MiMeDB: Showing metabocard for Xanthosine (MMDBc0000338)

Record Information

Version

1.0

Status

Detected and Quantified

Creation Date

2020-12-10 18:35:40 UTC

Update Date

2022-08-31 06:02:27 UTC

Metabolite ID

MMDBc0000338

Metabolite Identification

Common Name

Xanthosine

Description

Xanthosine, also known as xanthine riboside, belongs to the class of organic compounds known as purine nucleosides. Purine nucleosides are compounds comprising a purine base attached to a ribosyl or deoxyribosyl moiety. Xanthosine is a nucleoside derived from xanthine and ribose. Xanthosine exists in all living species, ranging from bacteria to plants to humans. In plants xanthosine is the biosynthetic precursor to 7-methylxanthosine which is produced by the action of the enzyme known as 7-methylxanthosine synthase. 7-Methylxanthosine in turn is the precursor to theobromine (the active alkaloid in chocolate), which in turn is the precursor to caffeine, the active alkaloid in coffee and tea. Within humans, xanthosine participates in a number of enzymatic reactions. In particular, xanthosine can be biosynthesized from xanthylic acid; which is catalyzed by the enzyme cytosolic purine 5'-nucleotidase. In addition, xanthosine can be converted into xanthine and ribose 1-phosphate; which is mediated by the enzyme purine nucleoside phosphorylase. Xanthosine monophosphate (XMP) is an intermediate in purine metabolism, formed from IMP (inosine monophosphate).

Structure

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

HMDB0000299
     RDKit          3D
Xanthosine
 32 34  0  0  0  0  0  0  0  0999 V2000
   -5.0067    0.4182    0.1166 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.9402   -0.2156    0.7502 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6340    0.5263    0.4664 C   0  0  1  0  0  0  0  0  0  0  0  0
   -1.5702   -0.0814    1.0815 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4917    0.1380    0.2334 C   0  0  1  0  0  0  0  0  0  0  0  0
    0.6755   -0.5961    0.5811 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.8007   -1.7835    1.1745 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.1211   -2.1026    1.3116 N   0  0  0  0  0  0  0  0  0  0  0  0
    2.8486   -1.0749    0.7835 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.2002   -0.8491    0.6468 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.1407   -1.7532    1.0839 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.6152    0.2873    0.0696 N   0  0  0  0  0  0  0  0  0  0  0  0
    3.7473    1.1878   -0.3669 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.1602    2.3705   -0.9673 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.4307    0.9588   -0.2292 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.9353   -0.1662    0.3436 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0880   -0.2610   -1.1025 C   0  0  2  0  0  0  0  0  0  0  0  0
   -0.3057    0.1663   -2.1617 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4024    0.4887   -1.0189 C   0  0  2  0  0  0  0  0  0  0  0  0
   -2.1694    1.7656   -1.5303 O   0  0  0  0  0  0  0  0  0  0  0  0
   -5.3116   -0.1290   -0.6555 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.8044   -1.2496    0.3711 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.1719   -0.2265    1.8297 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6865    1.5764    0.8417 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3244    1.2413    0.1944 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0432   -2.3859    1.4913 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.4603   -1.8406    2.0276 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.7331    2.7399   -1.8119 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2653   -1.3672   -1.1357 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.6039   -0.1954   -2.0099 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.2100   -0.0297   -1.5692 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0472    2.4422   -0.8396 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
  6  7  1  0
  7  8  2  0
  8  9  1  0
  9 10  2  0
 10 11  1  0
 10 12  1  0
 12 13  2  0
 13 14  1  0
 13 15  1  0
 15 16  2  0
  5 17  1  0
 17 18  1  0
 17 19  1  0
 19 20  1  0
 19  3  1  0
 16  6  1  0
 16  9  1  0
  1 21  1  0
  2 22  1  0
  2 23  1  0
  3 24  1  1
  5 25  1  6
  7 26  1  0
 11 27  1  0
 14 28  1  0
 17 29  1  1
 18 30  1  0
 19 31  1  6
 20 32  1  0
M  END

Xanthosine 5'-triphosphate.mol
  Mrv1652309042000002D          

 20 22  0  0  0  0            999 V2000
    3.0342    0.5318    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.2373    0.7453    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.6853    0.1322    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    1.8568   -0.6748    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    2.6105   -1.0103    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.1424   -1.0873    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    1.0561   -1.9078    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.5293   -0.5352    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    0.8648    0.2184    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2777   -0.7068    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6133   -1.4604    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4337   -1.3742    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6053   -0.5672    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3197   -0.1547    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.0342   -0.5672    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3197    0.6703    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6053    1.0828    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6053    1.9078    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8908    0.6703    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8908   -0.1547    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  3  2  1  6  0  0  0
  3  4  1  0  0  0  0
  4  5  1  1  0  0  0
  4  6  1  0  0  0  0
  6  7  1  1  0  0  0
  6  8  1  0  0  0  0
  8  9  1  0  0  0  0
  3  9  1  0  0  0  0
  8 10  1  6  0  0  0
 10 11  1  0  0  0  0
 11 12  2  0  0  0  0
 12 13  1  0  0  0  0
 13 14  1  0  0  0  0
 14 15  1  0  0  0  0
 14 16  2  0  0  0  0
 16 17  1  0  0  0  0
 17 18  1  0  0  0  0
 17 19  2  0  0  0  0
 19 20  1  0  0  0  0
 13 20  2  0  0  0  0
 10 20  1  0  0  0  0
M  END
> <DATABASE_ID>
MMDBc0000338

> <DATABASE_NAME>
MIME

> <SMILES>
OC[C@H]1O[C@H]([C@H](O)[C@@H]1O)N1C=NC2=C1N=C(O)N=C2O

> <INCHI_IDENTIFIER>
InChI=1S/C10H12N4O6/c15-1-3-5(16)6(17)9(20-3)14-2-11-4-7(14)12-10(19)13-8(4)18/h2-3,5-6,9,15-17H,1H2,(H2,12,13,18,19)/t3-,5-,6-,9-/m1/s1

> <INCHI_KEY>
UBORTCNDUKBEOP-UUOKFMHZSA-N

> <FORMULA>
C10H12N4O6

> <MOLECULAR_WEIGHT>
284.2255

> <EXACT_MASS>
284.075684136

> <JCHEM_ACCEPTOR_COUNT>
9

> <JCHEM_ATOM_COUNT>
32

> <JCHEM_AVERAGE_POLARIZABILITY>
25.54856291933196

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
5

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
9-[(2R,3R,4S,5R)-3,4-dihydroxy-5-(hydroxymethyl)oxolan-2-yl]-9H-purine-2,6-diol

> <ALOGPS_LOGP>
-1.60

> <JCHEM_LOGP>
-1.1903825390000002

> <ALOGPS_LOGS>
-1.01

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
3

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
12.473029142968798

> <JCHEM_PKA_STRONGEST_ACIDIC>
11.331641933271216

> <JCHEM_PKA_STRONGEST_BASIC>
0.07830393650019773

> <JCHEM_POLAR_SURFACE_AREA>
153.98000000000002

> <JCHEM_REFRACTIVITY>
62.40299999999999

> <JCHEM_ROTATABLE_BOND_COUNT>
2

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
2.78e+01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
9-[(2R,3R,4S,5R)-3,4-dihydroxy-5-(hydroxymethyl)oxolan-2-yl]purine-2,6-diol

> <JCHEM_VEBER_RULE>
0

$$$$

HMDB0000299
     RDKit          3D
Xanthosine
 32 34  0  0  0  0  0  0  0  0999 V2000
   -5.0067    0.4182    0.1166 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.9402   -0.2156    0.7502 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6340    0.5263    0.4664 C   0  0  1  0  0  0  0  0  0  0  0  0
   -1.5702   -0.0814    1.0815 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4917    0.1380    0.2334 C   0  0  1  0  0  0  0  0  0  0  0  0
    0.6755   -0.5961    0.5811 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.8007   -1.7835    1.1745 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.1211   -2.1026    1.3116 N   0  0  0  0  0  0  0  0  0  0  0  0
    2.8486   -1.0749    0.7835 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.2002   -0.8491    0.6468 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.1407   -1.7532    1.0839 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.6152    0.2873    0.0696 N   0  0  0  0  0  0  0  0  0  0  0  0
    3.7473    1.1878   -0.3669 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.1602    2.3705   -0.9673 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.4307    0.9588   -0.2292 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.9353   -0.1662    0.3436 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0880   -0.2610   -1.1025 C   0  0  2  0  0  0  0  0  0  0  0  0
   -0.3057    0.1663   -2.1617 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4024    0.4887   -1.0189 C   0  0  2  0  0  0  0  0  0  0  0  0
   -2.1694    1.7656   -1.5303 O   0  0  0  0  0  0  0  0  0  0  0  0
   -5.3116   -0.1290   -0.6555 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.8044   -1.2496    0.3711 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.1719   -0.2265    1.8297 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6865    1.5764    0.8417 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3244    1.2413    0.1944 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0432   -2.3859    1.4913 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.4603   -1.8406    2.0276 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.7331    2.7399   -1.8119 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2653   -1.3672   -1.1357 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.6039   -0.1954   -2.0099 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.2100   -0.0297   -1.5692 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0472    2.4422   -0.8396 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
  6  7  1  0
  7  8  2  0
  8  9  1  0
  9 10  2  0
 10 11  1  0
 10 12  1  0
 12 13  2  0
 13 14  1  0
 13 15  1  0
 15 16  2  0
  5 17  1  0
 17 18  1  0
 17 19  1  0
 19 20  1  0
 19  3  1  0
 16  6  1  0
 16  9  1  0
  1 21  1  0
  2 22  1  0
  2 23  1  0
  3 24  1  1
  5 25  1  6
  7 26  1  0
 11 27  1  0
 14 28  1  0
 17 29  1  1
 18 30  1  0
 19 31  1  6
 20 32  1  0
M  END

HEADER    PROTEIN                                 04-SEP-20   NONE
TITLE     NULL                                                        
COMPND    MOLECULE: Xanthosine 5'-triphosphate.mol                    
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   04-SEP-20         0                                  
HETATM    1  O   UNK     0       5.664   0.993   0.000  0.00  0.00           O+0
HETATM    2  C   UNK     0       4.176   1.391   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       3.146   0.247   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       3.466  -1.260   0.000  0.00  0.00           C+0
HETATM    5  O   UNK     0       4.873  -1.886   0.000  0.00  0.00           O+0
HETATM    6  C   UNK     0       2.132  -2.030   0.000  0.00  0.00           C+0
HETATM    7  O   UNK     0       1.971  -3.561   0.000  0.00  0.00           O+0
HETATM    8  C   UNK     0       0.988  -0.999   0.000  0.00  0.00           C+0
HETATM    9  O   UNK     0       1.614   0.408   0.000  0.00  0.00           O+0
HETATM   10  N   UNK     0      -0.518  -1.319   0.000  0.00  0.00           N+0
HETATM   11  C   UNK     0      -1.145  -2.726   0.000  0.00  0.00           C+0
HETATM   12  N   UNK     0      -2.676  -2.565   0.000  0.00  0.00           N+0
HETATM   13  C   UNK     0      -2.997  -1.059   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0      -4.330  -0.289   0.000  0.00  0.00           C+0
HETATM   15  O   UNK     0      -5.664  -1.059   0.000  0.00  0.00           O+0
HETATM   16  N   UNK     0      -4.330   1.251   0.000  0.00  0.00           N+0
HETATM   17  C   UNK     0      -2.997   2.021   0.000  0.00  0.00           C+0
HETATM   18  O   UNK     0      -2.997   3.561   0.000  0.00  0.00           O+0
HETATM   19  N   UNK     0      -1.663   1.251   0.000  0.00  0.00           N+0
HETATM   20  C   UNK     0      -1.663  -0.289   0.000  0.00  0.00           C+0
CONECT    1    2                                                            
CONECT    2    1    3                                                       
CONECT    3    2    4    9                                                  
CONECT    4    3    5    6                                                  
CONECT    5    4                                                            
CONECT    6    4    7    8                                                  
CONECT    7    6                                                            
CONECT    8    6    9   10                                                  
CONECT    9    8    3                                                       
CONECT   10    8   11   20                                                  
CONECT   11   10   12                                                       
CONECT   12   11   13                                                       
CONECT   13   12   14   20                                                  
CONECT   14   13   15   16                                                  
CONECT   15   14                                                            
CONECT   16   14   17                                                       
CONECT   17   16   18   19                                                  
CONECT   18   17                                                            
CONECT   19   17   20                                                       
CONECT   20   19   13   10                                                  
MASTER        0    0    0    0    0    0    0    0   20    0   44    0
END

COMPND    HMDB0000299
HETATM    1  O1  UNL     1      -5.007   0.418   0.117  1.00  0.00           O  
HETATM    2  C1  UNL     1      -3.940  -0.216   0.750  1.00  0.00           C  
HETATM    3  C2  UNL     1      -2.634   0.526   0.466  1.00  0.00           C  
HETATM    4  O2  UNL     1      -1.570  -0.081   1.081  1.00  0.00           O  
HETATM    5  C3  UNL     1      -0.492   0.138   0.233  1.00  0.00           C  
HETATM    6  N1  UNL     1       0.676  -0.596   0.581  1.00  0.00           N  
HETATM    7  C4  UNL     1       0.801  -1.783   1.175  1.00  0.00           C  
HETATM    8  N2  UNL     1       2.121  -2.103   1.312  1.00  0.00           N  
HETATM    9  C5  UNL     1       2.849  -1.075   0.784  1.00  0.00           C  
HETATM   10  C6  UNL     1       4.200  -0.849   0.647  1.00  0.00           C  
HETATM   11  O3  UNL     1       5.141  -1.753   1.084  1.00  0.00           O  
HETATM   12  N3  UNL     1       4.615   0.287   0.070  1.00  0.00           N  
HETATM   13  C7  UNL     1       3.747   1.188  -0.367  1.00  0.00           C  
HETATM   14  O4  UNL     1       4.160   2.370  -0.967  1.00  0.00           O  
HETATM   15  N4  UNL     1       2.431   0.959  -0.229  1.00  0.00           N  
HETATM   16  C8  UNL     1       1.935  -0.166   0.344  1.00  0.00           C  
HETATM   17  C9  UNL     1      -1.088  -0.261  -1.103  1.00  0.00           C  
HETATM   18  O5  UNL     1      -0.306   0.166  -2.162  1.00  0.00           O  
HETATM   19  C10 UNL     1      -2.402   0.489  -1.019  1.00  0.00           C  
HETATM   20  O6  UNL     1      -2.169   1.766  -1.530  1.00  0.00           O  
HETATM   21  H1  UNL     1      -5.312  -0.129  -0.655  1.00  0.00           H  
HETATM   22  H2  UNL     1      -3.804  -1.250   0.371  1.00  0.00           H  
HETATM   23  H3  UNL     1      -4.172  -0.227   1.830  1.00  0.00           H  
HETATM   24  H4  UNL     1      -2.687   1.576   0.842  1.00  0.00           H  
HETATM   25  H5  UNL     1      -0.324   1.241   0.194  1.00  0.00           H  
HETATM   26  H6  UNL     1      -0.043  -2.386   1.491  1.00  0.00           H  
HETATM   27  H7  UNL     1       5.460  -1.841   2.028  1.00  0.00           H  
HETATM   28  H8  UNL     1       3.733   2.740  -1.812  1.00  0.00           H  
HETATM   29  H9  UNL     1      -1.265  -1.367  -1.136  1.00  0.00           H  
HETATM   30  H10 UNL     1       0.604  -0.195  -2.010  1.00  0.00           H  
HETATM   31  H11 UNL     1      -3.210  -0.030  -1.569  1.00  0.00           H  
HETATM   32  H12 UNL     1      -2.047   2.442  -0.840  1.00  0.00           H  
CONECT    1    2   21
CONECT    2    3   22   23
CONECT    3    4   19   24
CONECT    4    5
CONECT    5    6   17   25
CONECT    6    7   16
CONECT    7    8    8   26
CONECT    8    9
CONECT    9   10   10   16
CONECT   10   11   12
CONECT   11   27
CONECT   12   13   13
CONECT   13   14   15
CONECT   14   28
CONECT   15   16   16
CONECT   17   18   19   29
CONECT   18   30
CONECT   19   20   31
CONECT   20   32
END

HMDB0000299
     RDKit          3D
Xanthosine
 32 34  0  0  0  0  0  0  0  0999 V2000
   -5.0067    0.4182    0.1166 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.9402   -0.2156    0.7502 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6340    0.5263    0.4664 C   0  0  1  0  0  0  0  0  0  0  0  0
   -1.5702   -0.0814    1.0815 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4917    0.1380    0.2334 C   0  0  1  0  0  0  0  0  0  0  0  0
    0.6755   -0.5961    0.5811 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.8007   -1.7835    1.1745 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.1211   -2.1026    1.3116 N   0  0  0  0  0  0  0  0  0  0  0  0
    2.8486   -1.0749    0.7835 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.2002   -0.8491    0.6468 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.1407   -1.7532    1.0839 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.6152    0.2873    0.0696 N   0  0  0  0  0  0  0  0  0  0  0  0
    3.7473    1.1878   -0.3669 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.1602    2.3705   -0.9673 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.4307    0.9588   -0.2292 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.9353   -0.1662    0.3436 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0880   -0.2610   -1.1025 C   0  0  2  0  0  0  0  0  0  0  0  0
   -0.3057    0.1663   -2.1617 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4024    0.4887   -1.0189 C   0  0  2  0  0  0  0  0  0  0  0  0
   -2.1694    1.7656   -1.5303 O   0  0  0  0  0  0  0  0  0  0  0  0
   -5.3116   -0.1290   -0.6555 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.8044   -1.2496    0.3711 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.1719   -0.2265    1.8297 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6865    1.5764    0.8417 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3244    1.2413    0.1944 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0432   -2.3859    1.4913 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.4603   -1.8406    2.0276 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.7331    2.7399   -1.8119 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2653   -1.3672   -1.1357 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.6039   -0.1954   -2.0099 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.2100   -0.0297   -1.5692 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0472    2.4422   -0.8396 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
  6  7  1  0
  7  8  2  0
  8  9  1  0
  9 10  2  0
 10 11  1  0
 10 12  1  0
 12 13  2  0
 13 14  1  0
 13 15  1  0
 15 16  2  0
  5 17  1  0
 17 18  1  0
 17 19  1  0
 19 20  1  0
 19  3  1  0
 16  6  1  0
 16  9  1  0
  1 21  1  0
  2 22  1  0
  2 23  1  0
  3 24  1  1
  5 25  1  6
  7 26  1  0
 11 27  1  0
 14 28  1  0
 17 29  1  1
 18 30  1  0
 19 31  1  6
 20 32  1  0
M  END

Synonyms

Value	Source
9-beta-D-Ribofuranosyl-3,9-dihydro-1H-purine-2,6-dione	ChEBI
9-beta-D-Ribofuranosylxanthine	ChEBI
Xanthine 9-beta-D-ribofuranoside	ChEBI
Xanthine riboside	ChEBI
9-b-D-Ribofuranosyl-3,9-dihydro-1H-purine-2,6-dione	Generator
9-Β-D-ribofuranosyl-3,9-dihydro-1H-purine-2,6-dione	Generator
9-b-D-Ribofuranosylxanthine	Generator
9-Β-D-ribofuranosylxanthine	Generator
Xanthine 9-b-D-ribofuranoside	Generator
Xanthine 9-β-D-ribofuranoside	Generator
3,9-Dihydro-9-b-D-ribofuranosyl-1H-purine-2,6-dione	HMDB
3,9-Dihydro-9-beta-delta-ribofuranosyl-1H-purine-2,6-dione	HMDB
3,9-Dihydro-9-D-ribofuranosyl-1H-purine-2,6-dione	HMDB
3,9-Dihydro-9-delta-ribofuranosyl-1H-purine-2,6-dione	HMDB
9-beta-delta-Ribofuranosylxanthine	HMDB
9-D-Ribofuranosylxanthine	HMDB
9-delta-Ribofuranosylxanthine	HMDB
9 beta-D-Ribofuranosylxanthine	HMDB

Molecular Formula

C₁₀H₁₂N₄O₆

Average Mass

284.2255

Monoisotopic Mass

284.075684136

IUPAC Name

9-[(2R,3R,4S,5R)-3,4-dihydroxy-5-(hydroxymethyl)oxolan-2-yl]-9H-purine-2,6-diol

Traditional Name

9-[(2R,3R,4S,5R)-3,4-dihydroxy-5-(hydroxymethyl)oxolan-2-yl]purine-2,6-diol

CAS Registry Number

Not Available

SMILES

OC[C@H]1O[C@H]([C@H](O)[C@@H]1O)N1C=NC2=C1N=C(O)N=C2O

InChI Identifier

InChI=1S/C10H12N4O6/c15-1-3-5(16)6(17)9(20-3)14-2-11-4-7(14)12-10(19)13-8(4)18/h2-3,5-6,9,15-17H,1H2,(H2,12,13,18,19)/t3-,5-,6-,9-/m1/s1

InChI Key

UBORTCNDUKBEOP-UUOKFMHZSA-N

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as purine nucleosides. Purine nucleosides are compounds comprising a purine base attached to a ribosyl or deoxyribosyl moiety.

Kingdom

Organic compounds

Super Class

Nucleosides, nucleotides, and analogues

Class

Purine nucleosides

Sub Class

Not Available

Direct Parent

Purine nucleosides

Alternative Parents

Substituents

Purine nucleoside
Glycosyl compound
N-glycosyl compound
Xanthine
6-oxopurine
Purinone
Pentose monosaccharide
Purine
Imidazopyrimidine
Alkaloid or derivatives
Pyrimidone
Pyrimidine
Monosaccharide
N-substituted imidazole
Imidazole
Heteroaromatic compound
Tetrahydrofuran
Azole
Vinylogous amide
Lactam
Urea
Secondary alcohol
Organoheterocyclic compound
Azacycle
Oxacycle
Organooxygen compound
Organonitrogen compound
Organic nitrogen compound
Hydrocarbon derivative
Organic oxide
Organopnictogen compound
Organic oxygen compound
Alcohol
Primary alcohol
Aromatic heteropolycyclic compound

Molecular Framework

Aromatic heteropolycyclic compounds

External Descriptors

xanthosines (CHEBI:18107 )
Purine alkaloids (C01762 )

Functional Ontology

Not Available

Physical Properties

State

Expected Solid

Predicted Properties

Property	Value	Source
Water Solubility	27.8 g/L	ALOGPS
logP	-1.6	ALOGPS
logP	-1.2	ChemAxon
logS	-1	ALOGPS
pKa (Strongest Acidic)	11.33	ChemAxon
pKa (Strongest Basic)	0.078	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	9	ChemAxon
Hydrogen Donor Count	5	ChemAxon
Polar Surface Area	153.98 Å²	ChemAxon
Rotatable Bond Count	2	ChemAxon
Refractivity	62.4 m³·mol⁻¹	ChemAxon
Polarizability	25.55 Å³	ChemAxon
Number of Rings	3	ChemAxon
Bioavailability	Yes	ChemAxon
Rule of Five	Yes	ChemAxon
Ghose Filter	No	ChemAxon
Veber's Rule	No	ChemAxon
MDDR-like Rule	No	ChemAxon

Spectra

Chromatographic Retention Times and Retention Indices

Retention Times

Not Available

Retention Indices

Not Available

Chromatographic Retention Times and Retention Indices

Retention Times

Not Available

Retention Indices

Not Available

Biological Properties

Cellular Locations

Cytoplasm

Biospecimen Locations

Blood
Feces
Placenta
Urine

Tissue Locations

Placenta

Associated OMIM IDs

114500 (Colorectal cancer)
610247 (Eosinophilic esophagitis)

Human Proteins and Enzymes

Protein ID	Protein Name	Protein Type	Uniprot ID	Species
MMDBp0191677	5'-nucleotidase	Unknown	P21589	Homo_sapiens
MMDBp0191680	Cytosolic 5'-nucleotidase 1B	Unknown	Q96P26	Homo_sapiens
MMDBp0191681	Cytosolic 5'-nucleotidase 1A	Unknown	Q9BXI3	Homo_sapiens
MMDBp0191682	5'(3')-deoxyribonucleotidase, cytosolic type	Unknown	Q8TCD5	Homo_sapiens
MMDBp0191684	5'(3')-deoxyribonucleotidase, mitochondrial	Unknown	Q9NPB1	Homo_sapiens
MMDBp0192097	Inosine triphosphate pyrophosphatase	Unknown	Q9BY32	Homo_sapiens
MMDBp0193860	Cytosolic 5'-nucleotidase 3	Enzyme	Q9H0P0	Homo_sapiens
MMDBp0193932	Cytosolic purine 5'-nucleotidase	Unknown	P49902	Homo_sapiens
MMDBp0193933	Purine nucleoside phosphorylase	Enzyme	P00491	Homo_sapiens

Human Pathways

Pathways

Name	SMPDB/PathBank

Microbial Pathways

Pathways

Not Available

Metabolic Reactions

Reactions

This table shows at most 20 reactions. For the full list of associated reactions:

See All Associated Reactions

Reaction ID	Precursor	Product	Enzyme	Reaction Type	Data Source	Reference

Health Effects and Bioactivity

Health Outcome/Bioactivity	Metabolite Response/Effect	Evidence Type	Host and Biospecimen	Data Source	Reference
Uremia		Association	Human Blood	HMDB	12675874

Microbial Sources

Superkingdom/Kingdom	Phylum	Total species	Hosts and Body Sites	Microbial Links
Bacteria	Firmicutes	389	Human feces; Human pleural fluid plaque; Pig ; Human ; Cattle	Indirect association between microbiota composition and metabolites measured in host biospecimen; Metabolic reconstruction
Bacteria	Proteobacteria	369	Human feces; Human sputum; Human ; Human unknown; Pig ; Human pleural fluid plaque; Human dental plaque; Human nasal swab; Human feces; pleural fluid plaque; bal; River trout ; Cattle	Metabolic reconstruction
Bacteria	Actinobacteria	129	Human feces; Human sputum; Human bronchial brush; Human nasopharyngeal swab; Human pleural fluid plaque; Human dental plaque; Human	Metabolic reconstruction
Bacteria	Verrucomicrobia	1	Human ; Human feces	Metabolic reconstruction
Bacteria	Bacteroidetes	126	Human feces; Human appendix biopsy; Human	Metabolic reconstruction
Bacteria	Synergistetes	4	Human feces	Metabolic reconstruction
Bacteria	Spirochaetes	5	Human feces; Human	Metabolic reconstruction
Archaea	Thaumarchaeota	1	Human feces	Metabolic reconstruction
Bacteria	Fusobacteria	20	Human feces; Human	Metabolic reconstruction
Archaea	Euryarchaeota	5	Human feces; Cattle ; Human	Metabolic reconstruction
Bacteria	Candidatus Melainabacteria	1	Human feces	Metabolic reconstruction
Bacteria	Tenericutes	4	Human feces	Metabolic reconstruction
Bacteria	Planctomycetes	2	Human feces	Metabolic reconstruction
Archaea	Crenarchaeota	1	Human feces	Metabolic reconstruction
Bacteria	Chlorobi	1
Bacteria/NULL	Proteobacteria	1	Human feces; Human sputum; Human ; Human unknown; Pig ; Human pleural fluid plaque; Human dental plaque; Human nasal swab; Human feces; pleural fluid plaque; bal; River trout ; Cattle	Metabolic reconstruction
Eukaryota/Fungi	Ascomycota	1	Human feces	Unknown

Exposure Sources

Other Exposures

Source Type	Data Source	Reference

Host Biospecimen and Location

Host and Biospecimen	Status	Mean	Std	Age	Sex	Health Condition	Data Source	Reference
Human Feces	Detected but not Quantified						HMDB
Human	Detected and Quantified	0.340	0.221	Adult (>18 years old)	Both	Uremia	HMDB	12675874
Human	Detected and Quantified	0.0842	0.0451	Adult (>18 years old)	Both	Normal	HMDB	12675874
Human	Detected and Quantified	0.59	0.36	Adult (>18 years old)	Female	Normal	HMDB	9129323
Human	Detected and Quantified	5.08	0.30	Adult (>18 years old)	Both	Normal	HMDB	16139832
Human Placenta	Detected but not Quantified			Not Specified	Not Specified	Normal	HMDB	34986597
Human Feces	Detected but not Quantified			Children (6 - 18 years old)	Not Specified	Normal	HMDB	27609529
Human Feces	Detected but not Quantified			Adult (>18 years old)	Both	Normal	HMDB	27543620
Human Feces	Detected but not Quantified			Adult (>18 years old)	Both	Normal	HMDB	25037050
Human Feces	Detected but not Quantified			Adult (>18 years old)	Both	Normal	HMDB	29808030
Human Urine	Detected but not Quantified			Adult (>18 years old)	Both	Normal	HMDB	32966057
Human Blood	Detected but not Quantified			Adult (>18 years old)	Both	Normal	HMDB	32966057

External Links

HMDB ID

HMDB0000299

DrugBank ID

Not Available

Phenol Explorer Compound ID

Not Available

FooDB ID

KNApSAcK ID

Chemspider ID

KEGG Compound ID

BioCyc ID

BiGG ID

Wikipedia Link

METLIN ID

PubChem Compound

PDB ID

Not Available

ChEBI ID

18107

Food Biomarker Ontology

Not Available

CMMC Knowledgebase

Not Available

General References

Liebich HM, Di Stefano C, Wixforth A, Schmid HR: Quantitation of urinary nucleosides by high-performance liquid chromatography. J Chromatogr A. 1997 Feb 28;763(1-2):193-7. doi: 10.1016/s0021-9673(96)00757-1. [PubMed:9129323 ]
Marti R, Nishigaki Y, Hirano M: Elevated plasma deoxyuridine in patients with thymidine phosphorylase deficiency. Biochem Biophys Res Commun. 2003 Mar 28;303(1):14-8. doi: 10.1016/s0006-291x(03)00294-8. [PubMed:12646159 ]
Dudley E, Lemiere F, Van Dongen W, Tuytten R, El-Sharkawi S, Brenton AG, Esmans EL, Newton RP: Analysis of urinary nucleosides. IV. Identification of urinary purine nucleosides by liquid chromatography/electrospray mass spectrometry. Rapid Commun Mass Spectrom. 2004;18(22):2730-8. doi: 10.1002/rcm.1685. [PubMed:15499664 ]
Khalil PN, Erb N, Khalil MN, Escherich G, Janka-Schaub GE: Validation and application of a high-performance liquid chromatographic-based assay for determination of the inosine 5'-monophosphate dehydrogenase activity in erythrocytes. J Chromatogr B Analyt Technol Biomed Life Sci. 2006 Sep 14;842(1):1-7. doi: 10.1016/j.jchromb.2006.04.040. Epub 2006 May 24. [PubMed:16725387 ]
Elshenawy S, Pinney SE, Stuart T, Doulias PT, Zura G, Parry S, Elovitz MA, Bennett MJ, Bansal A, Strauss JF 3rd, Ischiropoulos H, Simmons RA: The Metabolomic Signature of the Placenta in Spontaneous Preterm Birth. Int J Mol Sci. 2020 Feb 4;21(3). pii: ijms21031043. doi: 10.3390/ijms21031043. [PubMed:32033212 ]

Showing metabocard for Xanthosine (MMDBc0000338)

MOL for #<Metabolite:0x0000560be07b7270>

3D MOL for #<Metabolite:0x0000560be07b7270>

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3D-SDF for #<Metabolite:0x0000560be07b7270>

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3D PDB for #<Metabolite:0x0000560be07b7270>

SMILES for #<Metabolite:0x0000560be07b7270>

INCHI for #<Metabolite:0x0000560be07b7270>

Structure for #<Metabolite:0x0000560be07b7270>

3D Structure for #<Metabolite:0x0000560be07b7270>