Bovine Metabolome Database: Showing metabocard for GDP-L-fucose (BMDB0001095)

Identification Taxonomy Physical properties Pathways Spectra Concentrations Links References enzymes (5) Show 5 proteins XML

Record Information

Version

1.0

Creation Date

2016-09-30 22:41:04 UTC

Update Date

2020-06-04 18:58:18 UTC

BMDB ID

BMDB0001095

Secondary Accession Numbers

BMDB01095

Metabolite Identification

Common Name

GDP-L-fucose

Description

GDP-L-Fucose, also known as GDP fucose or fucose, GDP, 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. GDP-L-Fucose is possibly soluble (in water) and a moderately basic compound (based on its pKa). GDP-L-Fucose exists in all living organisms, ranging from bacteria to humans. GDP-L-Fucose participates in a number of enzymatic reactions, within cattle. In particular, GDP-L-Fucose can be converted into GDP-4-dehydro-6-deoxy-D-mannose through the action of the enzyme GDP-L-fucose synthase. In addition, GDP-L-Fucose can be biosynthesized from fucose 1-phosphate; which is mediated by the enzyme fucose-1-phosphate guanylyltransferase. In cattle, GDP-L-fucose is involved in the metabolic pathway called the fructose and mannose degradation pathway.

Structure

MOL SDF PDB SMILES InChI

Synonyms

Value	Source
(6-Deoxy-beta-L-galactopyranosyl) ester	HMDB
GDP Fucose	HMDB
GDP-beta-L-Fucose	HMDB
Guanosine diphosphate fucose	HMDB
Guanosine diphosphofucose	HMDB
Diphosphate fucose, guanosine	HMDB
Diphosphofucose, guanosine	HMDB
Fucose, GDP	HMDB
Fucose, guanosine diphosphate	HMDB
GDP-Fucose	HMDB
GDP-Β-L-fucose	HMDB
Guanosine 5'-diphosphate L-fucose	HMDB
Guanosine 5'-diphospho-fucose	HMDB
Guanosine 5'-diphosphofucose	HMDB
Guanosine 5’-diphosphate L-fucose	HMDB
Guanosine 5’-diphospho-fucose	HMDB
Guanosine 5’-diphosphofucose	HMDB
GDP-L-fucose	HMDB

Chemical Formula

C₁₆H₂₅N₅O₁₅P₂

Average Molecular Weight

589.3417

Monoisotopic Molecular Weight

589.082238179

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 Name

gdp-L-fucose

CAS Registry Number

15839-70-0

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 Key

LQEBEXMHBLQMDB-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.

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-fucose (CHEBI:17009 )

Ontology

Status

Detected and Quantified

Origin

Endogenous

Biofunction

Not Available

Application

Not Available

Cellular locations

Golgi

Physical Properties

State

Solid

Experimental 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

Predicted Properties

Property	Value	Source
logP	-1.7	ALOGPS
logP	-4.2	ChemAxon
logS	-1.9	ALOGPS
pKa (Strongest Acidic)	1.73	ChemAxon
pKa (Strongest Basic)	-3.6	ChemAxon
Physiological Charge	-2	ChemAxon
Hydrogen Acceptor Count	15	ChemAxon
Hydrogen Donor Count	9	ChemAxon
Polar Surface Area	307.2 Å²	ChemAxon
Rotatable Bond Count	8	ChemAxon
Refractivity	116.97 m³·mol⁻¹	ChemAxon
Polarizability	48.22 Å³	ChemAxon
Number of Rings	4	ChemAxon
Bioavailability	Yes	ChemAxon
Rule of Five	Yes	ChemAxon
Ghose Filter	Yes	ChemAxon
Veber's Rule	Yes	ChemAxon
MDDR-like Rule	Yes	ChemAxon

Spectra

Biological Properties

Cellular Locations

Golgi

Biospecimen Locations

Epidermis
Fibroblasts
Intestine
Kidney
Milk
Neuron
Placenta
Platelet
Prostate Tissue
Spleen

Pathways

Name	SMPDB/Pathwhiz	KEGG
Fructose and Mannose Degradation		Not Available

Normal Concentrations

Biospecimen	Status	Value	Age	Sex	Condition	Reference	Details
Epidermis	Expected but not Quantified	Not Quantified	Not Specified	Not Specified	Normal	Not Applicable	details
Fibroblasts	Expected but not Quantified	Not Quantified	Not Specified	Not Specified	Normal	Not Applicable	details
Intestine	Expected but not Quantified	Not Quantified	Not Specified	Not Specified	Normal	Not Applicable	details
Kidney	Expected but not Quantified	Not Quantified	Not Specified	Not Specified	Normal	Not Applicable	details
Milk	Detected and Quantified	0 - 67.400 uM	Not Specified	Not Specified	Normal	PMID: 7196410	details
Neuron	Expected but not Quantified	Not Quantified	Not Specified	Not Specified	Normal	Not Applicable	details
Placenta	Expected but not Quantified	Not Quantified	Not Specified	Not Specified	Normal	Not Applicable	details
Platelet	Expected but not Quantified	Not Quantified	Not Specified	Not Specified	Normal	Not Applicable	details
Prostate Tissue	Expected but not Quantified	Not Quantified	Not Specified	Not Specified	Normal	Not Applicable	details
Spleen	Expected but not Quantified	Not Quantified	Not Specified	Not Specified	Normal	Not Applicable	details

Abnormal Concentrations

Not Available

External Links

HMDB ID

HMDB0001095

DrugBank ID

Not Available

Phenol Explorer Compound ID

Not Available

FooDB ID

KNApSAcK ID

Chemspider ID

KEGG Compound ID

BioCyc ID

Not Available

BiGG ID

34623

Wikipedia Link

Not Available

METLIN ID

PubChem Compound

PDB ID

ChEBI ID

References

Synthesis Reference

Yamamoto, 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

Gil A, Sanchez-Medina F: Acid-soluble nucleotides of cow's, goat's and sheep's milks, at different stages of lactation. J Dairy Res. 1981 Feb;48(1):35-44. [PubMed:7196410 ]

Enzymes

Enzyme Details

1. Alpha-(1,6)-fucosyltransferase

General function:: Involved in glycoprotein 6-alpha-L-fucosyltransferase a
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:: Q9N0W2
Molecular weight:: 66493.0

Enzyme Details

2. Galactoside 3(4)-L-fucosyltransferase

General function:: Involved in 3-galactosyl-N-acetylglucosaminide 4-alpha-
Specific function:: May catalyze alpha-1,3 and alpha-1,4 glycosidic linkages involved in the expression of sialyl Lewis X and Lewis X/SSEA-1 antigens. It may be involved in blood group Lewis determination. Also acts on the corresponding 1,4-galactosyl derivative, forming 1,3-L-fucosyl links.
Gene Name:: FUT3
Uniprot ID:: Q11126
Molecular weight:: 42654.0

Enzyme Details

3. Galactoside 2-alpha-L-fucosyltransferase 2

General function:: Involved in galactoside 2-alpha-L-fucosyltransferase ac
Specific function:: Mediates the transfer of fucose to the terminal galactose on glycan chains of cell surface glycoproteins and glycolipids. The resulting epitope plays a role in cell-cell interaction including host-microbe interaction. Mediates interaction with intestinal microbiota influencing its composition. 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 membrane-associated blood group antigen synthesis pathway.
Gene Name:: FUT2
Uniprot ID:: Q28113
Molecular weight:: 39320.0

Enzyme Details

4. Fucose-1-phosphate guanylyltransferase

General function:: Not Available
Specific function:: Not Available
Gene Name:: FPGT
Uniprot ID:: E1B9U5
Molecular weight:: 67389.0

Reactions

Fucose 1-phosphate + Guanosine triphosphate → GDP-L-fucose + Pyrophosphate	details

Enzyme Details

5. Tissue specific transplantation antigen P35B

General function:: Not Available
Specific function:: Not Available
Gene Name:: TSTA3
Uniprot ID:: Q2KIT8
Molecular weight:: 36027.0

Reactions

GDP-L-fucose + NADP → GDP-4-Dehydro-6-deoxy-D-mannose + NADPH	details

Showing metabocard for GDP-L-fucose (BMDB0001095)

Structure for BMDB0001095 (GDP-L-fucose)

Enzymes

Reactions

Reactions