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Identification Taxonomy Ontology Physical properties Spectra Biological properties Concentrations Links References enzymes (4) Show 4 proteins XML

Record Information

Version

5.0

Status

Detected but not Quantified

Creation Date

2021-09-11 10:36:09 UTC

Update Date

2021-10-01 21:51:45 UTC

HMDB ID

HMDB0252660

Secondary Accession Numbers

None

Metabolite Identification

Common Name

GDP-fucose

Description

GDP-L-fucose 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. In humans, GDP-L-fucose is involved in the metabolic disorder called fructosuria. GDP-L-fucose is found, on average, in the highest concentration within milk (cow). This could make GDP-L-fucose a potential biomarker for the consumption of these foods. GDP-L-fucose is a primary metabolite. Primary metabolites are metabolically or physiologically essential metabolites. They are directly involved in an organism’s growth, development or reproduction. Based on a literature review a significant number of articles have been published on GDP-L-fucose. This compound has been identified in human blood as reported by (PMID: 31557052 ). Gdp-fucose is not a naturally occurring metabolite and is only found in those individuals exposed to this compound or its derivatives. Technically GDP-fucose is part of the human exposome. The exposome can be defined as the collection of all the exposures of an individual in a lifetime and how those exposures relate to health. An individual's exposure begins before birth and includes insults from environmental and occupational sources.

Structure

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


  Mrv1652305221920472D          

 38 41  0  0  0  0            999 V2000
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   -1.8505   -3.7149    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
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  4  1  1  0  0  0  0
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 38 30  1  0  0  0  0
 38 31  2  0  0  0  0
 38 35  1  0  0  0  0
 38 36  1  0  0  0  0
M  END

HMDB0252660
     RDKit          3D
GDP-fucose
 63 66  0  0  0  0  0  0  0  0999 V2000
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  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
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 31 32  1  0
  4 33  1  0
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 38 63  1  0
M  END


  Mrv1652305221920472D          

 38 41  0  0  0  0            999 V2000
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 37 28  1  0  0  0  0
 37 29  2  0  0  0  0
 37 32  1  0  0  0  0
 37 36  1  0  0  0  0
 38 30  1  0  0  0  0
 38 31  2  0  0  0  0
 38 35  1  0  0  0  0
 38 36  1  0  0  0  0
M  END
> <DATABASE_ID>
HMDB0252660

> <DATABASE_NAME>
hmdb

> <SMILES>
CC1OC(OP(O)(=O)OP(O)(=O)OCC2OC(C(O)C2O)N2C=NC3=C2NC(=N)N=C3O)C(O)C(O)C1O

> <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)

> <INCHI_KEY>
LQEBEXMHBLQMDB-UHFFFAOYSA-N

> <FORMULA>
C16H25N5O15P2

> <MOLECULAR_WEIGHT>
589.3417

> <EXACT_MASS>
589.082238179

> <JCHEM_ACCEPTOR_COUNT>
16

> <JCHEM_ATOM_COUNT>
63

> <JCHEM_AVERAGE_POLARIZABILITY>
50.35778180019027

> <JCHEM_BIOAVAILABILITY>
0

> <JCHEM_DONOR_COUNT>
10

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

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

> <JCHEM_VEBER_RULE>
0

$$$$

HMDB0252660
     RDKit          3D
GDP-fucose
 63 66  0  0  0  0  0  0  0  0999 V2000
   -8.2056   -1.5848    0.8199 C   0  0  0  0  0  0  0  0  0  0  0  0
   -7.3748   -0.4643    0.2305 C   0  0  0  0  0  0  0  0  0  0  0  0
   -6.3787   -0.1168    1.1640 O   0  0  0  0  0  0  0  0  0  0  0  0
   -5.3742    0.6356    0.5185 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.6140   -0.2645   -0.2022 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.0327   -0.3923    0.3828 P   0  0  0  0  0  5  0  0  0  0  0  0
   -3.0322   -0.5972    1.8946 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2069    1.0234   -0.0157 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3105   -1.6997   -0.4085 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9436   -2.2586    0.4303 P   0  0  0  0  0  5  0  0  0  0  0  0
   -1.0081   -1.7725    1.8468 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9701   -3.9549    0.3664 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.4196   -1.6878   -0.3902 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.3040   -1.1766    0.5352 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.5621   -0.6391   -0.1111 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.4456   -0.1263    0.8351 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.5696    0.1247    0.0853 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.7401    0.3653    0.9073 N   0  0  0  0  0  0  0  0  0  0  0  0
    5.9098    0.2055    2.2196 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.1708    0.5607    2.5170 N   0  0  0  0  0  0  0  0  0  0  0  0
    7.8235    0.9501    1.4107 C   0  0  0  0  0  0  0  0  0  0  0  0
    9.1039    1.4000    1.1656 C   0  0  0  0  0  0  0  0  0  0  0  0
    9.9773    1.5069    2.2240 O   0  0  0  0  0  0  0  0  0  0  0  0
    9.4310    1.7121   -0.1052 N   0  0  0  0  0  0  0  0  0  0  0  0
    8.5577    1.5984   -1.1218 C   0  0  0  0  0  0  0  0  0  0  0  0
    8.9439    1.9178   -2.3219 N   0  0  0  0  0  0  0  0  0  0  0  0
    7.3171    1.1568   -0.8493 N   0  0  0  0  0  0  0  0  0  0  0  0
    6.9077    0.8243    0.3852 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.7561   -1.0413   -0.8546 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.7975   -1.8690   -0.5022 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.3966   -1.7406   -0.7352 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.9392   -2.0921   -1.9963 O   0  0  0  0  0  0  0  0  0  0  0  0
   -5.9691    1.7311   -0.3098 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.9098    1.5071   -1.6647 O   0  0  0  0  0  0  0  0  0  0  0  0
   -7.4104    1.9787    0.0905 C   0  0  0  0  0  0  0  0  0  0  0  0
   -7.3920    2.5327    1.3674 O   0  0  0  0  0  0  0  0  0  0  0  0
   -8.2514    0.7460    0.0567 C   0  0  0  0  0  0  0  0  0  0  0  0
   -9.0474    0.6636   -1.0743 O   0  0  0  0  0  0  0  0  0  0  0  0
   -8.7084   -2.1825    0.0318 H   0  0  0  0  0  0  0  0  0  0  0  0
   -7.5061   -2.2419    1.3704 H   0  0  0  0  0  0  0  0  0  0  0  0
   -8.9838   -1.1465    1.4472 H   0  0  0  0  0  0  0  0  0  0  0  0
   -6.9316   -0.8277   -0.7047 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.7693    1.0913    1.3452 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4555    1.7764    0.5760 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7607   -4.2962   -0.1278 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.8555   -0.3417    1.1122 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.6261   -2.0225    1.2060 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.3699    0.1306   -0.8600 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.4341    1.0578   -0.5308 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.1178   -0.1557    2.8796 H   0  0  0  0  0  0  0  0  0  0  0  0
   10.9461    1.6951    2.0196 H   0  0  0  0  0  0  0  0  0  0  0  0
    8.2812    1.8365   -3.1241 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.6450    1.0699   -1.6359 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.9283   -0.6771   -1.8880 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.4185   -2.0240   -1.2820 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.4670   -2.6207   -0.0604 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.2139   -1.5110   -2.2956 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.4328    2.7034   -0.1193 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.0974    1.0772   -1.9847 H   0  0  0  0  0  0  0  0  0  0  0  0
   -7.8446    2.7354   -0.6129 H   0  0  0  0  0  0  0  0  0  0  0  0
   -6.5067    2.8998    1.6046 H   0  0  0  0  0  0  0  0  0  0  0  0
   -8.9474    0.7761    0.9328 H   0  0  0  0  0  0  0  0  0  0  0  0
   -9.0008    1.5357   -1.5510 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  1  0
 22 24  2  0
 24 25  1  0
 25 26  2  3
 25 27  1  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  0
  4 43  1  0
  8 44  1  0
 12 45  1  0
 14 46  1  0
 14 47  1  0
 15 48  1  0
 17 49  1  0
 19 50  1  0
 23 51  1  0
 26 52  1  0
 27 53  1  0
 29 54  1  0
 30 55  1  0
 31 56  1  0
 32 57  1  0
 33 58  1  0
 34 59  1  0
 35 60  1  0
 36 61  1  0
 37 62  1  0
 38 63  1  0
M  END

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     -10.769 -13.897   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0      -3.454  -6.934   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0      -1.173  -1.303   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0      -9.362 -14.523   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0      -2.208  -6.029   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       1.197  -0.533   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0      -9.201 -16.055   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0      -0.744  -6.505   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0      -7.794 -16.681   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0       0.161  -5.259   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0      -6.548 -15.776   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0       1.197  -2.073   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0       2.530   0.237   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0      -0.744  -4.013   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0      -6.709 -14.245   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0       3.864  -2.073   0.000  0.00  0.00           C+0
HETATM   17  N   UNK     0       5.198  -2.843   0.000  0.00  0.00           N+0
HETATM   18  N   UNK     0      -0.268  -0.057   0.000  0.00  0.00           N+0
HETATM   19  N   UNK     0       2.530  -2.843   0.000  0.00  0.00           N+0
HETATM   20  N   UNK     0       3.864  -0.533   0.000  0.00  0.00           N+0
HETATM   21  N   UNK     0      -0.268  -2.549   0.000  0.00  0.00           N+0
HETATM   22  O   UNK     0     -10.447 -16.960   0.000  0.00  0.00           O+0
HETATM   23  O   UNK     0      -0.268  -7.970   0.000  0.00  0.00           O+0
HETATM   24  O   UNK     0      -7.633 -18.213   0.000  0.00  0.00           O+0
HETATM   25  O   UNK     0       1.701  -5.259   0.000  0.00  0.00           O+0
HETATM   26  O   UNK     0      -5.141 -16.403   0.000  0.00  0.00           O+0
HETATM   27  O   UNK     0       2.530   1.777   0.000  0.00  0.00           O+0
HETATM   28  O   UNK     0      -5.444  -8.125   0.000  0.00  0.00           O+0
HETATM   29  O   UNK     0      -3.634 -10.617   0.000  0.00  0.00           O+0
HETATM   30  O   UNK     0      -7.156 -11.969   0.000  0.00  0.00           O+0
HETATM   31  O   UNK     0      -4.093 -11.647   0.000  0.00  0.00           O+0
HETATM   32  O   UNK     0      -3.293  -8.466   0.000  0.00  0.00           O+0
HETATM   33  O   UNK     0      -8.116 -13.618   0.000  0.00  0.00           O+0
HETATM   34  O   UNK     0      -2.208  -4.489   0.000  0.00  0.00           O+0
HETATM   35  O   UNK     0      -5.463 -13.339   0.000  0.00  0.00           O+0
HETATM   36  O   UNK     0      -5.785 -10.276   0.000  0.00  0.00           O+0
HETATM   37  P   UNK     0      -4.539  -9.371   0.000  0.00  0.00           P+0
HETATM   38  P   UNK     0      -5.624 -11.808   0.000  0.00  0.00           P+0
CONECT    1    4                                                            
CONECT    2    5   32                                                       
CONECT    3   18   21                                                       
CONECT    4    1    7   33                                                  
CONECT    5    2    8   34                                                  
CONECT    6   12   13   18                                                  
CONECT    7    4    9   22                                                  
CONECT    8    5   10   23                                                  
CONECT    9    7   11   24                                                  
CONECT   10    8   14   25                                                  
CONECT   11    9   15   26                                                  
CONECT   12    6   19   21                                                  
CONECT   13    6   20   27                                                  
CONECT   14   10   21   34                                                  
CONECT   15   11   33   35                                                  
CONECT   16   17   19   20                                                  
CONECT   17   16                                                            
CONECT   18    3    6                                                       
CONECT   19   12   16                                                       
CONECT   20   13   16                                                       
CONECT   21    3   12   14                                                  
CONECT   22    7                                                            
CONECT   23    8                                                            
CONECT   24    9                                                            
CONECT   25   10                                                            
CONECT   26   11                                                            
CONECT   27   13                                                            
CONECT   28   37                                                            
CONECT   29   37                                                            
CONECT   30   38                                                            
CONECT   31   38                                                            
CONECT   32    2   37                                                       
CONECT   33    4   15                                                       
CONECT   34    5   14                                                       
CONECT   35   15   38                                                       
CONECT   36   37   38                                                       
CONECT   37   28   29   32   36                                             
CONECT   38   30   31   35   36                                             
MASTER        0    0    0    0    0    0    0    0   38    0   82    0
END

COMPND    HMDB0252660
HETATM    1  C1  UNL     1      -8.206  -1.585   0.820  1.00  0.00           C  
HETATM    2  C2  UNL     1      -7.375  -0.464   0.230  1.00  0.00           C  
HETATM    3  O1  UNL     1      -6.379  -0.117   1.164  1.00  0.00           O  
HETATM    4  C3  UNL     1      -5.374   0.636   0.519  1.00  0.00           C  
HETATM    5  O2  UNL     1      -4.614  -0.264  -0.202  1.00  0.00           O  
HETATM    6  P1  UNL     1      -3.033  -0.392   0.383  1.00  0.00           P  
HETATM    7  O3  UNL     1      -3.032  -0.597   1.895  1.00  0.00           O  
HETATM    8  O4  UNL     1      -2.207   1.023  -0.016  1.00  0.00           O  
HETATM    9  O5  UNL     1      -2.310  -1.700  -0.408  1.00  0.00           O  
HETATM   10  P2  UNL     1      -0.944  -2.259   0.430  1.00  0.00           P  
HETATM   11  O6  UNL     1      -1.008  -1.772   1.847  1.00  0.00           O  
HETATM   12  O7  UNL     1      -0.970  -3.955   0.366  1.00  0.00           O  
HETATM   13  O8  UNL     1       0.420  -1.688  -0.390  1.00  0.00           O  
HETATM   14  C4  UNL     1       1.304  -1.177   0.535  1.00  0.00           C  
HETATM   15  C5  UNL     1       2.562  -0.639  -0.111  1.00  0.00           C  
HETATM   16  O9  UNL     1       3.446  -0.126   0.835  1.00  0.00           O  
HETATM   17  C6  UNL     1       4.570   0.125   0.085  1.00  0.00           C  
HETATM   18  N1  UNL     1       5.740   0.365   0.907  1.00  0.00           N  
HETATM   19  C7  UNL     1       5.910   0.206   2.220  1.00  0.00           C  
HETATM   20  N2  UNL     1       7.171   0.561   2.517  1.00  0.00           N  
HETATM   21  C8  UNL     1       7.824   0.950   1.411  1.00  0.00           C  
HETATM   22  C9  UNL     1       9.104   1.400   1.166  1.00  0.00           C  
HETATM   23  O10 UNL     1       9.977   1.507   2.224  1.00  0.00           O  
HETATM   24  N3  UNL     1       9.431   1.712  -0.105  1.00  0.00           N  
HETATM   25  C10 UNL     1       8.558   1.598  -1.122  1.00  0.00           C  
HETATM   26  N4  UNL     1       8.944   1.918  -2.322  1.00  0.00           N  
HETATM   27  N5  UNL     1       7.317   1.157  -0.849  1.00  0.00           N  
HETATM   28  C11 UNL     1       6.908   0.824   0.385  1.00  0.00           C  
HETATM   29  C12 UNL     1       4.756  -1.041  -0.855  1.00  0.00           C  
HETATM   30  O11 UNL     1       5.798  -1.869  -0.502  1.00  0.00           O  
HETATM   31  C13 UNL     1       3.397  -1.741  -0.735  1.00  0.00           C  
HETATM   32  O12 UNL     1       2.939  -2.092  -1.996  1.00  0.00           O  
HETATM   33  C14 UNL     1      -5.969   1.731  -0.310  1.00  0.00           C  
HETATM   34  O13 UNL     1      -5.910   1.507  -1.665  1.00  0.00           O  
HETATM   35  C15 UNL     1      -7.410   1.979   0.090  1.00  0.00           C  
HETATM   36  O14 UNL     1      -7.392   2.533   1.367  1.00  0.00           O  
HETATM   37  C16 UNL     1      -8.251   0.746   0.057  1.00  0.00           C  
HETATM   38  O15 UNL     1      -9.047   0.664  -1.074  1.00  0.00           O  
HETATM   39  H1  UNL     1      -8.708  -2.182   0.032  1.00  0.00           H  
HETATM   40  H2  UNL     1      -7.506  -2.242   1.370  1.00  0.00           H  
HETATM   41  H3  UNL     1      -8.984  -1.147   1.447  1.00  0.00           H  
HETATM   42  H4  UNL     1      -6.932  -0.828  -0.705  1.00  0.00           H  
HETATM   43  H5  UNL     1      -4.769   1.091   1.345  1.00  0.00           H  
HETATM   44  H6  UNL     1      -2.455   1.776   0.576  1.00  0.00           H  
HETATM   45  H7  UNL     1      -1.761  -4.296  -0.128  1.00  0.00           H  
HETATM   46  H8  UNL     1       0.855  -0.342   1.112  1.00  0.00           H  
HETATM   47  H9  UNL     1       1.626  -2.023   1.206  1.00  0.00           H  
HETATM   48  H10 UNL     1       2.370   0.131  -0.860  1.00  0.00           H  
HETATM   49  H11 UNL     1       4.434   1.058  -0.531  1.00  0.00           H  
HETATM   50  H12 UNL     1       5.118  -0.156   2.880  1.00  0.00           H  
HETATM   51  H13 UNL     1      10.946   1.695   2.020  1.00  0.00           H  
HETATM   52  H14 UNL     1       8.281   1.837  -3.124  1.00  0.00           H  
HETATM   53  H15 UNL     1       6.645   1.070  -1.636  1.00  0.00           H  
HETATM   54  H16 UNL     1       4.928  -0.677  -1.888  1.00  0.00           H  
HETATM   55  H17 UNL     1       6.418  -2.024  -1.282  1.00  0.00           H  
HETATM   56  H18 UNL     1       3.467  -2.621  -0.060  1.00  0.00           H  
HETATM   57  H19 UNL     1       2.214  -1.511  -2.296  1.00  0.00           H  
HETATM   58  H20 UNL     1      -5.433   2.703  -0.119  1.00  0.00           H  
HETATM   59  H21 UNL     1      -5.097   1.077  -1.985  1.00  0.00           H  
HETATM   60  H22 UNL     1      -7.845   2.735  -0.613  1.00  0.00           H  
HETATM   61  H23 UNL     1      -6.507   2.900   1.605  1.00  0.00           H  
HETATM   62  H24 UNL     1      -8.947   0.776   0.933  1.00  0.00           H  
HETATM   63  H25 UNL     1      -9.001   1.536  -1.551  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   24   24
CONECT   23   51
CONECT   24   25
CONECT   25   26   26   27
CONECT   26   52
CONECT   27   28   53
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

HMDB0252660
     RDKit          3D
GDP-fucose
 63 66  0  0  0  0  0  0  0  0999 V2000
   -8.2056   -1.5848    0.8199 C   0  0  0  0  0  0  0  0  0  0  0  0
   -7.3748   -0.4643    0.2305 C   0  0  0  0  0  0  0  0  0  0  0  0
   -6.3787   -0.1168    1.1640 O   0  0  0  0  0  0  0  0  0  0  0  0
   -5.3742    0.6356    0.5185 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.6140   -0.2645   -0.2022 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.0327   -0.3923    0.3828 P   0  0  0  0  0  5  0  0  0  0  0  0
   -3.0322   -0.5972    1.8946 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2069    1.0234   -0.0157 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3105   -1.6997   -0.4085 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9436   -2.2586    0.4303 P   0  0  0  0  0  5  0  0  0  0  0  0
   -1.0081   -1.7725    1.8468 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9701   -3.9549    0.3664 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.4196   -1.6878   -0.3902 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.3040   -1.1766    0.5352 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.5621   -0.6391   -0.1111 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.4456   -0.1263    0.8351 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.5696    0.1247    0.0853 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.7401    0.3653    0.9073 N   0  0  0  0  0  0  0  0  0  0  0  0
    5.9098    0.2055    2.2196 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.1708    0.5607    2.5170 N   0  0  0  0  0  0  0  0  0  0  0  0
    7.8235    0.9501    1.4107 C   0  0  0  0  0  0  0  0  0  0  0  0
    9.1039    1.4000    1.1656 C   0  0  0  0  0  0  0  0  0  0  0  0
    9.9773    1.5069    2.2240 O   0  0  0  0  0  0  0  0  0  0  0  0
    9.4310    1.7121   -0.1052 N   0  0  0  0  0  0  0  0  0  0  0  0
    8.5577    1.5984   -1.1218 C   0  0  0  0  0  0  0  0  0  0  0  0
    8.9439    1.9178   -2.3219 N   0  0  0  0  0  0  0  0  0  0  0  0
    7.3171    1.1568   -0.8493 N   0  0  0  0  0  0  0  0  0  0  0  0
    6.9077    0.8243    0.3852 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.7561   -1.0413   -0.8546 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.7975   -1.8690   -0.5022 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.3966   -1.7406   -0.7352 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.9392   -2.0921   -1.9963 O   0  0  0  0  0  0  0  0  0  0  0  0
   -5.9691    1.7311   -0.3098 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.9098    1.5071   -1.6647 O   0  0  0  0  0  0  0  0  0  0  0  0
   -7.4104    1.9787    0.0905 C   0  0  0  0  0  0  0  0  0  0  0  0
   -7.3920    2.5327    1.3674 O   0  0  0  0  0  0  0  0  0  0  0  0
   -8.2514    0.7460    0.0567 C   0  0  0  0  0  0  0  0  0  0  0  0
   -9.0474    0.6636   -1.0743 O   0  0  0  0  0  0  0  0  0  0  0  0
   -8.7084   -2.1825    0.0318 H   0  0  0  0  0  0  0  0  0  0  0  0
   -7.5061   -2.2419    1.3704 H   0  0  0  0  0  0  0  0  0  0  0  0
   -8.9838   -1.1465    1.4472 H   0  0  0  0  0  0  0  0  0  0  0  0
   -6.9316   -0.8277   -0.7047 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.7693    1.0913    1.3452 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4555    1.7764    0.5760 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7607   -4.2962   -0.1278 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.8555   -0.3417    1.1122 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.6261   -2.0225    1.2060 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.3699    0.1306   -0.8600 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.4341    1.0578   -0.5308 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.1178   -0.1557    2.8796 H   0  0  0  0  0  0  0  0  0  0  0  0
   10.9461    1.6951    2.0196 H   0  0  0  0  0  0  0  0  0  0  0  0
    8.2812    1.8365   -3.1241 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.6450    1.0699   -1.6359 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.9283   -0.6771   -1.8880 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.4185   -2.0240   -1.2820 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.4670   -2.6207   -0.0604 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.2139   -1.5110   -2.2956 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.4328    2.7034   -0.1193 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.0974    1.0772   -1.9847 H   0  0  0  0  0  0  0  0  0  0  0  0
   -7.8446    2.7354   -0.6129 H   0  0  0  0  0  0  0  0  0  0  0  0
   -6.5067    2.8998    1.6046 H   0  0  0  0  0  0  0  0  0  0  0  0
   -8.9474    0.7761    0.9328 H   0  0  0  0  0  0  0  0  0  0  0  0
   -9.0008    1.5357   -1.5510 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  1  0
 22 24  2  0
 24 25  1  0
 25 26  2  3
 25 27  1  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  0
  4 43  1  0
  8 44  1  0
 12 45  1  0
 14 46  1  0
 14 47  1  0
 15 48  1  0
 17 49  1  0
 19 50  1  0
 23 51  1  0
 26 52  1  0
 27 53  1  0
 29 54  1  0
 30 55  1  0
 31 56  1  0
 32 57  1  0
 33 58  1  0
 34 59  1  0
 35 60  1  0
 36 61  1  0
 37 62  1  0
 38 63  1  0
M  END

View in JSmol View NMR Assignments View Stereo Labels

Synonyms

Value	Source
Diphosphate fucose, guanosine	MeSH
Fucose, guanosine diphosphate	MeSH
Fucose, GDP	MeSH
Guanosine diphosphate fucose	MeSH
Guanosine diphosphofucose	MeSH
Diphosphofucose, guanosine	MeSH
GDP Fucose	MeSH

Chemical Formula

C₁₆H₂₅N₅O₁₅P₂

Average Molecular Weight

589.3417

Monoisotopic Molecular Weight

589.082238179

IUPAC Name

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

Traditional Name

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

CAS Registry Number

Not Available

SMILES

CC1OC(OP(O)(=O)OP(O)(=O)OCC2OC(C(O)C2O)N2C=NC3=C2NC(=N)N=C3O)C(O)C(O)C1O

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)

InChI Key

LQEBEXMHBLQMDB-UHFFFAOYSA-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

Not Available

Ontology

Physiological effect

Not Available

Disposition

Biological location

Non-excretory biofluid

Biofluid or Excreta

Blood (PMID: 31557052)

Source

Exogenous

Exogenous (PMID: 31557052)

Process

Not Available

Role

Not Available

Physical Properties

State

Not Available

Experimental Molecular Properties

Property	Value	Reference
Melting Point	Not Available	Not Available
Boiling Point	Not Available	Not Available
Water Solubility	Not Available	Not Available
LogP	Not Available	Not Available

Experimental Chromatographic Properties

Not Available

Predicted Molecular Properties

Property	Value	Source
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	50.36 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

Predicted Chromatographic Properties

Predicted Collision Cross Sections

Predictor	Adduct Type	CCS Value (Å²)	Reference
DeepCCS	[M+H]+	200.344	30932474
DeepCCS	[M-H]-	197.948	30932474
DeepCCS	[M-2H]-	231.162	30932474
DeepCCS	[M+Na]+	206.256	30932474
AllCCS	[M+H]+	219.5	32859911
AllCCS	[M+H-H2O]+	218.2	32859911
AllCCS	[M+NH4]+	220.7	32859911
AllCCS	[M+Na]+	221.0	32859911
AllCCS	[M-H]-	212.8	32859911
AllCCS	[M+Na-2H]-	213.8	32859911
AllCCS	[M+HCOO]-	215.1	32859911

Predicted Retention Times

Underivatized

Chromatographic Method	Retention Time	Reference
Predicted by Siyang on May 30, 2022	11.9414 minutes	33406817
Predicted by Siyang using ReTip algorithm on June 8, 2022	9.84 minutes	32390414
Fem_Long = Waters ACQUITY UPLC HSS T3 C18 with Water:MeOH and 0.1% Formic Acid	558.6 seconds	40023050
Fem_Lipids = Ascentis Express C18 with (60:40 water:ACN):(90:10 IPA:ACN) and 10mM NH4COOH + 0.1% Formic Acid	249.3 seconds	40023050
Life_Old = Waters ACQUITY UPLC BEH C18 with Water:(20:80 acetone:ACN) and 0.1% Formic Acid	21.1 seconds	40023050
Life_New = RP Waters ACQUITY UPLC HSS T3 C18 with Water:(30:70 MeOH:ACN) and 0.1% Formic Acid	178.1 seconds	40023050
RIKEN = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid	92.1 seconds	40023050
Eawag_XBridgeC18 = XBridge C18 3.5u 2.1x50 mm with Water:MeOH and 0.1% Formic Acid	363.8 seconds	40023050
BfG_NTS_RP1 =Agilent Zorbax Eclipse Plus C18 (2.1 mm x 150 mm, 3.5 um) with Water:ACN and 0.1% Formic Acid	309.4 seconds	40023050
HILIC_BDD_2 = Merck SeQuant ZIC-HILIC with ACN(0.1% formic acid):water(16 mM ammonium formate)	835.9 seconds	40023050
UniToyama_Atlantis = RP Waters Atlantis T3 (2.1 x 150 mm, 5 um) with ACN:Water and 0.1% Formic Acid	621.8 seconds	40023050
BDD_C18 = Hypersil Gold 1.9µm C18 with Water:ACN and 0.1% Formic Acid	128.9 seconds	40023050
UFZ_Phenomenex = Kinetex Core-Shell C18 2.6 um, 3.0 x 100 mm, Phenomenex with Water:MeOH and 0.1% Formic Acid	813.3 seconds	40023050
SNU_RIKEN_POS = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid	212.8 seconds	40023050
RPMMFDA = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid	313.1 seconds	40023050
MTBLS87 = Merck SeQuant ZIC-pHILIC column with ACN:Water and :ammonium carbonate	946.7 seconds	40023050
KI_GIAR_zic_HILIC_pH2_7 = Merck SeQuant ZIC-HILIC with ACN:Water and 0.1% FA	453.1 seconds	40023050
Meister zic-pHILIC pH9.3 = Merck SeQuant ZIC-pHILIC column with ACN:Water 5mM NH4Ac pH9.3 and 5mM ammonium acetate in water	638.5 seconds	40023050

Predicted Kovats Retention Indices

Underivatized

Metabolite	SMILES	Kovats RI Value	Column Type	Reference
GDP-fucose	CC1OC(OP(O)(=O)OP(O)(=O)OCC2OC(C(O)C2O)N2C=NC3=C2NC(=N)N=C3O)C(O)C(O)C1O	5140.9	Standard polar	33892256
GDP-fucose	CC1OC(OP(O)(=O)OP(O)(=O)OCC2OC(C(O)C2O)N2C=NC3=C2NC(=N)N=C3O)C(O)C(O)C1O	3381.9	Standard non polar	33892256
GDP-fucose	CC1OC(OP(O)(=O)OP(O)(=O)OCC2OC(C(O)C2O)N2C=NC3=C2NC(=N)N=C3O)C(O)C(O)C1O	5057.9	Semi standard non polar	33892256

Spectra

GC-MS Spectra

Spectrum Type	Description	Splash Key	Deposition Date	Source	View
Predicted GC-MS	Predicted GC-MS Spectrum - GDP-fucose GC-MS (TMS_1_1) - 70eV, Positive	Not Available	2021-11-04	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - GDP-fucose GC-MS (TMS_1_2) - 70eV, Positive	Not Available	2021-11-04	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - GDP-fucose GC-MS (TMS_1_3) - 70eV, Positive	Not Available	2021-11-04	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - GDP-fucose GC-MS (TMS_1_4) - 70eV, Positive	Not Available	2021-11-04	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - GDP-fucose GC-MS (TMS_1_5) - 70eV, Positive	Not Available	2021-11-04	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - GDP-fucose GC-MS (TMS_1_6) - 70eV, Positive	Not Available	2021-11-04	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - GDP-fucose GC-MS (TMS_1_7) - 70eV, Positive	Not Available	2021-11-04	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - GDP-fucose GC-MS (TMS_1_8) - 70eV, Positive	Not Available	2021-11-04	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - GDP-fucose GC-MS (TMS_1_9) - 70eV, Positive	Not Available	2021-11-04	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - GDP-fucose GC-MS (TMS_1_10) - 70eV, Positive	Not Available	2021-11-04	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - GDP-fucose GC-MS (TMS_2_1) - 70eV, Positive	Not Available	2021-11-04	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - GDP-fucose GC-MS (TMS_2_2) - 70eV, Positive	Not Available	2021-11-04	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - GDP-fucose GC-MS (TMS_2_3) - 70eV, Positive	Not Available	2021-11-04	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - GDP-fucose GC-MS (TMS_2_4) - 70eV, Positive	Not Available	2021-11-04	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - GDP-fucose GC-MS (TMS_2_5) - 70eV, Positive	Not Available	2021-11-04	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - GDP-fucose GC-MS (TMS_2_6) - 70eV, Positive	Not Available	2021-11-04	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - GDP-fucose GC-MS (TMS_2_7) - 70eV, Positive	Not Available	2021-11-04	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - GDP-fucose GC-MS (TMS_2_8) - 70eV, Positive	Not Available	2021-11-04	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - GDP-fucose GC-MS (TMS_2_9) - 70eV, Positive	Not Available	2021-11-04	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - GDP-fucose GC-MS (TMS_2_10) - 70eV, Positive	Not Available	2021-11-04	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - GDP-fucose GC-MS (TMS_2_11) - 70eV, Positive	Not Available	2021-11-04	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - GDP-fucose GC-MS (TMS_2_12) - 70eV, Positive	Not Available	2021-11-04	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - GDP-fucose GC-MS (TMS_2_13) - 70eV, Positive	Not Available	2021-11-04	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - GDP-fucose GC-MS (TMS_2_14) - 70eV, Positive	Not Available	2021-11-04	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - GDP-fucose GC-MS (TMS_2_15) - 70eV, Positive	Not Available	2021-11-04	Wishart Lab	View Spectrum

MS/MS Spectra

Spectrum Type	Description	Splash Key	Deposition Date	Source	View
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - GDP-fucose 10V, Negative-QTOF	splash10-000i-0000090000-2f459a27134486d5a1ca	2021-10-12	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - GDP-fucose 20V, Negative-QTOF	splash10-00c9-9401260000-711220911adf21a5b7e1	2021-10-12	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - GDP-fucose 40V, Negative-QTOF	splash10-00di-1501900000-83875d7712c17716a4b4	2021-10-12	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - GDP-fucose 10V, Positive-QTOF	splash10-0006-0100090000-a6f771b381799c776be6	2021-10-12	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - GDP-fucose 20V, Positive-QTOF	splash10-0f6x-5922540000-148431db11813e7bf59d	2021-10-12	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - GDP-fucose 40V, Positive-QTOF	splash10-0f7o-9741000000-f6a6f431ed8f9e6e28c1	2021-10-12	Wishart Lab	View Spectrum

NMR Spectra

Spectrum Type	Description	Deposition Date	Source	View
Predicted 1D NMR	¹³C NMR Spectrum (1D, 100 MHz, D₂O, predicted)	2021-10-13	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 100 MHz, D₂O, predicted)	2021-10-13	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 1000 MHz, D₂O, predicted)	2021-10-13	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 1000 MHz, D₂O, predicted)	2021-10-13	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 200 MHz, D₂O, predicted)	2021-10-13	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 200 MHz, D₂O, predicted)	2021-10-13	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 300 MHz, D₂O, predicted)	2021-10-13	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 300 MHz, D₂O, predicted)	2021-10-13	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 400 MHz, D₂O, predicted)	2021-10-13	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 400 MHz, D₂O, predicted)	2021-10-13	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 500 MHz, D₂O, predicted)	2021-10-13	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 500 MHz, D₂O, predicted)	2021-10-13	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 600 MHz, D₂O, predicted)	2021-10-13	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 600 MHz, D₂O, predicted)	2021-10-13	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 700 MHz, D₂O, predicted)	2021-10-13	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 700 MHz, D₂O, predicted)	2021-10-13	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 800 MHz, D₂O, predicted)	2021-10-13	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 800 MHz, D₂O, predicted)	2021-10-13	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 900 MHz, D₂O, predicted)	2021-10-13	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 900 MHz, D₂O, predicted)	2021-10-13	Wishart Lab	View Spectrum

Biological Properties

Cellular Locations

Not Available

Biospecimen Locations

Blood

Tissue Locations

Not Available

Pathways

Not Available

Name	SMPDB/PathBank	KEGG

Normal Concentrations

Biospecimen	Status	Value	Age	Sex	Condition	Reference	Details
Blood	Detected but not Quantified	Not Quantified	Not Specified	Not Specified	Normal	31557052	details

Abnormal Concentrations

Not Available

Associated Disorders and Diseases

Disease References

None

Associated OMIM IDs

None

External Links

DrugBank ID

Not Available

Phenol Explorer Compound ID

Not Available

FooDB ID

FDB021816

KNApSAcK ID

C00007245

Chemspider ID

438

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

451

PDB ID

Not Available

ChEBI ID

Not Available

Food Biomarker Ontology

Not Available

VMH ID

Not Available

MarkerDB ID

Not Available

Good Scents ID

Not Available

References

Synthesis Reference

Not Available

Material Safety Data Sheet (MSDS)

Not Available

General References

Barupal DK, Fiehn O: Generating the Blood Exposome Database Using a Comprehensive Text Mining and Database Fusion Approach. Environ Health Perspect. 2019 Sep;127(9):97008. doi: 10.1289/EHP4713. Epub 2019 Sep 26. [PubMed:31557052 ]

Enzymes

Enzyme Details

1. 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

Enzyme Details

2. GDP-fucose protein O-fucosyltransferase 1

General function:: Involved in peptide-O-fucosyltransferase activity
Specific function:: Catalyzes the reaction that attaches fucose through an O-glycosidic linkage to a conserved serine or threonine residue in EGF domains. Plays a crucial role in Notch signaling
Gene Name:: POFUT1
Uniprot ID:: Q9H488
Molecular weight:: 43955.4

Enzyme Details

3. Solute carrier family 35 member C2

General function:: Not Available
Specific function:: May play an important role in the cellular response to tissue hypoxia. May be either a GDP-fucose transporter that competes with SLC35C1 for GDP-fucose, or a factor that otherwise enhances the fucosylation of Notch and is required for optimal Notch signaling in mammalian cells.
Gene Name:: SLC35C2
Uniprot ID:: Q9NQQ7
Molecular weight:: 40431.35

Enzyme Details

4. GDP-fucose transporter 1

General function:: Not Available
Specific function:: Involved in GDP-fucose import from the cytoplasm into the Golgi lumen.
Gene Name:: SLC35C1
Uniprot ID:: Q96A29
Molecular weight:: 39808.415

Showing metabocard for GDP-fucose (HMDB0252660)

MOL for HMDB0252660 (GDP-fucose)

3D MOL for HMDB0252660 (GDP-fucose)

3D SDF for HMDB0252660 (GDP-fucose)

3D-SDF for HMDB0252660 (GDP-fucose)

PDB for HMDB0252660 (GDP-fucose)

3D PDB for HMDB0252660 (GDP-fucose)

SMILES for HMDB0252660 (GDP-fucose)

INCHI for HMDB0252660 (GDP-fucose)

Structure for HMDB0252660 (GDP-fucose)

3D Structure for HMDB0252660 (GDP-fucose)

Predicted Collision Cross Sections

Predicted Retention Times

Underivatized

Predicted Kovats Retention Indices

Underivatized

GC-MS Spectra

MS/MS Spectra

NMR Spectra

Enzymes