Cannabis Compound Database: Showing Compound Card for GDP-4-Dehydro-6-deoxy-D-mannose (CDB005258)

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Record Information

Version

1.0

Created at

2020-04-17 19:25:10 UTC

Updated at

2020-11-18 16:39:37 UTC

CannabisDB ID

CDB005258

Secondary Accession Numbers

Not Available

Cannabis Compound Identification

Common Name

GDP-4-Dehydro-6-deoxy-D-mannose

Description

GDP-4-Dehydro-6-deoxy-D-mannose, also known as GDP-4-dehydro-D-rhamnose or GDP-4-keto-6-deoxymannose, 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-4-Dehydro-6-deoxy-D-mannose is a strong basic compound (based on its pKa). GDP-4-Dehydro-6-deoxy-D-mannose exists in all living organisms, ranging from bacteria to humans. Within humans, GDP-4-dehydro-6-deoxy-D-mannose participates in a number of enzymatic reactions. In particular, GDP-4-dehydro-6-deoxy-D-mannose can be biosynthesized from guanosine diphosphate mannose through its interaction with the enzyme GDP-mannose 4,6 dehydratase. In addition, GDP-4-dehydro-6-deoxy-D-mannose can be biosynthesized from GDP-L-fucose through the action of the enzyme GDP-L-fucose synthase. In humans, GDP-4-dehydro-6-deoxy-D-mannose is involved in the metabolic disorder called fructosuria. Outside of the human body, GDP-4-Dehydro-6-deoxy-D-mannose has been detected, but not quantified in, several different foods, such as common walnuts, celeriacs, blackcurrants, triticales, and evergreen huckleberries. This could make GDP-4-dehydro-6-deoxy-D-mannose a potential biomarker for the consumption of these foods. A GDP-sugar having 4-dehydro-6-deoxy-alpha-D-mannose as the sugar portion. GDP-4-Dehydro-6-deoxy-D-mannose 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
GDP-4-Dehydro-6-deoxy-D-talose	ChEBI
GDP-4-Dehydro-D-rhamnose	ChEBI
GDP-4-Keto-6-deoxy-D-mannose	ChEBI
GDP-4-Keto-6-deoxymannose	ChEBI
GDP-4-oxo-6-Deoxy-D-mannose	ChEBI
Guanosine 5'-(trihydrogen diphosphate), p'-(6-deoxy-alpha-D-lyxo-hexopyranos-4-ulos-1-yl) ester	ChEBI
Guanosine diphosphate-4-keto-6-deoxy-D-mannose	ChEBI
GDP-4-Dehydro-alpha-D-rhamnose	Kegg
GDP-4-Dehydro-6-deoxy-alpha-D-mannose	Kegg
Guanosine 5'-(trihydrogen diphosphate), p'-(6-deoxy-a-D-lyxo-hexopyranos-4-ulos-1-yl) ester	Generator
Guanosine 5'-(trihydrogen diphosphate), p'-(6-deoxy-α-D-lyxo-hexopyranos-4-ulos-1-yl) ester	Generator
Guanosine 5'-(trihydrogen diphosphoric acid), p'-(6-deoxy-a-D-lyxo-hexopyranos-4-ulos-1-yl) ester	Generator
Guanosine 5'-(trihydrogen diphosphoric acid), p'-(6-deoxy-alpha-D-lyxo-hexopyranos-4-ulos-1-yl) ester	Generator
Guanosine 5'-(trihydrogen diphosphoric acid), p'-(6-deoxy-α-D-lyxo-hexopyranos-4-ulos-1-yl) ester	Generator
Guanosine diphosphoric acid-4-keto-6-deoxy-D-mannose	Generator
GDP-4-Dehydro-a-D-rhamnose	Generator
GDP-4-Dehydro-α-D-rhamnose	Generator
GDP-4-Dehydro-6-deoxy-a-D-mannose	Generator
GDP-4-Dehydro-6-deoxy-α-D-mannose	Generator
GDP-4-Keto-6-D-deoxymannose	HMDB
GDP-4-oxo-6-Deoxymannose	HMDB
Guanosine 5'-diphosphate 4-keto-6-deoxy-D-mannose	HMDB
Guanosine 5’-diphosphate 4-keto-6-deoxy-D-mannose	HMDB

Chemical Formula

C₁₆H₂₃N₅O₁₅P₂

Average Molecular Weight

587.33

Monoisotopic Molecular Weight

587.0666

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]({[(2R,3S,4R,6R)-3,4-dihydroxy-6-methyl-5-oxooxan-2-yl]oxy})phosphinic acid

Traditional Name

gdp-4-keto-6-deoxymannose

CAS Registry Number

18186-48-6

SMILES

C[C@H]1O[C@H](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)C1=O

InChI Identifier

InChI=1S/C16H23N5O15P2/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/h3-5,8-11,14-15,23-26H,2H2,1H3,(H,28,29)(H,30,31)(H3,17,19,20,27)/t4-,5-,8-,9+,10-,11+,14-,15-/m1/s1

InChI Key

PNHLMHWWFOPQLK-BKUUWRAGSA-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
Alkyl phosphate
Phosphoric acid ester
Oxane
Monosaccharide
Organic phosphoric acid derivative
N-substituted imidazole
Tetrahydrofuran
Vinylogous amide
Azole
Imidazole
Heteroaromatic compound
Cyclic ketone
Secondary alcohol
Ketone
Organoheterocyclic compound
Azacycle
Oxacycle
Hydrocarbon derivative
Primary amine
Organic oxide
Organopnictogen compound
Organic oxygen compound
Carbonyl group
Alcohol
Organic nitrogen compound
Organooxygen compound
Organonitrogen compound
Amine
Aromatic heteropolycyclic compound

Molecular Framework

Aromatic heteropolycyclic compounds

External Descriptors

GDP-sugar (CHEBI:16955 )

Ontology

Disposition

Route of exposure:

Enteral:

Ingestion

Source:

Biological:

Plant:

Animal

Biological location:

Subcellular:

Cytoplasm

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	-1.3	ALOGPS
logP	-3.6	ChemAxon
logS	-2	ALOGPS
pKa (Strongest Acidic)	1.73	ChemAxon
pKa (Strongest Basic)	-3.7	ChemAxon
Physiological Charge	-2	ChemAxon
Hydrogen Acceptor Count	15	ChemAxon
Hydrogen Donor Count	8	ChemAxon
Polar Surface Area	304.04 Å²	ChemAxon
Rotatable Bond Count	8	ChemAxon
Refractivity	116.2 m³·mol⁻¹	ChemAxon
Polarizability	48.01 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-4-Dehydro-6-deoxy-D-mannose, non-derivatized, Predicted GC-MS Spectrum - 70eV, Positive	splash10-00mo-7594640000-f6eaffb3b87a7209c04d	Spectrum
Predicted GC-MS	GDP-4-Dehydro-6-deoxy-D-mannose, 1 TMS, Predicted GC-MS Spectrum - 70eV, Positive	splash10-002f-6891604000-2d6996a185dcede1dcba	Spectrum
Predicted GC-MS	GDP-4-Dehydro-6-deoxy-D-mannose, "GDP-4-Dehydro-6-deoxy-D-mannose,1TMS,#1" TMS, Predicted GC-MS Spectrum - 70eV, Positive	Not Available	Spectrum
Predicted GC-MS	GDP-4-Dehydro-6-deoxy-D-mannose, TMS_1_2, Predicted GC-MS Spectrum - 70eV, Positive	Not Available	Spectrum
Predicted GC-MS	GDP-4-Dehydro-6-deoxy-D-mannose, TMS_1_3, Predicted GC-MS Spectrum - 70eV, Positive	Not Available	Spectrum
Predicted GC-MS	GDP-4-Dehydro-6-deoxy-D-mannose, TMS_1_4, Predicted GC-MS Spectrum - 70eV, Positive	Not Available	Spectrum
Predicted GC-MS	GDP-4-Dehydro-6-deoxy-D-mannose, TMS_1_5, Predicted GC-MS Spectrum - 70eV, Positive	Not Available	Spectrum
Predicted GC-MS	GDP-4-Dehydro-6-deoxy-D-mannose, TMS_1_6, Predicted GC-MS Spectrum - 70eV, Positive	Not Available	Spectrum
Predicted GC-MS	GDP-4-Dehydro-6-deoxy-D-mannose, TMS_1_7, Predicted GC-MS Spectrum - 70eV, Positive	Not Available	Spectrum
Predicted GC-MS	GDP-4-Dehydro-6-deoxy-D-mannose, TMS_1_8, Predicted GC-MS Spectrum - 70eV, Positive	Not Available	Spectrum
Predicted GC-MS	GDP-4-Dehydro-6-deoxy-D-mannose, TMS_1_9, Predicted GC-MS Spectrum - 70eV, Positive	Not Available	Spectrum
Predicted GC-MS	GDP-4-Dehydro-6-deoxy-D-mannose, TMS_1_10, Predicted GC-MS Spectrum - 70eV, Positive	Not Available	Spectrum
Predicted GC-MS	GDP-4-Dehydro-6-deoxy-D-mannose, TMS_2_1, Predicted GC-MS Spectrum - 70eV, Positive	Not Available	Spectrum
Predicted GC-MS	GDP-4-Dehydro-6-deoxy-D-mannose, TMS_2_2, Predicted GC-MS Spectrum - 70eV, Positive	Not Available	Spectrum
Predicted GC-MS	GDP-4-Dehydro-6-deoxy-D-mannose, TMS_2_3, Predicted GC-MS Spectrum - 70eV, Positive	Not Available	Spectrum
Predicted GC-MS	GDP-4-Dehydro-6-deoxy-D-mannose, TMS_2_4, Predicted GC-MS Spectrum - 70eV, Positive	Not Available	Spectrum
Predicted GC-MS	GDP-4-Dehydro-6-deoxy-D-mannose, TMS_2_5, Predicted GC-MS Spectrum - 70eV, Positive	Not Available	Spectrum
Predicted GC-MS	GDP-4-Dehydro-6-deoxy-D-mannose, TMS_2_6, Predicted GC-MS Spectrum - 70eV, Positive	Not Available	Spectrum
Predicted GC-MS	GDP-4-Dehydro-6-deoxy-D-mannose, TMS_2_7, Predicted GC-MS Spectrum - 70eV, Positive	Not Available	Spectrum
Predicted GC-MS	GDP-4-Dehydro-6-deoxy-D-mannose, TMS_2_8, Predicted GC-MS Spectrum - 70eV, Positive	Not Available	Spectrum
Predicted GC-MS	GDP-4-Dehydro-6-deoxy-D-mannose, TMS_2_9, Predicted GC-MS Spectrum - 70eV, Positive	Not Available	Spectrum
Predicted GC-MS	GDP-4-Dehydro-6-deoxy-D-mannose, TMS_2_10, Predicted GC-MS Spectrum - 70eV, Positive	Not Available	Spectrum
Predicted GC-MS	GDP-4-Dehydro-6-deoxy-D-mannose, TMS_2_11, Predicted GC-MS Spectrum - 70eV, Positive	Not Available	Spectrum
Predicted GC-MS	GDP-4-Dehydro-6-deoxy-D-mannose, TMS_2_12, Predicted GC-MS Spectrum - 70eV, Positive	Not Available	Spectrum
Predicted GC-MS	GDP-4-Dehydro-6-deoxy-D-mannose, TMS_2_13, 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-0910520000-fcbc13f148251be94ff4	2015-09-15	View Spectrum
Predicted MS/MS	Predicted LC-MS/MS Spectrum - 20V, Positive	splash10-0udi-0910000000-ed550a57c125fee026ee	2015-09-15	View Spectrum
Predicted MS/MS	Predicted LC-MS/MS Spectrum - 40V, Positive	splash10-0udi-1900000000-a873b451fb06d591cb14	2015-09-15	View Spectrum
Predicted MS/MS	Predicted LC-MS/MS Spectrum - 10V, Negative	splash10-0f79-3901480000-ab8899450fb110bccaf6	2015-09-15	View Spectrum
Predicted MS/MS	Predicted LC-MS/MS Spectrum - 20V, Negative	splash10-0udi-1901000000-c6a3e1a0d5247f947a8a	2015-09-15	View Spectrum
Predicted MS/MS	Predicted LC-MS/MS Spectrum - 40V, Negative	splash10-0pdl-3900000000-148e1fc1e5c7ae57395c	2015-09-15	View Spectrum
Predicted MS/MS	Predicted LC-MS/MS Spectrum - 10V, Negative	splash10-000i-0000090000-45b44004cbf29fe6aa8f	2021-09-24	View Spectrum
Predicted MS/MS	Predicted LC-MS/MS Spectrum - 20V, Negative	splash10-072c-7902450000-9b1901584b05fbc14f34	2021-09-24	View Spectrum
Predicted MS/MS	Predicted LC-MS/MS Spectrum - 40V, Negative	splash10-05fr-2721910000-5a19390a8eaa546bc477	2021-09-24	View Spectrum
Predicted MS/MS	Predicted LC-MS/MS Spectrum - 10V, Positive	splash10-0udi-0900030000-a9251fc5a1b28bbacc54	2021-09-24	View Spectrum
Predicted MS/MS	Predicted LC-MS/MS Spectrum - 20V, Positive	splash10-0udi-2911220000-4e86fd74cab914f8c823	2021-09-24	View Spectrum
Predicted MS/MS	Predicted LC-MS/MS Spectrum - 40V, Positive	splash10-0zgr-9631000000-4a357d49912c73e87853	2021-09-24	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
GDP-mannose 4,6 dehydratase	GMDS	6p25	O60547	details
GDP-L-fucose synthase	TSTA3	8q24.3	Q13630	details

Transporters

Not Available

Metal Bindings

Not Available

Receptors

Not Available

Transcriptional Factors

Not Available

Concentrations Data

Not Available

External Links

HMDB ID

HMDB0001346

DrugBank ID

Not Available

Phenol Explorer Compound ID

Not Available

FoodDB ID

KNApSAcK ID

Chemspider ID

KEGG Compound ID

BioCyc ID

GDP-4-DEHYDRO-6-DEOXY-D-MANNOSE

BiGG ID

37116

Wikipedia Link

Not Available

METLIN ID

6180

PubChem Compound

439446

PDB ID

Not Available

ChEBI ID

16955

References

General References

Not Available

Enzymes

Enzyme Details

1. GDP-mannose 4,6 dehydratase

General function:: Involved in catalytic activity
Specific function:: Conversion of GDP-D-mannose to GDP-4-keto-6-D-deoxymannose.
Gene Name:: GMDS
Uniprot ID:: O60547
Molecular weight:: 39053.295

Enzyme Details

2. 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

Showing Compound Card for GDP-4-Dehydro-6-deoxy-D-mannose (CDB005258)

Structure for CDB005258 (GDP-4-Dehydro-6-deoxy-D-mannose)

Enzymes