  1  1  0  0  0
  8  4  1  1  0  0  0
  5  9  1  0  0  0  0
  6  7  1  0  0  0  0
  6  8  1  0  0  0  0
  7  9  1  0  0  0  0
  8 10  1  0  0  0  0
M  END
Download

3D MOL for #<Metabolite:0x00007f1240cbc9e8>

HMDB0000098
     RDKit          3D
D-Xylose
 20 20  0  0  0  0  0  0  0  0999 V2000
   -2.1156   -0.5052    0.9038 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4403   -0.3744   -0.3190 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6857   -1.4629   -0.6348 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.6712   -1.2707   -0.6379 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.0092   -0.4946    0.6423 C   0  0  1  0  0  0  0  0  0  0  0  0
    2.3303   -0.6124    0.9895 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.6046    0.9395    0.3192 C   0  0  2  0  0  0  0  0  0  0  0  0
    0.7223    1.7268    1.4352 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7385    0.9350   -0.3144 C   0  0  1  0  0  0  0  0  0  0  0  0
   -0.6941    1.4850   -1.6145 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0488   -1.3903    1.2937 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2635   -0.3077   -1.0911 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.9039   -0.6100   -1.5230 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.2094   -2.2140   -0.6854 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.3077   -0.8123    1.4673 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.5819   -1.5531    0.9652 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.3550    1.2826   -0.4513 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.8891    2.6712    1.1988 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3842    1.6566    0.2682 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2140    0.9108   -2.2118 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
  4  5  1  0
  5  6  1  0
  5  7  1  0
  7  8  1  0
  7  9  1  0
  9 10  1  0
  9  2  1  0
  1 11  1  0
  2 12  1  0
  4 13  1  0
  4 14  1  0
  5 15  1  1
  6 16  1  0
  7 17  1  6
  8 18  1  0
  9 19  1  1
 10 20  1  0
M  END
Download

3D SDF for #<Metabolite:0x00007f1240cbc9e8>


  Mrv1652305271900082D          

 10 10  0  0  1  0            999 V2000
   12.6685  -10.4077    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   10.5250   -9.1702    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   11.9540   -8.3452    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   10.5250  -10.8202    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   13.3829   -9.1702    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   11.2395   -9.5827    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   11.9540   -9.1702    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   11.2395  -10.4077    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   12.6685   -9.5827    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   11.9540  -10.8202    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
  1  9  1  0  0  0  0
  1 10  1  0  0  0  0
  6  2  1  6  0  0  0
  7  3  1  1  0  0  0
  8  4  1  1  0  0  0
  5  9  1  0  0  0  0
  6  7  1  0  0  0  0
  6  8  1  0  0  0  0
  7  9  1  0  0  0  0
  8 10  1  0  0  0  0
M  END
> <DATABASE_ID>
MMDBc0000026

> <DATABASE_NAME>
MIME

> <SMILES>
O[C@@H]1COC(O)[C@H](O)[C@H]1O

> <INCHI_IDENTIFIER>
InChI=1S/C5H10O5/c6-2-1-10-5(9)4(8)3(2)7/h2-9H,1H2/t2-,3+,4-,5?/m1/s1

> <INCHI_KEY>
SRBFZHDQGSBBOR-IOVATXLUSA-N

> <FORMULA>
C5H10O5

> <MOLECULAR_WEIGHT>
150.1299

> <EXACT_MASS>
150.05282343

> <JCHEM_ACCEPTOR_COUNT>
5

> <JCHEM_ATOM_COUNT>
20

> <JCHEM_AVERAGE_POLARIZABILITY>
13.432709748510788

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
4

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(3R,4S,5R)-oxane-2,3,4,5-tetrol

> <ALOGPS_LOGP>
-2.57

> <JCHEM_LOGP>
-2.302204276

> <ALOGPS_LOGS>
0.91

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
1

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
12.786263151759016

> <JCHEM_PKA_STRONGEST_ACIDIC>
11.310624247742409

> <JCHEM_PKA_STRONGEST_BASIC>
-3.5265718350182684

> <JCHEM_POLAR_SURFACE_AREA>
90.15

> <JCHEM_REFRACTIVITY>
29.9609

> <JCHEM_ROTATABLE_BOND_COUNT>
0

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
1.22e+03 g/l

> <JCHEM_TRADITIONAL_IUPAC>
d-xylose

> <JCHEM_VEBER_RULE>
0

$$$$
Download

3D-SDF for #<Metabolite:0x00007f1240cbc9e8>

HMDB0000098
     RDKit          3D
D-Xylose
 20 20  0  0  0  0  0  0  0  0999 V2000
   -2.1156   -0.5052    0.9038 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4403   -0.3744   -0.3190 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6857   -1.4629   -0.6348 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.6712   -1.2707   -0.6379 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.0092   -0.4946    0.6423 C   0  0  1  0  0  0  0  0  0  0  0  0
    2.3303   -0.6124    0.9895 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.6046    0.9395    0.3192 C   0  0  2  0  0  0  0  0  0  0  0  0
    0.7223    1.7268    1.4352 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7385    0.9350   -0.3144 C   0  0  1  0  0  0  0  0  0  0  0  0
   -0.6941    1.4850   -1.6145 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0488   -1.3903    1.2937 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2635   -0.3077   -1.0911 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.9039   -0.6100   -1.5230 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.2094   -2.2140   -0.6854 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.3077   -0.8123    1.4673 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.5819   -1.5531    0.9652 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.3550    1.2826   -0.4513 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.8891    2.6712    1.1988 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3842    1.6566    0.2682 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2140    0.9108   -2.2118 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
  4  5  1  0
  5  6  1  0
  5  7  1  0
  7  8  1  0
  7  9  1  0
  9 10  1  0
  9  2  1  0
  1 11  1  0
  2 12  1  0
  4 13  1  0
  4 14  1  0
  5 15  1  1
  6 16  1  0
  7 17  1  6
  8 18  1  0
  9 19  1  1
 10 20  1  0
M  END
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PDB for #<Metabolite:0x00007f1240cbc9e8>

HEADER    PROTEIN                                 27-MAY-19   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   27-MAY-19         0                                  
HETATM    1  O   UNK     0      23.648 -19.428   0.000  0.00  0.00           O+0
HETATM    2  O   UNK     0      19.647 -17.118   0.000  0.00  0.00           O+0
HETATM    3  O   UNK     0      22.314 -15.578   0.000  0.00  0.00           O+0
HETATM    4  O   UNK     0      19.647 -20.198   0.000  0.00  0.00           O+0
HETATM    5  O   UNK     0      24.981 -17.118   0.000  0.00  0.00           O+0
HETATM    6  C   UNK     0      20.980 -17.888   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0      22.314 -17.118   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0      20.980 -19.428   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0      23.648 -17.888   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0      22.314 -20.198   0.000  0.00  0.00           C+0
CONECT    1    9   10                                                       
CONECT    2    6                                                            
CONECT    3    7                                                            
CONECT    4    8                                                            
CONECT    5    9                                                            
CONECT    6    2    7    8                                                  
CONECT    7    3    6    9                                                  
CONECT    8    4    6   10                                                  
CONECT    9    1    5    7                                                  
CONECT   10    1    8                                                       
MASTER        0    0    0    0    0    0    0    0   10    0   20    0
END
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3D PDB for #<Metabolite:0x00007f1240cbc9e8>

COMPND    HMDB0000098
HETATM    1  O1  UNL     1      -2.116  -0.505   0.904  1.00  0.00           O  
HETATM    2  C1  UNL     1      -1.440  -0.374  -0.319  1.00  0.00           C  
HETATM    3  O2  UNL     1      -0.686  -1.463  -0.635  1.00  0.00           O  
HETATM    4  C2  UNL     1       0.671  -1.271  -0.638  1.00  0.00           C  
HETATM    5  C3  UNL     1       1.009  -0.495   0.642  1.00  0.00           C  
HETATM    6  O3  UNL     1       2.330  -0.612   0.990  1.00  0.00           O  
HETATM    7  C4  UNL     1       0.605   0.940   0.319  1.00  0.00           C  
HETATM    8  O4  UNL     1       0.722   1.727   1.435  1.00  0.00           O  
HETATM    9  C5  UNL     1      -0.739   0.935  -0.314  1.00  0.00           C  
HETATM   10  O5  UNL     1      -0.694   1.485  -1.614  1.00  0.00           O  
HETATM   11  H1  UNL     1      -2.049  -1.390   1.294  1.00  0.00           H  
HETATM   12  H2  UNL     1      -2.263  -0.308  -1.091  1.00  0.00           H  
HETATM   13  H3  UNL     1       0.904  -0.610  -1.523  1.00  0.00           H  
HETATM   14  H4  UNL     1       1.209  -2.214  -0.685  1.00  0.00           H  
HETATM   15  H5  UNL     1       0.308  -0.812   1.467  1.00  0.00           H  
HETATM   16  H6  UNL     1       2.582  -1.553   0.965  1.00  0.00           H  
HETATM   17  H7  UNL     1       1.355   1.283  -0.451  1.00  0.00           H  
HETATM   18  H8  UNL     1       0.889   2.671   1.199  1.00  0.00           H  
HETATM   19  H9  UNL     1      -1.384   1.657   0.268  1.00  0.00           H  
HETATM   20  H10 UNL     1      -1.214   0.911  -2.212  1.00  0.00           H  
CONECT    1    2   11
CONECT    2    3    9   12
CONECT    3    4
CONECT    4    5   13   14
CONECT    5    6    7   15
CONECT    6   16
CONECT    7    8    9   17
CONECT    8   18
CONECT    9   10   19
CONECT   10   20
END
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SMILES for #<Metabolite:0x00007f1240cbc9e8>

O[C@@H]1COC(O)[C@H](O)[C@H]1O
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INCHI for #<Metabolite:0x00007f1240cbc9e8>

InChI=1S/C5H10O5/c6-2-1-10-5(9)4(8)3(2)7/h2-9H,1H2/t2-,3+,4-,5?/m1/s1
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Synonyms
ValueSource
(3R,4S,5R)-Tetrahydro-2H-pyran-2,3,4,5-tetrolChEBI
D-(+)-XyloseChEBI
D-XylopentoseChEBI
Wood sugarChEBI
Xylo-pfanKegg
D-Xylo-pentoseHMDB
XylomedHMDB
XyloseHMDB
XylosideHMDB
XylopyranoseHMDB
D XyloseHMDB
D-XylopyranoseHMDB
Aldehydo-D-xyloseHMDB
D-XyloseChEBI
Molecular FormulaC5H10O5
Average Mass150.1299
Monoisotopic Mass150.05282343
IUPAC Name(3R,4S,5R)-oxane-2,3,4,5-tetrol
Traditional Named-xylose
CAS Registry Number58-86-6
SMILES
O[C@@H]1COC(O)[C@H](O)[C@H]1O
InChI Identifier
InChI=1S/C5H10O5/c6-2-1-10-5(9)4(8)3(2)7/h2-9H,1H2/t2-,3+,4-,5?/m1/s1
InChI KeySRBFZHDQGSBBOR-IOVATXLUSA-N