Cannabis Compound Database: Showing Compound Card for GDP-L-fucose (CDB005259)

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Identification Taxonomy Ontology Physical properties Spectra Protein target Pathways Concentrations Links References enzymes (7) Show 8 proteins XML

Record Information

Version

1.0

Created at

2020-04-17 19:25:16 UTC

Updated at

2020-11-18 16:39:37 UTC

CannabisDB ID

CDB005259

Secondary Accession Numbers

Not Available

Cannabis Compound Identification

Common Name

GDP-L-fucose

Description

GDP-L-fucose, also known as GDP fucose or GDP-beta-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. GDP-L-fucose is a moderately basic compound (based on its pKa). GDP-L-fucose exists in all living organisms, ranging from bacteria to humans. Within humans, GDP-L-fucose participates in a number of enzymatic reactions. In particular, GDP-L-fucose can be converted into GDP-4-dehydro-6-deoxy-D-mannose through its interaction with the enzyme GDP-L-fucose synthase. In addition, GDP-L-fucose can be biosynthesized from fucose 1-phosphate through its interaction with the enzyme fucose-1-phosphate guanylyltransferase. In humans, GDP-L-fucose is involved in fructose intolerance, hereditary. Outside of the human body, GDP-L-fucose has been detected, but not quantified in, several different foods, such as wheats, rocket salad (ssp.), sacred lotus, macadamia nuts, and winter savories. This could make GDP-L-fucose a potential biomarker for the consumption of these foods. A GDP-fucose in which the fucosyl residue has L-configuration. GDP-L-fucose is expected to be in Cannabis as all living plants are known to produce and metabolize it.

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

589.34

Monoisotopic Molecular Weight

589.0822

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

Disposition

Source:

Endogenous

Platelet

Organ and components:

Subcellular:

Golgi

Tissue and substructures:

Placenta

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	No	ChemAxon
Rule of Five	No	ChemAxon
Ghose Filter	No	ChemAxon
Veber's Rule	No	ChemAxon
MDDR-like Rule	Yes	ChemAxon

Spectra

EI-MS/GC-MS

Type	Description	Splash Key	View
Predicted GC-MS	GDP-L-fucose, non-derivatized, Predicted GC-MS Spectrum - 70eV, Positive	splash10-05bf-6985780000-f2b6a0fdececb1ffd409	Spectrum
Predicted GC-MS	GDP-L-fucose, 1 TMS, Predicted GC-MS Spectrum - 70eV, Positive	splash10-0007-6173159000-1cf7c64a7a19bbd73e28	Spectrum
Predicted GC-MS	GDP-L-fucose, "GDP-L-fucose,1TMS,#1" TMS, Predicted GC-MS Spectrum - 70eV, Positive	Not Available	Spectrum
Predicted GC-MS	GDP-L-fucose, TMS_1_2, Predicted GC-MS Spectrum - 70eV, Positive	Not Available	Spectrum
Predicted GC-MS	GDP-L-fucose, TMS_1_3, Predicted GC-MS Spectrum - 70eV, Positive	Not Available	Spectrum
Predicted GC-MS	GDP-L-fucose, TMS_1_4, Predicted GC-MS Spectrum - 70eV, Positive	Not Available	Spectrum
Predicted GC-MS	GDP-L-fucose, TMS_1_5, Predicted GC-MS Spectrum - 70eV, Positive	Not Available	Spectrum
Predicted GC-MS	GDP-L-fucose, TMS_1_6, Predicted GC-MS Spectrum - 70eV, Positive	Not Available	Spectrum
Predicted GC-MS	GDP-L-fucose, TMS_1_7, Predicted GC-MS Spectrum - 70eV, Positive	Not Available	Spectrum
Predicted GC-MS	GDP-L-fucose, TMS_1_8, Predicted GC-MS Spectrum - 70eV, Positive	Not Available	Spectrum
Predicted GC-MS	GDP-L-fucose, TMS_1_9, Predicted GC-MS Spectrum - 70eV, Positive	Not Available	Spectrum
Predicted GC-MS	GDP-L-fucose, TMS_2_1, Predicted GC-MS Spectrum - 70eV, Positive	Not Available	Spectrum
Predicted GC-MS	GDP-L-fucose, TMS_2_2, Predicted GC-MS Spectrum - 70eV, Positive	Not Available	Spectrum
Predicted GC-MS	GDP-L-fucose, TMS_2_3, Predicted GC-MS Spectrum - 70eV, Positive	Not Available	Spectrum
Predicted GC-MS	GDP-L-fucose, TMS_2_4, Predicted GC-MS Spectrum - 70eV, Positive	Not Available	Spectrum
Predicted GC-MS	GDP-L-fucose, TMS_2_5, Predicted GC-MS Spectrum - 70eV, Positive	Not Available	Spectrum
Predicted GC-MS	GDP-L-fucose, TMS_2_6, Predicted GC-MS Spectrum - 70eV, Positive	Not Available	Spectrum
Predicted GC-MS	GDP-L-fucose, TMS_2_7, Predicted GC-MS Spectrum - 70eV, Positive	Not Available	Spectrum
Predicted GC-MS	GDP-L-fucose, TMS_2_8, Predicted GC-MS Spectrum - 70eV, Positive	Not Available	Spectrum
Predicted GC-MS	GDP-L-fucose, TMS_2_9, Predicted GC-MS Spectrum - 70eV, Positive	Not Available	Spectrum
Predicted GC-MS	GDP-L-fucose, TMS_2_10, Predicted GC-MS Spectrum - 70eV, Positive	Not Available	Spectrum
Predicted GC-MS	GDP-L-fucose, TMS_2_11, Predicted GC-MS Spectrum - 70eV, Positive	Not Available	Spectrum
Predicted GC-MS	GDP-L-fucose, TMS_2_12, Predicted GC-MS Spectrum - 70eV, Positive	Not Available	Spectrum
Predicted GC-MS	GDP-L-fucose, TMS_2_13, Predicted GC-MS Spectrum - 70eV, Positive	Not Available	Spectrum
Predicted GC-MS	GDP-L-fucose, TMS_2_14, Predicted GC-MS Spectrum - 70eV, Positive	Not Available	Spectrum

MS/MS

Type	Description	Splash Key	View
Predicted MS/MS	Predicted LC-MS/MS Spectrum - 10V, Positive	splash10-0udi-0910420000-6f2823064a15be7fc9a8	2015-09-15	View Spectrum
Predicted MS/MS	Predicted LC-MS/MS Spectrum - 20V, Positive	splash10-0udi-0910000000-866d48af83abebf46339	2015-09-15	View Spectrum
Predicted MS/MS	Predicted LC-MS/MS Spectrum - 40V, Positive	splash10-0udi-1900000000-8b884fd821ce0574d9f1	2015-09-15	View Spectrum
Predicted MS/MS	Predicted LC-MS/MS Spectrum - 10V, Negative	splash10-0ukl-2801490000-f519f8992a1d7307dde6	2015-09-15	View Spectrum
Predicted MS/MS	Predicted LC-MS/MS Spectrum - 20V, Negative	splash10-0udi-1901000000-5004fbddcfb22c8ecd5f	2015-09-15	View Spectrum
Predicted MS/MS	Predicted LC-MS/MS Spectrum - 40V, Negative	splash10-0pdl-3900000000-4c564cfa5a166417a5fa	2015-09-15	View Spectrum
Predicted MS/MS	Predicted LC-MS/MS Spectrum - 10V, Negative	splash10-000i-0000090000-2f459a27134486d5a1ca	2021-09-22	View Spectrum
Predicted MS/MS	Predicted LC-MS/MS Spectrum - 20V, Negative	splash10-00c9-9401260000-e8773e96d7afecfae815	2021-09-22	View Spectrum
Predicted MS/MS	Predicted LC-MS/MS Spectrum - 40V, Negative	splash10-00di-1501900000-343d428ef047e4949795	2021-09-22	View Spectrum
Predicted MS/MS	Predicted LC-MS/MS Spectrum - 10V, Positive	splash10-0006-0100090000-a6f771b381799c776be6	2021-09-23	View Spectrum
Predicted MS/MS	Predicted LC-MS/MS Spectrum - 20V, Positive	splash10-0f6x-5922540000-c4c21e0fb882f03ef863	2021-09-23	View Spectrum
Predicted MS/MS	Predicted LC-MS/MS Spectrum - 40V, Positive	splash10-0f7x-9740000000-e90684222b98c6e2cd5a	2021-09-23	View Spectrum

NMR

Not Available

Pathways

Name	SMPDB/Pathwhiz	KEGG
Fructose and Mannose Degradation
Fructosuria		Not Available
Fructose intolerance, hereditary		Not Available

Protein Targets

Enzymes

Protein Name	Gene Name	Locus	Uniprot ID	Details
Fucose-1-phosphate guanylyltransferase	FPGT	1p31.1	O14772	details
Galactoside 2-alpha-L-fucosyltransferase 2	FUT2	19q13.3	Q10981	details
Galactoside 2-alpha-L-fucosyltransferase 1	FUT1	19q13.3	P19526	details
GDP-L-fucose synthase	TSTA3	8q24.3	Q13630	details
Alpha-(1,3)-fucosyltransferase	FUT5	19p13.3	Q11128	details
Alpha-(1,6)-fucosyltransferase	FUT8	14q24.3	Q9BYC5	details
Galactoside 3(4)-L-fucosyltransferase	FUT3	19p13.3	P21217	details

Transporters

Not Available

Metal Bindings

Not Available

Receptors

Protein Name	Gene Name	Locus	Uniprot ID	Details
Alpha-(1,6)-fucosyltransferase	FUT8	14q24.3	Q9BYC5	details

Transcriptional Factors

Not Available

Concentrations Data

Not Available

External Links

HMDB ID

HMDB0001095

DrugBank ID

Not Available

Phenol Explorer Compound ID

Not Available

FoodDB 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

General References

Not Available

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

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

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

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

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

Enzyme Details

6. 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

Enzyme Details

7. 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

Showing Compound Card for GDP-L-fucose (CDB005259)

Structure for CDB005259 (GDP-L-fucose)

Enzymes