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Showing metabocard for GDP-L-fucose (HMDB0001095)

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Record Information
Version5.0
StatusExpected but not Quantified
Creation Date2005-11-16 15:48:42 UTC
Update Date2021-09-14 15:40:13 UTC
HMDB IDHMDB0001095
Secondary Accession Numbers
  • HMDB0062554
  • HMDB01095
  • HMDB62554
Metabolite Identification
Common NameGDP-L-fucose
DescriptionGDP-L-fucose is a sugar nucleotide and a readily available source of fucose. Fucose is a deoxyhexose that is found in nearly all plant and animal species. The monosaccharide plays several important metabolic roles in complex carbohydrates and in glycoproteins. Fucosylated oligosaccharides are involved in cell-cell recognition, selectin-mediated leukocyte-endothelial adhesion, and mouse embryogenesis. They form the basis of the Lewis-type blood group antigens, are involved in the formation of atherosclerosis, and mediate host-bacterial interactions. A decrease in the availability of fucose is associated with leukocyte adhesion deficiency type-II disorder, and fucosylated glycoproteins have been implicated in memory processes. Fucose is made available during the synthesis of fucosylated glycolipids, oligosaccharides, and glycoproteins via a sugar nucleotide intermediate, specifically GDP-L-fucose. GTP-L-fucose pyrophosphorylase (GFPP, E. C. 2.7.7.30) catalyzes the reversible condensation of guanosine triphosphate and beta-L-fucose-1-phosphate to form the nucleotide-sugar GDP-L-fucose. The enzyme functions primarily in the mammalian liver and kidney to salvage free L-fucose during the breakdown of glycolipids and glycoproteins. (PMID: 16086588 ).
Structure
Data?1582752176
MOL3D MOLSDF3D SDFPDB3D PDBSMILESInChI

MOL for HMDB0001095 (GDP-L-fucose)

  Mrv1652309042000182D          

 38 41  0  0  1  0            999 V2000
    3.6062    1.4009    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    2.8194    1.6514    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.6027   -0.2364    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    4.0897    2.0607    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8194    2.4805    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.0995    1.2279    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    2.9252    0.2505    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.3557   -1.0092    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    3.6132    2.7382    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    2.0995    2.8934    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.3868    1.6514    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.2688   -0.2223    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    2.5300   -1.0092    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    3.8426   -1.6690    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
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    2.0960    3.7121    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
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 34 35  1  0  0  0  0
M  END
Download

3D MOL for HMDB0001095 (GDP-L-fucose)

HMDB0001095
     RDKit          3D
GDP-L-fucose
 63 66  0  0  0  0  0  0  0  0999 V2000
    7.3952    1.6877   -0.9006 C   0  0  0  0  0  0  0  0  0  0  0  0
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    5.3870    0.9014   -0.0659 O   0  0  0  0  0  0  0  0  0  0  0  0
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 37 62  1  6
 38 63  1  0
M  END
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3D SDF for HMDB0001095 (GDP-L-fucose)

  Mrv1652309042000182D          

 38 41  0  0  1  0            999 V2000
    3.6062    1.4009    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    2.8194    1.6514    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.6027   -0.2364    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    4.0897    2.0607    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8194    2.4805    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.0995    1.2279    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    2.9252    0.2505    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.3557   -1.0092    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    3.6132    2.7382    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    2.0995    2.8934    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.3868    1.6514    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.2688   -0.2223    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    2.5300   -1.0092    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    3.8426   -1.6690    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.3868    2.4805    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    2.0960    3.7121    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.6739    1.2421    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.4820    0.0247    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.0607   -1.6760    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.7692   -0.3776    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0529   -0.3776    0.0000 P   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8786   -0.3776    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0494    0.4410    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0635   -1.2879    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
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   -2.5194   -0.3811    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
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   -2.5194   -2.0254    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
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   -3.9450   -2.8440    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
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 10 16  2  0  0  0  0
 11 17  1  0  0  0  0
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 13 19  1  6  0  0  0
 18 20  1  0  0  0  0
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 25 26  1  0  0  0  0
 25 27  1  0  0  0  0
 25 28  2  0  0  0  0
 26 29  1  0  0  0  0
 29 30  1  0  0  0  0
 29 31  1  0  0  0  0
 30 32  1  0  0  0  0
 30 33  1  1  0  0  0
 31 34  1  0  0  0  0
 32 35  1  0  0  0  0
 32 36  1  6  0  0  0
 34 37  1  6  0  0  0
 35 38  1  6  0  0  0
  5  9  1  0  0  0  0
 11 15  1  0  0  0  0
 12 13  1  0  0  0  0
 34 35  1  0  0  0  0
M  END
> <DATABASE_ID>
HMDB0001095

> <DATABASE_NAME>
hmdb

> <SMILES>
C[C@@H]1OC(OP(O)(=O)OP(O)(=O)OC[C@H]2O[C@H]([C@H](O)[C@@H]2O)N2C=NC3=C2N=C(N)NC3=O)[C@@H](O)[C@H](O)[C@@H]1O

> <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-QIXZNPMTSA-N

> <FORMULA>
C16H25N5O15P2

> <MOLECULAR_WEIGHT>
589.3417

> <EXACT_MASS>
589.082238179

> <JCHEM_ACCEPTOR_COUNT>
15

> <JCHEM_ATOM_COUNT>
63

> <JCHEM_AVERAGE_POLARIZABILITY>
48.2224639920485

> <JCHEM_BIOAVAILABILITY>
0

> <JCHEM_DONOR_COUNT>
9

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
[({[(2R,3S,4R,5R)-5-(2-amino-6-oxo-6,9-dihydro-1H-purin-9-yl)-3,4-dihydroxyoxolan-2-yl]methoxy}(hydroxy)phosphoryl)oxy]({[(3S,4R,5S,6S)-3,4,5-trihydroxy-6-methyloxan-2-yl]oxy})phosphinic acid

> <ALOGPS_LOGP>
-1.69

> <JCHEM_LOGP>
-4.240674166333333

> <ALOGPS_LOGS>
-1.92

> <JCHEM_MDDR_LIKE_RULE>
1

> <JCHEM_NUMBER_OF_RINGS>
4

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-2

> <JCHEM_PKA>
3.1763296428152783

> <JCHEM_PKA_STRONGEST_ACIDIC>
1.7326083975660058

> <JCHEM_PKA_STRONGEST_BASIC>
-3.6122141796192597

> <JCHEM_POLAR_SURFACE_AREA>
307.2

> <JCHEM_REFRACTIVITY>
116.96759999999996

> <JCHEM_ROTATABLE_BOND_COUNT>
8

> <JCHEM_RULE_OF_FIVE>
0

> <ALOGPS_SOLUBILITY>
7.04e+00 g/l

> <JCHEM_TRADITIONAL_IUPAC>
gdp-L-fucose

> <JCHEM_VEBER_RULE>
0

$$$$
Download

3D-SDF for HMDB0001095 (GDP-L-fucose)

HMDB0001095
     RDKit          3D
GDP-L-fucose
 63 66  0  0  0  0  0  0  0  0999 V2000
    7.3952    1.6877   -0.9006 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.5063    0.4487   -0.7118 C   0  0  2  0  0  0  0  0  0  0  0  0
    5.3870    0.9014   -0.0659 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.4822   -0.1527    0.2868 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.8656   -0.6055   -0.8668 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.9423    0.5659   -1.6377 P   0  0  0  0  0  5  0  0  0  0  0  0
    2.5956    1.7218   -0.7501 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.8565    1.0578   -2.9908 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.4807   -0.0756   -2.3057 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.7218   -0.8539   -1.0654 P   0  0  0  0  0  5  0  0  0  0  0  0
    1.4601   -2.0942   -0.5997 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.9209    0.2893    0.2924 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8952   -1.1290   -1.0934 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6031    0.0640   -1.4716 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3968    0.2924   -0.2258 C   0  0  1  0  0  0  0  0  0  0  0  0
   -3.4234    1.1239   -0.1507 O   0  0  0  0  0  0  0  0  0  0  0  0
   -4.1323    0.7231    1.0165 C   0  0  1  0  0  0  0  0  0  0  0  0
   -5.4679    1.2040    1.0299 N   0  0  0  0  0  0  0  0  0  0  0  0
   -5.8672    2.2565    1.7489 C   0  0  0  0  0  0  0  0  0  0  0  0
   -7.1856    2.4925    1.5396 N   0  0  0  0  0  0  0  0  0  0  0  0
   -7.5784    1.5500    0.6802 C   0  0  0  0  0  0  0  0  0  0  0  0
   -8.8440    1.3110    0.1705 C   0  0  0  0  0  0  0  0  0  0  0  0
   -9.7866    2.0613    0.4774 O   0  0  0  0  0  0  0  0  0  0  0  0
   -9.0127    0.2590   -0.6448 N   0  0  0  0  0  0  0  0  0  0  0  0
   -7.9320   -0.5423   -0.9462 C   0  0  0  0  0  0  0  0  0  0  0  0
   -8.2965   -1.7060   -1.7023 N   0  0  0  0  0  0  0  0  0  0  0  0
   -6.7269   -0.3143   -0.4700 N   0  0  0  0  0  0  0  0  0  0  0  0
   -6.5247    0.7197    0.3423 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.0803   -0.8024    0.9063 C   0  0  2  0  0  0  0  0  0  0  0  0
   -4.3778   -1.4109    2.0944 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5738   -0.9473    0.5807 C   0  0  2  0  0  0  0  0  0  0  0  0
   -1.9025   -0.8530    1.7829 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.1336   -1.2352    1.0409 C   0  0  1  0  0  0  0  0  0  0  0  0
    5.1584   -2.4125    0.2731 O   0  0  0  0  0  0  0  0  0  0  0  0
    6.5878   -0.9391    1.3884 C   0  0  2  0  0  0  0  0  0  0  0  0
    6.6987    0.0043    2.4037 O   0  0  0  0  0  0  0  0  0  0  0  0
    7.2975   -0.5400    0.1237 C   0  0  2  0  0  0  0  0  0  0  0  0
    8.5387   -0.0321    0.4596 O   0  0  0  0  0  0  0  0  0  0  0  0
    6.7475    2.5569   -1.1520 H   0  0  0  0  0  0  0  0  0  0  0  0
    8.1723    1.4594   -1.6243 H   0  0  0  0  0  0  0  0  0  0  0  0
    7.8570    1.8662    0.0973 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.3230    0.0456   -1.7276 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.7638    0.4042    0.9128 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.2824    1.9098   -2.8127 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.6332   -0.0028    0.8322 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8926    0.8330   -1.6880 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2781   -0.1425   -2.3441 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5699    0.9282    0.4252 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5452    1.0234    1.8841 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.2351    2.8312    2.4273 H   0  0  0  0  0  0  0  0  0  0  0  0
   -9.9489    0.0839   -1.0323 H   0  0  0  0  0  0  0  0  0  0  0  0
   -8.7921   -2.4487   -1.1126 H   0  0  0  0  0  0  0  0  0  0  0  0
   -8.1084   -1.8247   -2.6842 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.6258   -1.1864    0.0501 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.5382   -2.3531    1.9318 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3449   -1.8764    0.0318 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3776   -0.0334    1.9163 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.6270   -1.4960    1.9959 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.9865   -2.9284    0.4585 H   0  0  0  0  0  0  0  0  0  0  0  0
    7.0486   -1.8982    1.7213 H   0  0  0  0  0  0  0  0  0  0  0  0
    7.6558    0.2530    2.4529 H   0  0  0  0  0  0  0  0  0  0  0  0
    7.4602   -1.4536   -0.4772 H   0  0  0  0  0  0  0  0  0  0  0  0
    9.2783   -0.6388    0.1859 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  2  0
  6  8  1  0
  6  9  1  0
  9 10  1  0
 10 11  2  0
 10 12  1  0
 10 13  1  0
 13 14  1  0
 14 15  1  0
 15 16  1  0
 16 17  1  0
 17 18  1  0
 18 19  1  0
 19 20  2  0
 20 21  1  0
 21 22  1  0
 22 23  2  0
 22 24  1  0
 24 25  1  0
 25 26  1  0
 25 27  2  0
 27 28  1  0
 17 29  1  0
 29 30  1  0
 29 31  1  0
 31 32  1  0
  4 33  1  0
 33 34  1  0
 33 35  1  0
 35 36  1  0
 35 37  1  0
 37 38  1  0
 37  2  1  0
 31 15  1  0
 28 18  1  0
 28 21  2  0
  1 39  1  0
  1 40  1  0
  1 41  1  0
  2 42  1  6
  4 43  1  0
  8 44  1  0
 12 45  1  0
 14 46  1  0
 14 47  1  0
 15 48  1  1
 17 49  1  1
 19 50  1  0
 24 51  1  0
 26 52  1  0
 26 53  1  0
 29 54  1  6
 30 55  1  0
 31 56  1  6
 32 57  1  0
 33 58  1  1
 34 59  1  0
 35 60  1  1
 36 61  1  0
 37 62  1  6
 38 63  1  0
M  END
Download

PDB for HMDB0001095 (GDP-L-fucose)

HEADER    PROTEIN                                 04-SEP-20   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   04-SEP-20         0                                  
HETATM    1  N   UNK     0       6.732   2.615   0.000  0.00  0.00           N+0
HETATM    2  C   UNK     0       5.263   3.083   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       6.725  -0.441   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       7.634   3.847   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       5.263   4.630   0.000  0.00  0.00           C+0
HETATM    6  N   UNK     0       3.919   2.292   0.000  0.00  0.00           N+0
HETATM    7  O   UNK     0       5.460   0.468   0.000  0.00  0.00           O+0
HETATM    8  C   UNK     0       6.264  -1.884   0.000  0.00  0.00           C+0
HETATM    9  N   UNK     0       6.745   5.111   0.000  0.00  0.00           N+0
HETATM   10  C   UNK     0       3.919   5.401   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0       2.589   3.083   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0       4.235  -0.415   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0       4.723  -1.884   0.000  0.00  0.00           C+0
HETATM   14  O   UNK     0       7.173  -3.115   0.000  0.00  0.00           O+0
HETATM   15  N   UNK     0       2.589   4.630   0.000  0.00  0.00           N+0
HETATM   16  O   UNK     0       3.913   6.929   0.000  0.00  0.00           O+0
HETATM   17  N   UNK     0       1.258   2.319   0.000  0.00  0.00           N+0
HETATM   18  C   UNK     0       2.766   0.046   0.000  0.00  0.00           C+0
HETATM   19  O   UNK     0       3.847  -3.129   0.000  0.00  0.00           O+0
HETATM   20  O   UNK     0       1.436  -0.705   0.000  0.00  0.00           O+0
HETATM   21  P   UNK     0      -0.099  -0.705   0.000  0.00  0.00           P+0
HETATM   22  O   UNK     0      -1.640  -0.705   0.000  0.00  0.00           O+0
HETATM   23  O   UNK     0      -0.092   0.823   0.000  0.00  0.00           O+0
HETATM   24  O   UNK     0      -0.119  -2.404   0.000  0.00  0.00           O+0
HETATM   25  P   UNK     0      -3.162  -0.705   0.000  0.00  0.00           P+0
HETATM   26  O   UNK     0      -4.703  -0.711   0.000  0.00  0.00           O+0
HETATM   27  O   UNK     0      -3.155   0.823   0.000  0.00  0.00           O+0
HETATM   28  O   UNK     0      -3.181  -2.286   0.000  0.00  0.00           O+0
HETATM   29  C   UNK     0      -6.027  -1.475   0.000  0.00  0.00           C+0
HETATM   30  C   UNK     0      -6.027  -3.003   0.000  0.00  0.00           C+0
HETATM   31  O   UNK     0      -7.364  -0.711   0.000  0.00  0.00           O+0
HETATM   32  C   UNK     0      -7.364  -3.781   0.000  0.00  0.00           C+0
HETATM   33  O   UNK     0      -4.703  -3.781   0.000  0.00  0.00           O+0
HETATM   34  C   UNK     0      -8.701  -1.475   0.000  0.00  0.00           C+0
HETATM   35  C   UNK     0      -8.701  -3.003   0.000  0.00  0.00           C+0
HETATM   36  O   UNK     0      -7.364  -5.309   0.000  0.00  0.00           O+0
HETATM   37  C   UNK     0     -10.012  -0.711   0.000  0.00  0.00           C+0
HETATM   38  O   UNK     0     -10.012  -3.781   0.000  0.00  0.00           O+0
CONECT    1    2    3    4                                                  
CONECT    2    1    5    6                                                  
CONECT    3    1    7    8                                                  
CONECT    4    1    9                                                       
CONECT    5    2   10    9                                                  
CONECT    6    2   11                                                       
CONECT    7    3   12                                                       
CONECT    8    3   13   14                                                  
CONECT    9    4    5                                                       
CONECT   10    5   15   16                                                  
CONECT   11    6   17   15                                                  
CONECT   12    7   18   13                                                  
CONECT   13    8   19   12                                                  
CONECT   14    8                                                            
CONECT   15   10   11                                                       
CONECT   16   10                                                            
CONECT   17   11                                                            
CONECT   18   12   20                                                       
CONECT   19   13                                                            
CONECT   20   18   21                                                       
CONECT   21   20   22   23   24                                             
CONECT   22   21   25                                                       
CONECT   23   21                                                            
CONECT   24   21                                                            
CONECT   25   22   26   27   28                                             
CONECT   26   25   29                                                       
CONECT   27   25                                                            
CONECT   28   25                                                            
CONECT   29   26   30   31                                                  
CONECT   30   29   32   33                                                  
CONECT   31   29   34                                                       
CONECT   32   30   35   36                                                  
CONECT   33   30                                                            
CONECT   34   31   37   35                                                  
CONECT   35   32   38   34                                                  
CONECT   36   32                                                            
CONECT   37   34                                                            
CONECT   38   35                                                            
MASTER        0    0    0    0    0    0    0    0   38    0   82    0
END
Download

3D PDB for HMDB0001095 (GDP-L-fucose)

COMPND    HMDB0001095
HETATM    1  C1  UNL     1       7.395   1.688  -0.901  1.00  0.00           C  
HETATM    2  C2  UNL     1       6.506   0.449  -0.712  1.00  0.00           C  
HETATM    3  O1  UNL     1       5.387   0.901  -0.066  1.00  0.00           O  
HETATM    4  C3  UNL     1       4.482  -0.153   0.287  1.00  0.00           C  
HETATM    5  O2  UNL     1       3.866  -0.606  -0.867  1.00  0.00           O  
HETATM    6  P1  UNL     1       2.942   0.566  -1.638  1.00  0.00           P  
HETATM    7  O3  UNL     1       2.596   1.722  -0.750  1.00  0.00           O  
HETATM    8  O4  UNL     1       3.857   1.058  -2.991  1.00  0.00           O  
HETATM    9  O5  UNL     1       1.481  -0.076  -2.306  1.00  0.00           O  
HETATM   10  P2  UNL     1       0.722  -0.854  -1.065  1.00  0.00           P  
HETATM   11  O6  UNL     1       1.460  -2.094  -0.600  1.00  0.00           O  
HETATM   12  O7  UNL     1       0.921   0.289   0.292  1.00  0.00           O  
HETATM   13  O8  UNL     1      -0.895  -1.129  -1.093  1.00  0.00           O  
HETATM   14  C4  UNL     1      -1.603   0.064  -1.472  1.00  0.00           C  
HETATM   15  C5  UNL     1      -2.397   0.292  -0.226  1.00  0.00           C  
HETATM   16  O9  UNL     1      -3.423   1.124  -0.151  1.00  0.00           O  
HETATM   17  C6  UNL     1      -4.132   0.723   1.017  1.00  0.00           C  
HETATM   18  N1  UNL     1      -5.468   1.204   1.030  1.00  0.00           N  
HETATM   19  C7  UNL     1      -5.867   2.257   1.749  1.00  0.00           C  
HETATM   20  N2  UNL     1      -7.186   2.492   1.540  1.00  0.00           N  
HETATM   21  C8  UNL     1      -7.578   1.550   0.680  1.00  0.00           C  
HETATM   22  C9  UNL     1      -8.844   1.311   0.170  1.00  0.00           C  
HETATM   23  O10 UNL     1      -9.787   2.061   0.477  1.00  0.00           O  
HETATM   24  N3  UNL     1      -9.013   0.259  -0.645  1.00  0.00           N  
HETATM   25  C10 UNL     1      -7.932  -0.542  -0.946  1.00  0.00           C  
HETATM   26  N4  UNL     1      -8.296  -1.706  -1.702  1.00  0.00           N  
HETATM   27  N5  UNL     1      -6.727  -0.314  -0.470  1.00  0.00           N  
HETATM   28  C11 UNL     1      -6.525   0.720   0.342  1.00  0.00           C  
HETATM   29  C12 UNL     1      -4.080  -0.802   0.906  1.00  0.00           C  
HETATM   30  O11 UNL     1      -4.378  -1.411   2.094  1.00  0.00           O  
HETATM   31  C13 UNL     1      -2.574  -0.947   0.581  1.00  0.00           C  
HETATM   32  O12 UNL     1      -1.903  -0.853   1.783  1.00  0.00           O  
HETATM   33  C14 UNL     1       5.134  -1.235   1.041  1.00  0.00           C  
HETATM   34  O13 UNL     1       5.158  -2.412   0.273  1.00  0.00           O  
HETATM   35  C15 UNL     1       6.588  -0.939   1.388  1.00  0.00           C  
HETATM   36  O14 UNL     1       6.699   0.004   2.404  1.00  0.00           O  
HETATM   37  C16 UNL     1       7.297  -0.540   0.124  1.00  0.00           C  
HETATM   38  O15 UNL     1       8.539  -0.032   0.460  1.00  0.00           O  
HETATM   39  H1  UNL     1       6.747   2.557  -1.152  1.00  0.00           H  
HETATM   40  H2  UNL     1       8.172   1.459  -1.624  1.00  0.00           H  
HETATM   41  H3  UNL     1       7.857   1.866   0.097  1.00  0.00           H  
HETATM   42  H4  UNL     1       6.323   0.046  -1.728  1.00  0.00           H  
HETATM   43  H5  UNL     1       3.764   0.404   0.913  1.00  0.00           H  
HETATM   44  H6  UNL     1       4.282   1.910  -2.813  1.00  0.00           H  
HETATM   45  H7  UNL     1       1.633  -0.003   0.832  1.00  0.00           H  
HETATM   46  H8  UNL     1      -0.893   0.833  -1.688  1.00  0.00           H  
HETATM   47  H9  UNL     1      -2.278  -0.143  -2.344  1.00  0.00           H  
HETATM   48  H10 UNL     1      -1.570   0.928   0.425  1.00  0.00           H  
HETATM   49  H11 UNL     1      -3.545   1.023   1.884  1.00  0.00           H  
HETATM   50  H12 UNL     1      -5.235   2.831   2.427  1.00  0.00           H  
HETATM   51  H13 UNL     1      -9.949   0.084  -1.032  1.00  0.00           H  
HETATM   52  H14 UNL     1      -8.792  -2.449  -1.113  1.00  0.00           H  
HETATM   53  H15 UNL     1      -8.108  -1.825  -2.684  1.00  0.00           H  
HETATM   54  H16 UNL     1      -4.626  -1.186   0.050  1.00  0.00           H  
HETATM   55  H17 UNL     1      -4.538  -2.353   1.932  1.00  0.00           H  
HETATM   56  H18 UNL     1      -2.345  -1.876   0.032  1.00  0.00           H  
HETATM   57  H19 UNL     1      -1.378  -0.033   1.916  1.00  0.00           H  
HETATM   58  H20 UNL     1       4.627  -1.496   1.996  1.00  0.00           H  
HETATM   59  H21 UNL     1       5.987  -2.928   0.459  1.00  0.00           H  
HETATM   60  H22 UNL     1       7.049  -1.898   1.721  1.00  0.00           H  
HETATM   61  H23 UNL     1       7.656   0.253   2.453  1.00  0.00           H  
HETATM   62  H24 UNL     1       7.460  -1.454  -0.477  1.00  0.00           H  
HETATM   63  H25 UNL     1       9.278  -0.639   0.186  1.00  0.00           H  
CONECT    1    2   39   40   41
CONECT    2    3   37   42
CONECT    3    4
CONECT    4    5   33   43
CONECT    5    6
CONECT    6    7    7    8    9
CONECT    8   44
CONECT    9   10
CONECT   10   11   11   12   13
CONECT   12   45
CONECT   13   14
CONECT   14   15   46   47
CONECT   15   16   31   48
CONECT   16   17
CONECT   17   18   29   49
CONECT   18   19   28
CONECT   19   20   20   50
CONECT   20   21
CONECT   21   22   28   28
CONECT   22   23   23   24
CONECT   24   25   51
CONECT   25   26   27   27
CONECT   26   52   53
CONECT   27   28
CONECT   29   30   31   54
CONECT   30   55
CONECT   31   32   56
CONECT   32   57
CONECT   33   34   35   58
CONECT   34   59
CONECT   35   36   37   60
CONECT   36   61
CONECT   37   38   62
CONECT   38   63
END
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SMILES for HMDB0001095 (GDP-L-fucose)

C[C@@H]1OC(OP(O)(=O)OP(O)(=O)OC[C@H]2O[C@H]([C@H](O)[C@@H]2O)N2C=NC3=C2N=C(N)NC3=O)[C@@H](O)[C@H](O)[C@@H]1O
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INCHI for HMDB0001095 (GDP-L-fucose)

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
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View in JSmolView NMR AssignmentsView Stereo Labels
Synonyms
Chemical FormulaC16H25N5O15P2
Average Molecular Weight589.3417
Monoisotopic Molecular Weight589.082238179
IUPAC Name[({[(2R,3S,4R,5R)-5-(2-amino-6-oxo-6,9-dihydro-1H-purin-9-yl)-3,4-dihydroxyoxolan-2-yl]methoxy}(hydroxy)phosphoryl)oxy]({[(3S,4R,5S,6S)-3,4,5-trihydroxy-6-methyloxan-2-yl]oxy})phosphinic acid
Traditional Namegdp-L-fucose
CAS Registry Number15839-70-0
SMILES
C[C@@H]1OC(OP(O)(=O)OP(O)(=O)OC[C@H]2O[C@H]([C@H](O)[C@@H]2O)N2C=NC3=C2N=C(N)NC3=O)[C@@H](O)[C@H](O)[C@@H]1O
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 KeyLQEBEXMHBLQMDB-QIXZNPMTSA-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.
KingdomOrganic compounds
Super ClassNucleosides, nucleotides, and analogues
ClassPurine nucleotides
Sub ClassPurine nucleotide sugars
Direct ParentPurine 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 FrameworkAromatic heteropolycyclic compounds
External Descriptors
Ontology
Physiological effectNot Available
Disposition
Biological locationSource
Process
Naturally occurring process
RoleNot Available
Physical Properties
StateSolid
Experimental Molecular Properties
PropertyValueReference
Melting PointNot AvailableNot Available
Boiling PointNot AvailableNot Available
Water SolubilityNot AvailableNot Available
LogPNot AvailableNot Available
Experimental Chromatographic Properties

Experimental Collision Cross Sections

Adduct TypeData SourceCCS Value (Å2)Reference
[M-H]-MetCCS_train_neg206.72430932474
[M+H]+MetCCS_train_pos217.19130932474
[M-H]-Not Available206.724http://allccs.zhulab.cn/database/detail?ID=AllCCS00000115
[M+H]+Not Available217.916http://allccs.zhulab.cn/database/detail?ID=AllCCS00000115
Predicted Molecular Properties
Predicted Chromatographic Properties
Spectra
Biological Properties
Cellular Locations
  • Golgi apparatus
Biospecimen LocationsNot Available
Tissue Locations
  • Epidermis
  • Fibroblasts
  • Intestine
  • Kidney
  • Neuron
  • Placenta
  • Platelet
  • Prostate
  • Spleen
Pathways
Normal Concentrations
Not Available
Abnormal Concentrations
Not Available
Associated Disorders and Diseases
Disease ReferencesNone
Associated OMIM IDsNone
DrugBank IDNot Available
Phenol Explorer Compound IDNot Available
FooDB IDFDB030882
KNApSAcK IDC00007245
Chemspider ID388350
KEGG Compound IDC00325
BioCyc IDNot Available
BiGG ID34623
Wikipedia LinkNot Available
METLIN ID6001
PubChem Compound439211
PDB IDGFB
ChEBI ID17009
Food Biomarker OntologyNot Available
VMH IDGDPFUC
MarkerDB IDNot Available
Good Scents IDNot Available
References
Synthesis ReferenceYamamoto, Kenji; Maruyama, Takashi; Kumagai, Hidehiko; Tochikura, Tatsurokuro; Seno, Taiko; Yamaguchi, Hideo. Preparation of GDP-L-fucose by using microbial enzymes. Agricultural and Biological Chemistry (1984), 48(3), 823-4.
Material Safety Data Sheet (MSDS)Not Available
General References

Enzymes

Enzyme Details
1. Fucose-1-phosphate guanylyltransferase
General function:
Involved in fucose-1-phosphate guanylyltransferase acti
Specific function:
Catalyzes the formation of GDP-L-fucose from GTP and L-fucose-1-phosphate. Functions as a salvage pathway to reutilize L-fucose arising from the turnover of glycoproteins and glycolipids.
Gene Name:
FPGT
Uniprot ID:
O14772
Molecular weight:
37630.405
Reactions
Guanosine triphosphate + Fucose 1-phosphate → Pyrophosphate + GDP-L-fucosedetails
Enzyme Details
2. Galactoside 2-alpha-L-fucosyltransferase 2
General function:
Involved in galactoside 2-alpha-L-fucosyltransferase activity
Specific function:
Creates a soluble precursor oligosaccharide FuC-alpha ((1,2)Galbeta-) called the H antigen which is an essential substrate for the final step in the soluble A and B antigen synthesis pathway. H and Se enzymes fucosylate the same acceptor substrates but exhibit different Km values.
Gene Name:
FUT2
Uniprot ID:
Q10981
Molecular weight:
39016.84
Reactions
GDP-L-fucose + beta-D-galactosyl-(1->3)-N-acetyl-beta-D-glucosaminyl-(1->3)-beta-D-galactosyl-(1->4)-beta-D-glucosyl-(1<->1)-ceramide → Guanosine diphosphate + alpha-L-fucosyl-(1->2)-beta-D-galactosyl-(1->3)-N-acetyl-beta-D-glucosaminyl-(1->3)-beta-D-galactosyl-(1->4)-beta-D-glucosyl-(1<->1)-ceramidedetails
Enzyme Details
3. Galactoside 2-alpha-L-fucosyltransferase 1
General function:
Involved in galactoside 2-alpha-L-fucosyltransferase activity
Specific function:
Creates a soluble precursor oligosaccharide FuC-alpha ((1,2)Galbeta-) called the H antigen which is an essential substrate for the final step in the soluble A and B antigen synthesis pathway. H and Se enzymes fucosylate the same acceptor substrates but exhibit different Km values.
Gene Name:
FUT1
Uniprot ID:
P19526
Molecular weight:
41251.11
Reactions
GDP-L-fucose + beta-D-galactosyl-(1->3)-N-acetyl-beta-D-glucosaminyl-(1->3)-beta-D-galactosyl-(1->4)-beta-D-glucosyl-(1<->1)-ceramide → Guanosine diphosphate + alpha-L-fucosyl-(1->2)-beta-D-galactosyl-(1->3)-N-acetyl-beta-D-glucosaminyl-(1->3)-beta-D-galactosyl-(1->4)-beta-D-glucosyl-(1<->1)-ceramidedetails
Enzyme Details
4. GDP-L-fucose synthase
General function:
Involved in catalytic activity
Specific function:
Two step NADP-dependent conversion of GDP-4-dehydro-6-deoxy-D-mannose to GDP-fucose, involving an epimerase and a reductase reaction.
Gene Name:
TSTA3
Uniprot ID:
Q13630
Molecular weight:
35892.46
Reactions
GDP-L-fucose + NADP → GDP-4-Dehydro-6-deoxy-D-mannose + NADPHdetails
GDP-L-fucose + NADP → GDP-4-Dehydro-6-deoxy-D-mannose + NADPH + Hydrogen Iondetails
Enzyme Details
5. Alpha-(1,3)-fucosyltransferase
General function:
Involved in fucosyltransferase activity
Specific function:
May catalyze alpha-1,3 glycosidic linkages involved in the expression of VIM-2, Lewis X/SSEA-1 and sialyl Lewis X antigens.
Gene Name:
FUT5
Uniprot ID:
Q11128
Molecular weight:
42988.655
Reactions
GDP-L-fucose + beta-D-galactosyl-(1->3)-N-acetyl-D-glucosaminyl-R → Guanosine diphosphate + beta-D-galactosyl-(1->3)-(alpha-L-fucosyl-(1->4))-N-acetyl-beta-D-glucosaminyl-Rdetails
Enzyme Details
6. Alpha-(1,3)-fucosyltransferase
General function:
Involved in fucosyltransferase activity
Specific function:
Transfers a fucose to lacto-N-neotetraose but not to either alpha2,3-sialyl lacto-N-neotetraose or lacto-N-tetraose. Can catalyze the last step in the biosynthesis of Lewis antigen, the addition of a fucose to precursor polysaccharides
Gene Name:
FUT9
Uniprot ID:
Q9Y231
Molecular weight:
42040.7
Enzyme Details
7. Alpha-(1,6)-fucosyltransferase
General function:
Involved in glycoprotein 6-alpha-L-fucosyltransferase activity
Specific function:
Catalyzes the addition of fucose in alpha 1-6 linkage to the first GlcNAc residue, next to the peptide chains in N-glycans.
Gene Name:
FUT8
Uniprot ID:
Q9BYC5
Molecular weight:
66515.32
Reactions
GDP-L-fucose + N(4)-(N-acetyl-beta-D-glucosaminyl-(1->2)-alpha-D-mannosyl-(1->3)-(N-acetyl-beta-D-glucosaminyl-(1->2)-alpha-D-mannosyl-(1->6))-beta-D-mannosyl-(1->4)-N-acetyl-beta-D-glucosaminyl-(1->4)-N-acetyl-beta-D-glucosaminyl)asparagine → Guanosine diphosphate + N(4)-(N-acetyl-beta-D-glucosaminyl-(1->2)-alpha-D-mannosyl-(1->3)-(N-acetyl-beta-D-glucosaminyl-(1->2)-alpha-D-mannosyl-(1->6))-beta-D-mannosyl-(1->4)-N-acetyl-beta-D-glucosaminyl-(1->4)-(alpha-L-fucosyl-(1->6))-N-acetyl-beta-D-glucosaminyl)asparaginedetails
Enzyme Details
8. Alpha-(1,3)-fucosyltransferase
General function:
Involved in fucosyltransferase activity
Specific function:
Enzyme involved in the biosynthesis of the E-Selectin ligand, sialyl-Lewis X. Catalyzes the transfer of fucose from GDP-beta-fucose to alpha-2,3 sialylated substrates.
Gene Name:
FUT6
Uniprot ID:
P51993
Molecular weight:
41859.42
Reactions
GDP-L-fucose + beta-D-galactosyl-(1->3)-N-acetyl-D-glucosaminyl-R → Guanosine diphosphate + beta-D-galactosyl-(1->3)-(alpha-L-fucosyl-(1->4))-N-acetyl-beta-D-glucosaminyl-Rdetails
Enzyme Details
9. Alpha-(1,3)-fucosyltransferase
General function:
Involved in fucosyltransferase activity
Specific function:
May catalyze alpha-1,3 glycosidic linkages involved in the expression of sialyl Lewis X antigens.
Gene Name:
FUT7
Uniprot ID:
Q11130
Molecular weight:
39238.495
Reactions
GDP-L-fucose + alpha-2,3-Neu-N-acetyl-1,4-beta-D-galactosyl-N-acetyl-D-glucosaminyl-R → Guanosine diphosphate + alpha-2,3-Neu-N-acetyl-1,4-beta-D-galactosyl-(alpha-1,3-L-fucosyl)-N-acetyl-D-glucosaminyl-Rdetails
Enzyme Details
10. Galactoside 3(4)-L-fucosyltransferase
General function:
Not Available
Specific function:
May catalyze alpha-1,3 and alpha-1,4 glycosidic linkages involved in the expression of Vim-2, Lewis A, Lewis B, sialyl Lewis X and Lewis X/SSEA-1 antigens. May be involved in blood group Lewis determination; Lewis-positive (Le(+)) individuals have an active enzyme while Lewis-negative (Le(-)) individuals have an inactive enzyme. Also acts on the corresponding 1,4-galactosyl derivative, forming 1,3-L-fucosyl links.
Gene Name:
FUT3
Uniprot ID:
P21217
Molecular weight:
42116.69
Reactions
GDP-L-fucose + beta-D-galactosyl-(1->3)-N-acetyl-D-glucosaminyl-R → Guanosine diphosphate + beta-D-galactosyl-(1->3)-(alpha-L-fucosyl-(1->4))-N-acetyl-beta-D-glucosaminyl-Rdetails