MiMeDB: Showing metabocard for GDP-beta-L-fucose (MMDBc0054491)

Record Information

Version

1.0

Status

Detected and Quantified

Creation Date

2022-06-05 23:15:31 UTC

Update Date

2022-08-12 20:09:00 UTC

Metabolite ID

MMDBc0054491

Metabolite Identification

Common Name

GDP-beta-L-fucose

Description

guanosine 5'-diphospho-fucose, also known as GDP-beta-L-fucose or diphosphate fucose, guanosine, belongs to the class of organic compounds known as purine nucleotide sugars. These are purine nucleotides bound to a saccharide derivative through the terminal phosphate group. guanosine 5'-diphospho-fucose is a strong basic compound (based on its pKa).

Structure

MOL SDF PDB SMILES InChI


  Mrv1652303231704552D          

 47 50  0  0  1  0            999 V2000
   -0.9818    2.6724    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3984    2.0890    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   -0.1435    2.8736    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6955    3.4867    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4406    4.2713    0.0000 P   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2252    4.5263    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.3440    4.0164    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1857    5.0560    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7377    5.6691    0.0000 P   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3508    5.1170    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1246    6.2211    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2897    6.2821    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0348    7.0668    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   -0.4828    6.4537    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5868    7.6799    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3319    8.4645    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   -1.0769    9.2491    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8839    9.0776    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5249    8.6360    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    0.2821    8.8075    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2700    9.4206    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.0271    8.0229    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    0.5792    7.4098    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.8341    8.1944    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2278    7.2383    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   -0.7798    7.8514    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.3242    6.6252    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.0865    1.4216    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3984    0.7541    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   -0.9818    0.1708    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1435   -0.0305    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6284   -0.6979    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1435   -1.3654    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.6411   -1.1104    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.6411   -0.2854    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.3556    0.1271    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    2.0701   -0.2854    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.7845    0.1271    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    2.0701   -1.1104    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.3556   -1.5229    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.3556   -2.3479    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1831    1.0091    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   -1.9181    1.3836    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8505    0.5241    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1831    1.8341    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   -0.5156    1.3491    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8505    2.3190    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  2  1  1  6  0  0  0
  2  3  1  1  0  0  0
  3  4  1  0  0  0  0
  4  5  1  0  0  0  0
  5  6  1  0  0  0  0
  5  7  2  0  0  0  0
  5  8  1  0  0  0  0
  8  9  1  0  0  0  0
  9 10  1  0  0  0  0
  9 11  2  0  0  0  0
  9 12  1  0  0  0  0
 13 12  1  1  0  0  0
 13 14  1  6  0  0  0
 13 15  1  0  0  0  0
 15 16  1  0  0  0  0
 16 17  1  6  0  0  0
 16 18  1  1  0  0  0
 16 19  1  0  0  0  0
 19 20  1  6  0  0  0
 19 21  1  1  0  0  0
 19 22  1  0  0  0  0
 22 23  1  6  0  0  0
 22 24  1  1  0  0  0
 22 25  1  0  0  0  0
 13 25  1  0  0  0  0
 25 26  1  1  0  0  0
 25 27  1  1  0  0  0
  2 28  1  0  0  0  0
 28 29  1  0  0  0  0
 29 30  1  6  0  0  0
 29 31  1  1  0  0  0
 31 32  1  0  0  0  0
 32 33  2  0  0  0  0
 33 34  1  0  0  0  0
 34 35  2  0  0  0  0
 31 35  1  0  0  0  0
 35 36  1  0  0  0  0
 36 37  1  0  0  0  0
 37 38  2  0  0  0  0
 37 39  1  0  0  0  0
 39 40  2  0  0  0  0
 34 40  1  0  0  0  0
 40 41  1  0  0  0  0
 29 42  1  0  0  0  0
 42 43  1  1  0  0  0
 42 44  1  6  0  0  0
 42 45  1  0  0  0  0
  2 45  1  0  0  0  0
 45 46  1  1  0  0  0
 45 47  1  1  0  0  0
M  END


  Mrv1652303231704552D          

 47 50  0  0  1  0            999 V2000
   -0.9818    2.6724    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3984    2.0890    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   -0.1435    2.8736    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6955    3.4867    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4406    4.2713    0.0000 P   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2252    4.5263    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.3440    4.0164    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1857    5.0560    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7377    5.6691    0.0000 P   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3508    5.1170    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1246    6.2211    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2897    6.2821    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0348    7.0668    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   -0.4828    6.4537    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5868    7.6799    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3319    8.4645    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   -1.0769    9.2491    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8839    9.0776    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5249    8.6360    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    0.2821    8.8075    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2700    9.4206    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.0271    8.0229    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    0.5792    7.4098    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.8341    8.1944    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2278    7.2383    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   -0.7798    7.8514    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.3242    6.6252    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.0865    1.4216    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3984    0.7541    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   -0.9818    0.1708    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1435   -0.0305    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6284   -0.6979    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1435   -1.3654    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.6411   -1.1104    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.6411   -0.2854    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.3556    0.1271    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    2.0701   -0.2854    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.7845    0.1271    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    2.0701   -1.1104    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.3556   -1.5229    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.3556   -2.3479    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1831    1.0091    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   -1.9181    1.3836    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8505    0.5241    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1831    1.8341    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   -0.5156    1.3491    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8505    2.3190    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  2  1  1  6  0  0  0
  2  3  1  1  0  0  0
  3  4  1  0  0  0  0
  4  5  1  0  0  0  0
  5  6  1  0  0  0  0
  5  7  2  0  0  0  0
  5  8  1  0  0  0  0
  8  9  1  0  0  0  0
  9 10  1  0  0  0  0
  9 11  2  0  0  0  0
  9 12  1  0  0  0  0
 13 12  1  1  0  0  0
 13 14  1  6  0  0  0
 13 15  1  0  0  0  0
 15 16  1  0  0  0  0
 16 17  1  6  0  0  0
 16 18  1  1  0  0  0
 16 19  1  0  0  0  0
 19 20  1  6  0  0  0
 19 21  1  1  0  0  0
 19 22  1  0  0  0  0
 22 23  1  6  0  0  0
 22 24  1  1  0  0  0
 22 25  1  0  0  0  0
 13 25  1  0  0  0  0
 25 26  1  1  0  0  0
 25 27  1  1  0  0  0
  2 28  1  0  0  0  0
 28 29  1  0  0  0  0
 29 30  1  6  0  0  0
 29 31  1  1  0  0  0
 31 32  1  0  0  0  0
 32 33  2  0  0  0  0
 33 34  1  0  0  0  0
 34 35  2  0  0  0  0
 31 35  1  0  0  0  0
 35 36  1  0  0  0  0
 36 37  1  0  0  0  0
 37 38  2  0  0  0  0
 37 39  1  0  0  0  0
 39 40  2  0  0  0  0
 34 40  1  0  0  0  0
 40 41  1  0  0  0  0
 29 42  1  0  0  0  0
 42 43  1  1  0  0  0
 42 44  1  6  0  0  0
 42 45  1  0  0  0  0
  2 45  1  0  0  0  0
 45 46  1  1  0  0  0
 45 47  1  1  0  0  0
M  END
> <DATABASE_ID>
MMDBc0054491

> <DATABASE_NAME>
MIME

> <SMILES>
[H][C@]1(COP(O)(=O)OP(O)(=O)O[C@@]2([H])O[C@@]([H])(C)[C@@]([H])(O)[C@@]([H])(O)[C@]2([H])O)O[C@@]([H])(N2C=NC3=C2NC(=N)N=C3O)[C@]([H])(O)[C@]1([H])O

> <INCHI_IDENTIFIER>
InChI=1S/C16H25N5O15P2/c1-4-7(22)9(24)11(26)15(33-4)35-38(30,31)36-37(28,29)32-2-5-8(23)10(25)14(34-5)21-3-18-6-12(21)19-16(17)20-13(6)27/h3-5,7-11,14-15,22-26H,2H2,1H3,(H,28,29)(H,30,31)(H3,17,19,20,27)/t4-,5+,7+,8+,9+,10+,11-,14+,15+/m0/s1

> <INCHI_KEY>
LQEBEXMHBLQMDB-JGQUBWHWSA-N

> <FORMULA>
C16H25N5O15P2

> <MOLECULAR_WEIGHT>
589.344

> <EXACT_MASS>
589.082239121

> <JCHEM_ACCEPTOR_COUNT>
16

> <JCHEM_ATOM_COUNT>
63

> <JCHEM_AVERAGE_POLARIZABILITY>
50.0448086851553

> <JCHEM_BIOAVAILABILITY>
0

> <JCHEM_DONOR_COUNT>
10

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
{[(2R,3S,4R,5R)-3,4-dihydroxy-5-(6-hydroxy-2-imino-3,9-dihydro-2H-purin-9-yl)oxolan-2-yl]methoxy}({[hydroxy({[(3S,4R,5S,6S)-3,4,5-trihydroxy-6-methyloxan-2-yl]oxy})phosphoryl]oxy})phosphinic acid

> <ALOGPS_LOGP>
-1.45

> <JCHEM_LOGP>
-4.7463169002200365

> <ALOGPS_LOGS>
-1.92

> <JCHEM_MDDR_LIKE_RULE>
1

> <JCHEM_NUMBER_OF_RINGS>
4

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-2

> <JCHEM_PKA>
2.7816533430109756

> <JCHEM_PKA_STRONGEST_ACIDIC>
1.7078968338117804

> <JCHEM_PKA_STRONGEST_BASIC>
3.3839265821482374

> <JCHEM_POLAR_SURFACE_AREA>
308.19000000000005

> <JCHEM_REFRACTIVITY>
127.54869999999997

> <JCHEM_ROTATABLE_BOND_COUNT>
8

> <JCHEM_RULE_OF_FIVE>
0

> <ALOGPS_SOLUBILITY>
7.02e+00 g/l

> <JCHEM_TRADITIONAL_IUPAC>
[(2R,3S,4R,5R)-3,4-dihydroxy-5-(6-hydroxy-2-imino-3H-purin-9-yl)oxolan-2-yl]methoxy([hydroxy([(3S,4R,5S,6S)-3,4,5-trihydroxy-6-methyloxan-2-yl]oxy)phosphoryl]oxy)phosphinic acid

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 23-MAR-17   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   23-MAR-17         0                                  
HETATM    1  H   UNK     0      -1.833   4.988   0.000  0.00  0.00           H+0
HETATM    2  C   UNK     0      -0.744   3.899   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0      -0.268   5.364   0.000  0.00  0.00           C+0
HETATM    4  O   UNK     0      -1.298   6.509   0.000  0.00  0.00           O+0
HETATM    5  P   UNK     0      -0.822   7.973   0.000  0.00  0.00           P+0
HETATM    6  O   UNK     0      -2.287   8.449   0.000  0.00  0.00           O+0
HETATM    7  O   UNK     0       0.642   7.497   0.000  0.00  0.00           O+0
HETATM    8  O   UNK     0      -0.347   9.438   0.000  0.00  0.00           O+0
HETATM    9  P   UNK     0      -1.377  10.582   0.000  0.00  0.00           P+0
HETATM   10  O   UNK     0      -2.521   9.552   0.000  0.00  0.00           O+0
HETATM   11  O   UNK     0      -0.233  11.613   0.000  0.00  0.00           O+0
HETATM   12  O   UNK     0      -2.407  11.727   0.000  0.00  0.00           O+0
HETATM   13  C   UNK     0      -1.932  13.191   0.000  0.00  0.00           C+0
HETATM   14  H   UNK     0      -0.901  12.047   0.000  0.00  0.00           H+0
HETATM   15  O   UNK     0      -2.962  14.336   0.000  0.00  0.00           O+0
HETATM   16  C   UNK     0      -2.486  15.800   0.000  0.00  0.00           C+0
HETATM   17  H   UNK     0      -2.010  17.265   0.000  0.00  0.00           H+0
HETATM   18  C   UNK     0      -3.517  16.945   0.000  0.00  0.00           C+0
HETATM   19  C   UNK     0      -0.980  16.121   0.000  0.00  0.00           C+0
HETATM   20  H   UNK     0       0.527  16.441   0.000  0.00  0.00           H+0
HETATM   21  O   UNK     0      -0.504  17.585   0.000  0.00  0.00           O+0
HETATM   22  C   UNK     0       0.051  14.976   0.000  0.00  0.00           C+0
HETATM   23  H   UNK     0       1.081  13.832   0.000  0.00  0.00           H+0
HETATM   24  O   UNK     0       1.557  15.296   0.000  0.00  0.00           O+0
HETATM   25  C   UNK     0      -0.425  13.511   0.000  0.00  0.00           C+0
HETATM   26  H   UNK     0      -1.456  14.656   0.000  0.00  0.00           H+0
HETATM   27  O   UNK     0       0.605  12.367   0.000  0.00  0.00           O+0
HETATM   28  O   UNK     0       0.161   2.654   0.000  0.00  0.00           O+0
HETATM   29  C   UNK     0      -0.744   1.408   0.000  0.00  0.00           C+0
HETATM   30  H   UNK     0      -1.833   0.319   0.000  0.00  0.00           H+0
HETATM   31  N   UNK     0      -0.268  -0.057   0.000  0.00  0.00           N+0
HETATM   32  C   UNK     0      -1.173  -1.303   0.000  0.00  0.00           C+0
HETATM   33  N   UNK     0      -0.268  -2.549   0.000  0.00  0.00           N+0
HETATM   34  C   UNK     0       1.197  -2.073   0.000  0.00  0.00           C+0
HETATM   35  C   UNK     0       1.197  -0.533   0.000  0.00  0.00           C+0
HETATM   36  N   UNK     0       2.530   0.237   0.000  0.00  0.00           N+0
HETATM   37  C   UNK     0       3.864  -0.533   0.000  0.00  0.00           C+0
HETATM   38  N   UNK     0       5.198   0.237   0.000  0.00  0.00           N+0
HETATM   39  N   UNK     0       3.864  -2.073   0.000  0.00  0.00           N+0
HETATM   40  C   UNK     0       2.530  -2.843   0.000  0.00  0.00           C+0
HETATM   41  O   UNK     0       2.530  -4.383   0.000  0.00  0.00           O+0
HETATM   42  C   UNK     0      -2.208   1.884   0.000  0.00  0.00           C+0
HETATM   43  H   UNK     0      -3.581   2.583   0.000  0.00  0.00           H+0
HETATM   44  O   UNK     0      -3.454   0.978   0.000  0.00  0.00           O+0
HETATM   45  C   UNK     0      -2.208   3.424   0.000  0.00  0.00           C+0
HETATM   46  H   UNK     0      -0.963   2.518   0.000  0.00  0.00           H+0
HETATM   47  O   UNK     0      -3.454   4.329   0.000  0.00  0.00           O+0
CONECT    1    2                                                            
CONECT    2    1    3   28   45                                             
CONECT    3    2    4                                                       
CONECT    4    3    5                                                       
CONECT    5    4    6    7    8                                             
CONECT    6    5                                                            
CONECT    7    5                                                            
CONECT    8    5    9                                                       
CONECT    9    8   10   11   12                                             
CONECT   10    9                                                            
CONECT   11    9                                                            
CONECT   12    9   13                                                       
CONECT   13   12   14   15   25                                             
CONECT   14   13                                                            
CONECT   15   13   16                                                       
CONECT   16   15   17   18   19                                             
CONECT   17   16                                                            
CONECT   18   16                                                            
CONECT   19   16   20   21   22                                             
CONECT   20   19                                                            
CONECT   21   19                                                            
CONECT   22   19   23   24   25                                             
CONECT   23   22                                                            
CONECT   24   22                                                            
CONECT   25   22   13   26   27                                             
CONECT   26   25                                                            
CONECT   27   25                                                            
CONECT   28    2   29                                                       
CONECT   29   28   30   31   42                                             
CONECT   30   29                                                            
CONECT   31   29   32   35                                                  
CONECT   32   31   33                                                       
CONECT   33   32   34                                                       
CONECT   34   33   35   40                                                  
CONECT   35   34   31   36                                                  
CONECT   36   35   37                                                       
CONECT   37   36   38   39                                                  
CONECT   38   37                                                            
CONECT   39   37   40                                                       
CONECT   40   39   34   41                                                  
CONECT   41   40                                                            
CONECT   42   29   43   44   45                                             
CONECT   43   42                                                            
CONECT   44   42                                                            
CONECT   45   42    2   46   47                                             
CONECT   46   45                                                            
CONECT   47   45                                                            
MASTER        0    0    0    0    0    0    0    0   47    0  100    0
END

Synonyms

Value	Source
GDP-beta-L-Fucose	Kegg
GDP-b-L-Fucose	Generator
GDP-Β-L-fucose	Generator
Diphosphate fucose, guanosine	HMDB
Diphosphofucose, guanosine	HMDB
Fucose, GDP	HMDB
Fucose, guanosine diphosphate	HMDB
GDP Fucose	HMDB
Guanosine diphosphate fucose	HMDB
Guanosine diphosphofucose	HMDB

Molecular Formula

C₁₆H₂₅N₅O₁₅P₂

Average Mass

589.344

Monoisotopic Mass

589.082239121

IUPAC Name

{[(2R,3S,4R,5R)-3,4-dihydroxy-5-(6-hydroxy-2-imino-3,9-dihydro-2H-purin-9-yl)oxolan-2-yl]methoxy}({[hydroxy({[(3S,4R,5S,6S)-3,4,5-trihydroxy-6-methyloxan-2-yl]oxy})phosphoryl]oxy})phosphinic acid

Traditional Name

[(2R,3S,4R,5R)-3,4-dihydroxy-5-(6-hydroxy-2-imino-3H-purin-9-yl)oxolan-2-yl]methoxy([hydroxy([(3S,4R,5S,6S)-3,4,5-trihydroxy-6-methyloxan-2-yl]oxy)phosphoryl]oxy)phosphinic acid

CAS Registry Number

Not Available

SMILES

[H][C@]1(COP(O)(=O)OP(O)(=O)O[C@@]2([H])O[C@@]([H])(C)[C@@]([H])(O)[C@@]([H])(O)[C@]2([H])O)O[C@@]([H])(N2C=NC3=C2NC(=N)N=C3O)[C@]([H])(O)[C@]1([H])O

InChI Identifier

InChI=1S/C16H25N5O15P2/c1-4-7(22)9(24)11(26)15(33-4)35-38(30,31)36-37(28,29)32-2-5-8(23)10(25)14(34-5)21-3-18-6-12(21)19-16(17)20-13(6)27/h3-5,7-11,14-15,22-26H,2H2,1H3,(H,28,29)(H,30,31)(H3,17,19,20,27)/t4-,5+,7+,8+,9+,10+,11-,14+,15+/m0/s1

InChI Key

LQEBEXMHBLQMDB-JGQUBWHWSA-N

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as purine nucleotide sugars. These are purine nucleotides bound to a saccharide derivative through the terminal phosphate group.

Kingdom

Organic compounds

Super Class

Nucleosides, nucleotides, and analogues

Class

Purine nucleotides

Sub Class

Purine nucleotide sugars

Direct Parent

Purine nucleotide sugars

Alternative Parents

Substituents

Purine nucleotide sugar
Purine ribonucleoside diphosphate
Purine ribonucleoside monophosphate
Pentose phosphate
Pentose-5-phosphate
Glycosyl compound
N-glycosyl compound
6-oxopurine
Hypoxanthine
Monosaccharide phosphate
Organic pyrophosphate
Imidazopyrimidine
Purine
Aminopyrimidine
Monoalkyl phosphate
Pyrimidone
Pyrimidine
Monosaccharide
N-substituted imidazole
Organic phosphoric acid derivative
Oxane
Phosphoric acid ester
Alkyl phosphate
Tetrahydrofuran
Vinylogous amide
Azole
Imidazole
Heteroaromatic compound
Secondary alcohol
Organoheterocyclic compound
Azacycle
Polyol
Oxacycle
Hydrocarbon derivative
Organooxygen compound
Organic oxide
Organopnictogen compound
Alcohol
Primary amine
Organonitrogen compound
Amine
Organic oxygen compound
Organic nitrogen compound
Aromatic heteropolycyclic compound

Molecular Framework

Aromatic heteropolycyclic compounds

External Descriptors

GDP-L-fucose (CHEBI:13332 )

Functional Ontology

Not Available

Physical Properties

State

Expected Solid

Predicted Properties

Property	Value	Source
Water Solubility	7.02 g/L	ALOGPS
logP	-1.4	ALOGPS
logP	-4.7	ChemAxon
logS	-1.9	ALOGPS
pKa (Strongest Acidic)	1.71	ChemAxon
pKa (Strongest Basic)	3.38	ChemAxon
Physiological Charge	-2	ChemAxon
Hydrogen Acceptor Count	16	ChemAxon
Hydrogen Donor Count	10	ChemAxon
Polar Surface Area	308.19 Å²	ChemAxon
Rotatable Bond Count	8	ChemAxon
Refractivity	127.55 m³·mol⁻¹	ChemAxon
Polarizability	50.04 Å³	ChemAxon
Number of Rings	4	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 GC-MS	Predicted GC-MS Spectrum - GC-MS (Non-derivatized) - 70eV, Positive	splash10-05bf-9783680000-b41cb630b018ecbde457	2017-09-20	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (1 TMS) - 70eV, Positive	splash10-0006-6973605000-c45a685e630952dfe864	2017-10-06	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Positive	splash10-0udi-0910420000-f17d0e7a837317cda320	2017-10-06	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Positive	splash10-0udi-0910000000-b98c6683a197770e15a2	2017-10-06	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Positive	splash10-0udi-0900000000-5a6c05a30625c67a5f09	2017-10-06	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Negative	splash10-0fe3-2701490000-f34518fa366b43c12b3d	2017-10-06	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Negative	splash10-0udi-2901100000-e85209998edf794b7b0a	2017-10-06	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Negative	splash10-0pdl-3900000000-2bf9d67c6016478647ff	2017-10-06	View Spectrum

Biological Properties

Cellular Locations

Not Available

Biospecimen Locations

Not Available

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

Reaction ID	Precursor	Product	Enzyme	Reaction Type	Data Source	Reference
MMDBr0013818	GDP-beta-L-fucose	GDP-4-dehydro-6-deoxy-Œ±-D-mannose	GDP-L-fucose synthase	Synthesis	RHEA	34755880
MMDBr0015536	beta-D-Gal-(1->3)-alpha-D-GalNAc-(1->3)-alpha-D-GalNAc-di-trans,octa-cis-undecaprenyl diphosphate	alpha-L-Fuc-(1->2)-beta-D-Gal-(1->3)-alpha-D-GalNAc-(1->3)-alpha-D-GalNAc-di-trans,octa-cis-undecaprenyl diphosphate	O-antigen biosynthesis glycosyltransferase WbnK	Glycosylation	RHEA	34755880
MMDBr0024472	GDP-beta-L-fucose	Hydrogen Ion	Alpha-(1,3)-fucosyltransferase FucT	Addition of fucose in alpha 1-3 linkage	RHEA	34755880

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
Bacteria	Proteobacteria	4	Human ; Human feces; Human feces; pleural fluid plaque; bal; Human stool

Exposure Sources

Source Type	Source Sub-type	Species	Data Source	Reference

Host Biospecimen and Location

Host and Biospecimen	Status	Mean	Std	Min	Max	Units	Age	Sex	Health Condition	Data Source	Reference

External Links

HMDB ID

HMDB0062554

DrugBank ID

Not Available

Phenol Explorer Compound ID

Not Available

FooDB ID

Not Available

KNApSAcK ID

C00007245

Chemspider ID

Not Available

KEGG Compound ID

C00325

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

10918995

PDB ID

Not Available

ChEBI ID

13332

Food Biomarker Ontology

Not Available

References

Synthesis Reference

Not Available

General References

Bansal P, Morgat A, Axelsen KB, Muthukrishnan V, Coudert E, Aimo L, Hyka-Nouspikel N, Gasteiger E, Kerhornou A, Neto TB, Pozzato M, Blatter MC, Ignatchenko A, Redaschi N, Bridge A: Rhea, the reaction knowledgebase in 2022. Nucleic Acids Res. 2022 Jan 7;50(D1):D693-D700. doi: 10.1093/nar/gkab1016. [PubMed:34755880 ]

Showing metabocard for GDP-beta-L-fucose (MMDBc0054491)

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