MiMeDB: Showing metabocard for UDP-D-Xylose (MMDBc0048830)

Record Information

Version

1.0

Status

Detected and Quantified

Creation Date

2022-04-29 22:11:35 UTC

Update Date

2024-04-30 20:37:15 UTC

Metabolite ID

MMDBc0048830

Metabolite Identification

Common Name

UDP-D-Xylose

Description

Uridine diphosphate xylose is important intermediate in the Nucleotide sugars metabolism and chondroitin sulfate biosynthesis (KEGG). The decarboxylation product of UDPglucuronic acid, which is used for formation of the xylosides of seryl hydroxyl groups in mucoprotein synthesis.

Structure

MOL SDF PDB SMILES InChI


  Mrv1652305221920112D          

 42 44  0  0  1  0            999 V2000
   -2.4757    3.8205    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9908    4.4879    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.2893    9.8372    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0231    6.9486    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.4608   10.6442    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   -0.7615    6.6937    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   -3.2962    3.9067    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.8477   11.1962    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   -1.4289    7.1786    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   -2.0964    6.6937    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    3.0631   10.9413    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   -1.8414    5.9090    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    2.8916   10.1343    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   -3.1468    5.3278    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.6318    4.6604    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3264    5.2416    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    5.2454   10.8991    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.7811    3.2393    0.0000 O   0  5  0  0  0  0  0  0  0  0  0  0
    4.0192   12.0032    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4289    8.0036    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8810    6.9486    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.4500   11.4933    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.4824    6.0815    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.7243    8.7951    0.0000 O   0  5  0  0  0  0  0  0  0  0  0  0
    1.2342    7.2259    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.1284    9.2439    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.7424    8.9009    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.5047    9.5823    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.1946    7.7556    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0164    5.9090    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.1069    9.8794    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.7639    8.2654    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.9793    8.0105    0.0000 P   0  0  0  0  0  0  0  0  0  0  0  0
    1.9354    9.0724    0.0000 P   0  0  0  0  0  0  0  0  0  0  0  0
    4.6323   11.4512    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6324    7.5085    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.6762   10.3893    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1640    7.5531    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6797    6.1103    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.2346   11.7483    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4669    5.1739    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.2785   10.6864    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
  2  1  2  0  0  0  0
  5  3  1  0  0  0  0
  6  4  1  1  0  0  0
  7  1  1  0  0  0  0
  8  5  1  0  0  0  0
  9  6  1  0  0  0  0
 10  9  1  0  0  0  0
 11  8  1  0  0  0  0
 12 10  1  0  0  0  0
 13 11  1  0  0  0  0
 15  7  2  0  0  0  0
 15 14  1  0  0  0  0
 16  2  1  0  0  0  0
 12 16  1  1  0  0  0
 16 14  1  0  0  0  0
  5 17  1  6  0  0  0
 18  7  1  0  0  0  0
  8 19  1  6  0  0  0
  9 20  1  6  0  0  0
 10 21  1  6  0  0  0
 11 22  1  6  0  0  0
 23 14  2  0  0  0  0
 28  3  1  0  0  0  0
 28 13  1  0  0  0  0
 29  4  1  0  0  0  0
 30  6  1  0  0  0  0
 30 12  1  0  0  0  0
 13 31  1  6  0  0  0
 33 24  1  0  0  0  0
 33 25  2  0  0  0  0
 33 29  1  0  0  0  0
 33 32  1  0  0  0  0
 34 26  1  0  0  0  0
 34 27  2  0  0  0  0
 34 31  1  0  0  0  0
 34 32  1  0  0  0  0
  5 35  1  1  0  0  0
  6 36  1  6  0  0  0
  8 37  1  6  0  0  0
  9 38  1  1  0  0  0
 10 39  1  1  0  0  0
 11 40  1  1  0  0  0
 12 41  1  6  0  0  0
 13 42  1  1  0  0  0
M  CHG  2  18  -1  24  -1
M  END


  Mrv1652305221920112D          

 42 44  0  0  1  0            999 V2000
   -2.4757    3.8205    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9908    4.4879    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.2893    9.8372    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0231    6.9486    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.4608   10.6442    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   -0.7615    6.6937    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   -3.2962    3.9067    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.8477   11.1962    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   -1.4289    7.1786    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   -2.0964    6.6937    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    3.0631   10.9413    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   -1.8414    5.9090    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    2.8916   10.1343    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   -3.1468    5.3278    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.6318    4.6604    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3264    5.2416    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    5.2454   10.8991    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.7811    3.2393    0.0000 O   0  5  0  0  0  0  0  0  0  0  0  0
    4.0192   12.0032    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4289    8.0036    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8810    6.9486    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.4500   11.4933    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.4824    6.0815    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.7243    8.7951    0.0000 O   0  5  0  0  0  0  0  0  0  0  0  0
    1.2342    7.2259    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.1284    9.2439    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.7424    8.9009    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.5047    9.5823    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.1946    7.7556    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0164    5.9090    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.1069    9.8794    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.7639    8.2654    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.9793    8.0105    0.0000 P   0  0  0  0  0  0  0  0  0  0  0  0
    1.9354    9.0724    0.0000 P   0  0  0  0  0  0  0  0  0  0  0  0
    4.6323   11.4512    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6324    7.5085    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.6762   10.3893    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1640    7.5531    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6797    6.1103    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.2346   11.7483    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4669    5.1739    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.2785   10.6864    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
  2  1  2  0  0  0  0
  5  3  1  0  0  0  0
  6  4  1  1  0  0  0
  7  1  1  0  0  0  0
  8  5  1  0  0  0  0
  9  6  1  0  0  0  0
 10  9  1  0  0  0  0
 11  8  1  0  0  0  0
 12 10  1  0  0  0  0
 13 11  1  0  0  0  0
 15  7  2  0  0  0  0
 15 14  1  0  0  0  0
 16  2  1  0  0  0  0
 12 16  1  1  0  0  0
 16 14  1  0  0  0  0
  5 17  1  6  0  0  0
 18  7  1  0  0  0  0
  8 19  1  6  0  0  0
  9 20  1  6  0  0  0
 10 21  1  6  0  0  0
 11 22  1  6  0  0  0
 23 14  2  0  0  0  0
 28  3  1  0  0  0  0
 28 13  1  0  0  0  0
 29  4  1  0  0  0  0
 30  6  1  0  0  0  0
 30 12  1  0  0  0  0
 13 31  1  6  0  0  0
 33 24  1  0  0  0  0
 33 25  2  0  0  0  0
 33 29  1  0  0  0  0
 33 32  1  0  0  0  0
 34 26  1  0  0  0  0
 34 27  2  0  0  0  0
 34 31  1  0  0  0  0
 34 32  1  0  0  0  0
  5 35  1  1  0  0  0
  6 36  1  6  0  0  0
  8 37  1  6  0  0  0
  9 38  1  1  0  0  0
 10 39  1  1  0  0  0
 11 40  1  1  0  0  0
 12 41  1  6  0  0  0
 13 42  1  1  0  0  0
M  CHG  2  18  -1  24  -1
M  END
> <DATABASE_ID>
MMDBc0048830

> <DATABASE_NAME>
MIME

> <SMILES>
[H][C@]1(COP([O-])(=O)OP(O)(=O)O[C@@]2([H])OC[C@@]([H])(O)[C@]([H])(O)[C@@]2([H])O)O[C@@]([H])(N2C=CC([O-])=NC2=O)[C@]([H])(O)[C@]1([H])O

> <INCHI_IDENTIFIER>
InChI=1S/C14H22N2O16P2/c17-5-3-28-13(11(22)8(5)19)31-34(26,27)32-33(24,25)29-4-6-9(20)10(21)12(30-6)16-2-1-7(18)15-14(16)23/h1-2,5-6,8-13,17,19-22H,3-4H2,(H,24,25)(H,26,27)(H,15,18,23)/p-2/t5-,6-,8+,9-,10-,11-,12-,13-/m1/s1

> <INCHI_KEY>
DQQDLYVHOTZLOR-OCIMBMBZSA-L

> <FORMULA>
C14H20N2O16P2

> <MOLECULAR_WEIGHT>
534.2599

> <EXACT_MASS>
534.028805626

> <JCHEM_ACCEPTOR_COUNT>
14

> <JCHEM_ATOM_COUNT>
54

> <JCHEM_AVERAGE_POLARIZABILITY>
42.81120190982726

> <JCHEM_BIOAVAILABILITY>
0

> <JCHEM_DONOR_COUNT>
6

> <JCHEM_FORMAL_CHARGE>
-2

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
1-[(2R,3R,4S,5R)-3,4-dihydroxy-5-({[hydroxy({[(2R,3R,4S,5R)-3,4,5-trihydroxyoxan-2-yl]oxy})phosphoryl phosphono]oxy}methyl)oxolan-2-yl]-2-oxo-1,2-dihydropyrimidin-4-olate

> <ALOGPS_LOGP>
-1.69

> <JCHEM_LOGP>
-3.9987723323333335

> <ALOGPS_LOGS>
-1.11

> <JCHEM_MDDR_LIKE_RULE>
1

> <JCHEM_NUMBER_OF_RINGS>
3

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-2

> <JCHEM_PKA>
3.1763411018919383

> <JCHEM_PKA_STRONGEST_ACIDIC>
1.7326517523572988

> <JCHEM_PKA_STRONGEST_BASIC>
-3.526611516883185

> <JCHEM_POLAR_SURFACE_AREA>
280.46

> <JCHEM_REFRACTIVITY>
110.24359999999999

> <JCHEM_ROTATABLE_BOND_COUNT>
8

> <JCHEM_RULE_OF_FIVE>
0

> <ALOGPS_SOLUBILITY>
4.44e+01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
1-[(2R,3R,4S,5R)-3,4-dihydroxy-5-({[hydroxy([(2R,3R,4S,5R)-3,4,5-trihydroxyoxan-2-yl]oxy)phosphoryl phosphono]oxy}methyl)oxolan-2-yl]-2-oxopyrimidin-4-olate

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 22-MAY-19   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   22-MAY-19         0                                  
HETATM    1  C   UNK     0      -4.621   7.132   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0      -3.716   8.377   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       8.007  18.363   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       0.043  12.971   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       8.327  19.869   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0      -1.421  12.495   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0      -6.153   7.293   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0       7.182  20.900   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0      -2.667  13.400   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0      -3.913  12.495   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0       5.718  20.424   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0      -3.437  11.030   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0       5.398  18.917   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0      -5.874   9.945   0.000  0.00  0.00           C+0
HETATM   15  N   UNK     0      -6.779   8.699   0.000  0.00  0.00           N+0
HETATM   16  N   UNK     0      -4.343   9.784   0.000  0.00  0.00           N+0
HETATM   17  O   UNK     0       9.791  20.345   0.000  0.00  0.00           O+0
HETATM   18  O   UNK     0      -7.058   6.047   0.000  0.00  0.00           O-1
HETATM   19  O   UNK     0       7.503  22.406   0.000  0.00  0.00           O+0
HETATM   20  O   UNK     0      -2.667  14.940   0.000  0.00  0.00           O+0
HETATM   21  O   UNK     0      -5.378  12.971   0.000  0.00  0.00           O+0
HETATM   22  O   UNK     0       4.573  21.454   0.000  0.00  0.00           O+0
HETATM   23  O   UNK     0      -6.500  11.352   0.000  0.00  0.00           O+0
HETATM   24  O   UNK     0       1.352  16.418   0.000  0.00  0.00           O-1
HETATM   25  O   UNK     0       2.304  13.488   0.000  0.00  0.00           O+0
HETATM   26  O   UNK     0       2.106  17.255   0.000  0.00  0.00           O+0
HETATM   27  O   UNK     0       5.119  16.615   0.000  0.00  0.00           O+0
HETATM   28  O   UNK     0       6.542  17.887   0.000  0.00  0.00           O+0
HETATM   29  O   UNK     0       0.363  14.477   0.000  0.00  0.00           O+0
HETATM   30  O   UNK     0      -1.897  11.030   0.000  0.00  0.00           O+0
HETATM   31  O   UNK     0       3.933  18.442   0.000  0.00  0.00           O+0
HETATM   32  O   UNK     0       3.293  15.429   0.000  0.00  0.00           O+0
HETATM   33  P   UNK     0       1.828  14.953   0.000  0.00  0.00           P+0
HETATM   34  P   UNK     0       3.613  16.935   0.000  0.00  0.00           P+0
HETATM   35  H   UNK     0       8.647  21.376   0.000  0.00  0.00           H+0
HETATM   36  H   UNK     0      -1.181  14.016   0.000  0.00  0.00           H+0
HETATM   37  H   UNK     0       6.862  19.393   0.000  0.00  0.00           H+0
HETATM   38  H   UNK     0      -4.040  14.099   0.000  0.00  0.00           H+0
HETATM   39  H   UNK     0      -5.002  11.406   0.000  0.00  0.00           H+0
HETATM   40  H   UNK     0       6.038  21.930   0.000  0.00  0.00           H+0
HETATM   41  H   UNK     0      -2.738   9.658   0.000  0.00  0.00           H+0
HETATM   42  H   UNK     0       4.253  19.948   0.000  0.00  0.00           H+0
CONECT    1    2    7                                                       
CONECT    2    1   16                                                       
CONECT    3    5   28                                                       
CONECT    4    6   29                                                       
CONECT    5    3    8   17   35                                             
CONECT    6    4    9   30   36                                             
CONECT    7    1   15   18                                                  
CONECT    8    5   11   19   37                                             
CONECT    9    6   10   20   38                                             
CONECT   10    9   12   21   39                                             
CONECT   11    8   13   22   40                                             
CONECT   12   10   16   30   41                                             
CONECT   13   11   28   31   42                                             
CONECT   14   15   16   23                                                  
CONECT   15    7   14                                                       
CONECT   16    2   12   14                                                  
CONECT   17    5                                                            
CONECT   18    7                                                            
CONECT   19    8                                                            
CONECT   20    9                                                            
CONECT   21   10                                                            
CONECT   22   11                                                            
CONECT   23   14                                                            
CONECT   24   33                                                            
CONECT   25   33                                                            
CONECT   26   34                                                            
CONECT   27   34                                                            
CONECT   28    3   13                                                       
CONECT   29    4   33                                                       
CONECT   30    6   12                                                       
CONECT   31   13   34                                                       
CONECT   32   33   34                                                       
CONECT   33   24   25   29   32                                             
CONECT   34   26   27   31   32                                             
CONECT   35    5                                                            
CONECT   36    6                                                            
CONECT   37    8                                                            
CONECT   38    9                                                            
CONECT   39   10                                                            
CONECT   40   11                                                            
CONECT   41   12                                                            
CONECT   42   13                                                            
MASTER        0    0    0    0    0    0    0    0   42    0   88    0
END

Synonyms

Value	Source
UDP-alpha-D-Xylose	ChEBI
UDP-alpha-D-Xylose dianion	ChEBI
UDP-a-D-Xylose	Generator
UDP-Α-D-xylose	Generator
UDP-a-D-Xylose dianion	Generator
UDP-Α-D-xylose dianion	Generator

Molecular Formula

C₁₄H₂₀N₂O₁₆P₂

Average Mass

534.2599

Monoisotopic Mass

534.028805626

IUPAC Name

1-[(2R,3R,4S,5R)-3,4-dihydroxy-5-({[hydroxy({[(2R,3R,4S,5R)-3,4,5-trihydroxyoxan-2-yl]oxy})phosphoryl phosphono]oxy}methyl)oxolan-2-yl]-2-oxo-1,2-dihydropyrimidin-4-olate

Traditional Name

1-[(2R,3R,4S,5R)-3,4-dihydroxy-5-({[hydroxy([(2R,3R,4S,5R)-3,4,5-trihydroxyoxan-2-yl]oxy)phosphoryl phosphono]oxy}methyl)oxolan-2-yl]-2-oxopyrimidin-4-olate

CAS Registry Number

Not Available

SMILES

[H][C@]1(COP([O-])(=O)OP(O)(=O)O[C@@]2([H])OC[C@@]([H])(O)[C@]([H])(O)[C@@]2([H])O)O[C@@]([H])(N2C=CC([O-])=NC2=O)[C@]([H])(O)[C@]1([H])O

InChI Identifier

InChI=1S/C14H22N2O16P2/c17-5-3-28-13(11(22)8(5)19)31-34(26,27)32-33(24,25)29-4-6-9(20)10(21)12(30-6)16-2-1-7(18)15-14(16)23/h1-2,5-6,8-13,17,19-22H,3-4H2,(H,24,25)(H,26,27)(H,15,18,23)/p-2/t5-,6-,8+,9-,10-,11-,12-,13-/m1/s1

InChI Key

DQQDLYVHOTZLOR-OCIMBMBZSA-L

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as pyrimidine ribonucleoside diphosphates. These are pyrimidine ribonucleotides with diphosphate group linked to the ribose moiety.

Kingdom

Organic compounds

Super Class

Nucleosides, nucleotides, and analogues

Class

Pyrimidine nucleotides

Sub Class

Pyrimidine ribonucleotides

Direct Parent

Pyrimidine ribonucleoside diphosphates

Alternative Parents

Substituents

Pyrimidine ribonucleoside diphosphate
Pentose phosphate
Pentose-5-phosphate
Glycosyl compound
N-glycosyl compound
Monosaccharide phosphate
Organic pyrophosphate
Pyrimidone
Hydropyrimidine
Monosaccharide
Organic phosphoric acid derivative
Oxane
Phosphoric acid ester
Pyrimidine
Alkyl phosphate
Heteroaromatic compound
Vinylogous amide
Tetrahydrofuran
Lactam
Urea
Secondary alcohol
Azacycle
Oxacycle
Polyol
Organoheterocyclic compound
Alcohol
Hydrocarbon derivative
Organic oxide
Organic nitrogen compound
Organonitrogen compound
Organooxygen compound
Organic oxygen compound
Organopnictogen compound
Organic anion
Aromatic heteromonocyclic compound

Molecular Framework

Aromatic heteromonocyclic compounds

External Descriptors

nucleotide-sugar oxoanion (CHEBI:57632 )

Functional Ontology

Not Available

Physical Properties

State

Expected Solid

Predicted Properties

Property	Value	Source
Water Solubility	44.4 g/L	ALOGPS
logP	-1.7	ALOGPS
logP	-4	ChemAxon
logS	-1.1	ALOGPS
pKa (Strongest Acidic)	1.73	ChemAxon
pKa (Strongest Basic)	-3.5	ChemAxon
Physiological Charge	-2	ChemAxon
Hydrogen Acceptor Count	14	ChemAxon
Hydrogen Donor Count	6	ChemAxon
Polar Surface Area	280.46 Å²	ChemAxon
Rotatable Bond Count	8	ChemAxon
Refractivity	110.24 m³·mol⁻¹	ChemAxon
Polarizability	42.81 Å³	ChemAxon
Number of Rings	3	ChemAxon
Bioavailability	No	ChemAxon
Rule of Five	No	ChemAxon
Ghose Filter	No	ChemAxon
Veber's Rule	No	ChemAxon
MDDR-like Rule	Yes	ChemAxon

Spectra

Spectrum Type	Description	Splash Key	Deposition Date	View
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Positive	splash10-000i-0300190000-c82186e086ad12d7f048	2016-08-03	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Positive	splash10-03gi-0661090000-e50c51155436fc000036	2016-08-03	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Positive	splash10-05ur-9500000000-a508624fffd0623f8974	2016-08-03	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Negative	splash10-001l-8100190000-eefddd6f1f288d1ddd68	2016-08-03	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Negative	splash10-003r-6942070000-e60d3fa9feacb604a3c6	2016-08-03	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Negative	splash10-005c-9110000000-4be1f1cda4e8bc2c2cb9	2016-08-03	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 100 MHz, H₂O, predicted)		2022-08-18	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 100 MHz, H₂O, predicted)		2022-08-18	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 1000 MHz, H₂O, predicted)		2022-08-18	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 1000 MHz, H₂O, predicted)		2022-08-18	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 200 MHz, H₂O, predicted)		2022-08-18	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 200 MHz, H₂O, predicted)		2022-08-18	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 300 MHz, H₂O, predicted)		2022-08-18	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 300 MHz, H₂O, predicted)		2022-08-18	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 400 MHz, H₂O, predicted)		2022-08-18	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 400 MHz, H₂O, predicted)		2022-08-18	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 500 MHz, H₂O, predicted)		2022-08-18	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 500 MHz, H₂O, predicted)		2022-08-18	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 600 MHz, H₂O, predicted)		2022-08-18	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 600 MHz, H₂O, predicted)		2022-08-18	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 700 MHz, H₂O, predicted)		2022-08-18	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 700 MHz, H₂O, predicted)		2022-08-18	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 800 MHz, H₂O, predicted)		2022-08-18	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 800 MHz, H₂O, predicted)		2022-08-18	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 900 MHz, H₂O, predicted)		2022-08-18	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 900 MHz, H₂O, predicted)		2022-08-18	View Spectrum

Biological Properties

Cellular Locations

Endoplasmic reticulum
Golgi apparatus

Biospecimen Locations

Adipose Tissue
Epidermis
Feces
Fibroblasts
Intestine
Kidney
Liver
Neuron
Spleen
Testis

Tissue Locations

Not Available

Associated OMIM IDs

114500 (Colorectal cancer)
610247 (Eosinophilic esophagitis)

Human Proteins and Enzymes

Protein ID	Protein Name	Protein Type	Uniprot ID	Species

Human Pathways

Pathways

Name	SMPDB/PathBank

Metabolic Reactions

Reactions

Reaction ID	Precursor	Product	Enzyme	Reaction Type	Data Source	Reference
MMDBr0002317	UDP-Glucuronic acid	UDP-D-Xylose	UDP-glucuronate decarboxylase 1		VMH; KEGG	30371894
MMDBr0010273	UDP-Glucuronic acid	UDP-D-Xylose	UDP-glucuronate decarboxylase 1		VMH; KEGG	30371894

Health Effects and Bioactivity

Health Outcome/Bioactivity	Metabolite Response/Effect	Evidence Type	Host and Biospecimen	Data Source	Reference

Microbial Sources

Superkingdom/Kingdom	Phylum	Total species	Hosts and Body Sites	Microbial Links
Eukaryota/Fungi	Basidiomycota	4

Exposure Sources

Source Type	Source Sub-type	Species	Data Source	Reference

Host Biospecimen and Location

Host and Biospecimen	Status	Age	Sex	Health Condition	Data Source	Reference
Human Feces	Detected but not Quantified				HMDB
Human Adipose tissue	Detected but not Quantified	Not Specified	Not Specified	Normal	HMDB	34986597
Human Epidermis	Detected but not Quantified	Not Specified	Not Specified	Normal	HMDB	34986597
Human Fibroblasts	Detected but not Quantified	Not Specified	Not Specified	Normal	HMDB	34986597
Human Intestine	Detected but not Quantified	Not Specified	Not Specified	Normal	HMDB	34986597
Human Kidney	Detected but not Quantified	Not Specified	Not Specified	Normal	HMDB	34986597
Human Liver	Detected but not Quantified	Not Specified	Not Specified	Normal	HMDB	34986597
Human Neuron	Detected but not Quantified	Not Specified	Not Specified	Normal	HMDB	34986597
Human Spleen	Detected but not Quantified	Not Specified	Not Specified	Normal	HMDB	34986597
Human Testis	Detected but not Quantified	Not Specified	Not Specified	Normal	HMDB	34986597

External Links

HMDB ID

Not Available

DrugBank ID

Not Available

Phenol Explorer Compound ID

Not Available

FooDB ID

FDB005661

KNApSAcK ID

Not Available

Chemspider ID

Not Available

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

16667349

PDB ID

Not Available

ChEBI ID

57632

Food Biomarker Ontology

Not Available

References

Synthesis Reference

Not Available

General References

Gallai V, Mazzotta G, Montesi S, Sarchielli P, Del Gatto F: Effects of uridine in the treatment of diabetic neuropathy: an electrophysiological study. Acta Neurol Scand. 1992 Jul;86(1):3-7. doi: 10.1111/j.1600-0404.1992.tb08045.x. [PubMed:1325728 ]
Moore A, Findlay K, Morris ID: In-vitro DNA synthesis in Leydig and other interstitial cells of the rat testis. J Endocrinol. 1992 Aug;134(2):247-55. doi: 10.1677/joe.0.1340247. [PubMed:1402535 ]
Bjarnason I, Smethurst P, Macpherson A, Walker F, McElnay JC, Passmore AP, Menzies IS: Glucose and citrate reduce the permeability changes caused by indomethacin in humans. Gastroenterology. 1992 May;102(5):1546-50. doi: 10.1016/0016-5085(92)91712-d. [PubMed:1568563 ]
Okuyama A, Koh E, Kondoh N, Nakamura M, Namiki M, Fujioka H, Mizutani S, Kiyohara H, Sonoda T: In vitro temperature sensitivity of DNA, RNA, and protein syntheses throughout puberty in human testis. Arch Androl. 1991 Jan-Feb;26(1):7-13. doi: 10.3109/01485019108987619. [PubMed:1706913 ]
Nakamura M, Namiki M, Okuyama A, Koh E, Kondoh N, Takeyama M, Fujioka H, Nishimune Y, Matsumoto K, Matsuda M: Optimal temperature for synthesis of DNA, RNA, and protein by human testis in vitro. Arch Androl. 1988;20(1):41-4. doi: 10.3109/01485018808987051. [PubMed:2455487 ]
Nakamura M, Nonomura N, Namiki M, Okuyama A, Koh E, Kondoh N, Fujioka H, Nishimune Y, Matsumoto K, Matsuda M: DNA and RNA synthesis by postpubertal undescended testis in vitro. Arch Androl. 1989;22(1):91-4. doi: 10.3109/01485018908986756. [PubMed:2469403 ]
Pierard-Franchimont C, Damseaux M, Melotte P, Pierard GE: The fate of hypodermis after liposuction surgery. J Am Acad Dermatol. 1988 Oct;19(4):723-8. doi: 10.1016/s0190-9622(88)70228-5. [PubMed:3183095 ]
Nasrallah SM, Al-Khalidi UA: Clinical value of 14C-phenylacetic oil as a fat absorption test. Lancet. 1980 Feb 2;1(8162):229-31. doi: 10.1016/s0140-6736(80)90717-5. [PubMed:6101679 ]
Pal'tsyn AA, Pobedina VG, Chervonskaia NV, Badikova AK, Sanovich EIa: [Method of electron-autoradiographic study of nucleic acid biosynthesis in bacteria during phagocytosis]. Biull Eksp Biol Med. 1981 Jun;91(6):763-5. [PubMed:6168317 ]
Cherwinski HM, Cohn RG, Cheung P, Webster DJ, Xu YZ, Caulfield JP, Young JM, Nakano G, Ransom JT: The immunosuppressant leflunomide inhibits lymphocyte proliferation by inhibiting pyrimidine biosynthesis. J Pharmacol Exp Ther. 1995 Nov;275(2):1043-9. [PubMed:7473131 ]
Thorell L, Sjoberg LB, Hernell O: Nucleotides in human milk: sources and metabolism by the newborn infant. Pediatr Res. 1996 Dec;40(6):845-52. doi: 10.1203/00006450-199612000-00012. [PubMed:8947961 ]
Saliba F, Hagipantelli R, Misset JL, Bastian G, Vassal G, Bonnay M, Herait P, Cote C, Mahjoubi M, Mignard D, Cvitkovic E: Pathophysiology and therapy of irinotecan-induced delayed-onset diarrhea in patients with advanced colorectal cancer: a prospective assessment. J Clin Oncol. 1998 Aug;16(8):2745-51. doi: 10.1200/JCO.1998.16.8.2745. [PubMed:9704727 ]
Kost S, Keinert K, Glaser FH: [D-xylose test of resorption as a method to determine radiation side effects in the small intestine]. Strahlenther Onkol. 1998 Sep;174(9):462-7. doi: 10.1007/BF03038624. [PubMed:9765687 ]
Yamamoto T, Moriwaki Y, Cheng J, Takahashi S, Tsutsumi Z, Ka T, Hada T: Effect of inosine on the plasma concentration of uridine and purine bases. Metabolism. 2002 Apr;51(4):438-42. doi: 10.1053/meta.2002.31322. [PubMed:11912550 ]
Molina JM, Tourneur M, Sarfati C, Chevret S, de Gouvello A, Gobert JG, Balkan S, Derouin F: Fumagillin treatment of intestinal microsporidiosis. N Engl J Med. 2002 Jun 20;346(25):1963-9. doi: 10.1056/NEJMoa012924. [PubMed:12075057 ]
Chilov D, Fux C, Joch H, Fussenegger M: Identification of a novel proliferation-inducing determinant using lentiviral expression cloning. Nucleic Acids Res. 2003 Sep 15;31(18):e113. doi: 10.1093/nar/gng115. [PubMed:12954789 ]
Yong J, Wan L, Dreyfuss G: Why do cells need an assembly machine for RNA-protein complexes? Trends Cell Biol. 2004 May;14(5):226-32. doi: 10.1016/j.tcb.2004.03.010. [PubMed:15130578 ]
Sterling JD, Atmodjo MA, Inwood SE, Kumar Kolli VS, Quigley HF, Hahn MG, Mohnen D: Functional identification of an Arabidopsis pectin biosynthetic homogalacturonan galacturonosyltransferase. Proc Natl Acad Sci U S A. 2006 Mar 28;103(13):5236-41. doi: 10.1073/pnas.0600120103. Epub 2006 Mar 15. [PubMed:16540543 ]
Ostergaard M, Hansen GA, Vorum H, Honore B: Proteomic profiling of fibroblasts reveals a modulating effect of extracellular calumenin on the organization of the actin cytoskeleton. Proteomics. 2006 Jun;6(12):3509-19. doi: 10.1002/pmic.200500686. [PubMed:16691550 ]
Kucera O, Lotkova H, Kand'ar R, Hezova R, Muzakova V, Cervinkova Z: The model of D-galactosamine-induced injury of rat hepatocytes in primary culture. Acta Medica (Hradec Kralove). 2006;49(1):59-65. [PubMed:16696445 ]

Showing metabocard for UDP-D-Xylose (MMDBc0048830)

MOL for #<Metabolite:0x00007fecebc8fe80>

3D MOL for #<Metabolite:0x00007fecebc8fe80>

3D SDF for #<Metabolite:0x00007fecebc8fe80>

3D-SDF for #<Metabolite:0x00007fecebc8fe80>

PDB for #<Metabolite:0x00007fecebc8fe80>

3D PDB for #<Metabolite:0x00007fecebc8fe80>

SMILES for #<Metabolite:0x00007fecebc8fe80>

INCHI for #<Metabolite:0x00007fecebc8fe80>

Structure for #<Metabolite:0x00007fecebc8fe80>

3D Structure for #<Metabolite:0x00007fecebc8fe80>