Bovine Metabolome Database: Showing metabocard for GDP-4-Dehydro-6-deoxy-D-mannose (BMDB0001346)

Identification Taxonomy Physical properties Pathways Spectra Concentrations Links References enzymes (2) Show 2 proteins XML

Record Information

Version

1.0

Creation Date

2016-09-30 22:44:29 UTC

Update Date

2020-05-21 16:28:32 UTC

BMDB ID

BMDB0001346

Secondary Accession Numbers

BMDB01346

Metabolite 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 possibly soluble (in water) and 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. GDP-4-Dehydro-6-deoxy-D-mannose participates in a number of enzymatic reactions, within cattle. 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; which is mediated by the enzyme GDP-L-fucose synthase. In cattle, GDP-4-dehydro-6-deoxy-D-mannose is involved in the metabolic pathway called the fructose and mannose degradation pathway.

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

587.3258

Monoisotopic Molecular Weight

587.066588115

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

Status

Expected but not Quantified

Origin

Endogenous

Biofunction

Not Available

Application

Not Available

Cellular locations

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	Yes	ChemAxon
Rule of Five	Yes	ChemAxon
Ghose Filter	Yes	ChemAxon
Veber's Rule	Yes	ChemAxon
MDDR-like Rule	Yes	ChemAxon

Spectra

Spectrum Type	Description	Splash Key
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (Non-derivatized) - 70eV, Positive	splash10-00mo-7594640000-f6eaffb3b87a7209c04d	View in MoNA
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (1 TMS) - 70eV, Positive	splash10-002f-6891604000-2d6996a185dcede1dcba	View in MoNA
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS ("GDP-4-Dehydro-6-deoxy-D-mannose,1TMS,#1" TMS) - 70eV, Positive	Not Available	View in JSpectraViewer
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_1_2) - 70eV, Positive	Not Available	View in JSpectraViewer
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_1_3) - 70eV, Positive	Not Available	View in JSpectraViewer
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_1_4) - 70eV, Positive	Not Available	View in JSpectraViewer
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_1_5) - 70eV, Positive	Not Available	View in JSpectraViewer
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_1_6) - 70eV, Positive	Not Available	View in JSpectraViewer
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_1_7) - 70eV, Positive	Not Available	View in JSpectraViewer
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_1_8) - 70eV, Positive	Not Available	View in JSpectraViewer
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_1_9) - 70eV, Positive	Not Available	View in JSpectraViewer
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_1_10) - 70eV, Positive	Not Available	View in JSpectraViewer
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_2_1) - 70eV, Positive	Not Available	View in JSpectraViewer
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_2_2) - 70eV, Positive	Not Available	View in JSpectraViewer
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_2_3) - 70eV, Positive	Not Available	View in JSpectraViewer
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_2_4) - 70eV, Positive	Not Available	View in JSpectraViewer
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_2_5) - 70eV, Positive	Not Available	View in JSpectraViewer
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_2_6) - 70eV, Positive	Not Available	View in JSpectraViewer
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_2_7) - 70eV, Positive	Not Available	View in JSpectraViewer
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_2_8) - 70eV, Positive	Not Available	View in JSpectraViewer
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_2_9) - 70eV, Positive	Not Available	View in JSpectraViewer
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_2_10) - 70eV, Positive	Not Available	View in JSpectraViewer
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_2_11) - 70eV, Positive	Not Available	View in JSpectraViewer
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_2_12) - 70eV, Positive	Not Available	View in JSpectraViewer
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_2_13) - 70eV, Positive	Not Available	View in JSpectraViewer
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Positive	splash10-0udi-0910520000-fcbc13f148251be94ff4	View in MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Positive	splash10-0udi-0910000000-ed550a57c125fee026ee	View in MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Positive	splash10-0udi-1900000000-a873b451fb06d591cb14	View in MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Negative	splash10-0f79-3901480000-ab8899450fb110bccaf6	View in MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Negative	splash10-0udi-1901000000-c6a3e1a0d5247f947a8a	View in MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Negative	splash10-0pdl-3900000000-148e1fc1e5c7ae57395c	View in MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Negative	splash10-000i-0000090000-45b44004cbf29fe6aa8f	View in MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Negative	splash10-072c-7902450000-9b1901584b05fbc14f34	View in MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Negative	splash10-05fr-2721910000-5a19390a8eaa546bc477	View in MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Positive	splash10-0udi-0900030000-a9251fc5a1b28bbacc54	View in MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Positive	splash10-0udi-2911220000-4e86fd74cab914f8c823	View in MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Positive	splash10-0zgr-9631000000-4a357d49912c73e87853	View in MoNA
1D NMR	¹H NMR Spectrum (1D, 100 MHz, D₂O, predicted)	Not Available	View in JSpectraViewer
1D NMR	¹³C NMR Spectrum (1D, 100 MHz, D₂O, predicted)	Not Available	View in JSpectraViewer
1D NMR	¹H NMR Spectrum (1D, 200 MHz, D₂O, predicted)	Not Available	View in JSpectraViewer
1D NMR	¹³C NMR Spectrum (1D, 200 MHz, D₂O, predicted)	Not Available	View in JSpectraViewer
1D NMR	¹H NMR Spectrum (1D, 300 MHz, D₂O, predicted)	Not Available	View in JSpectraViewer
1D NMR	¹³C NMR Spectrum (1D, 300 MHz, D₂O, predicted)	Not Available	View in JSpectraViewer
1D NMR	¹H NMR Spectrum (1D, 400 MHz, D₂O, predicted)	Not Available	View in JSpectraViewer
1D NMR	¹³C NMR Spectrum (1D, 400 MHz, D₂O, predicted)	Not Available	View in JSpectraViewer
1D NMR	¹H NMR Spectrum (1D, 500 MHz, D₂O, predicted)	Not Available	View in JSpectraViewer
1D NMR	¹³C NMR Spectrum (1D, 500 MHz, D₂O, predicted)	Not Available	View in JSpectraViewer
1D NMR	¹H NMR Spectrum (1D, 600 MHz, D₂O, predicted)	Not Available	View in JSpectraViewer
1D NMR	¹³C NMR Spectrum (1D, 600 MHz, D₂O, predicted)	Not Available	View in JSpectraViewer
1D NMR	¹H NMR Spectrum (1D, 700 MHz, D₂O, predicted)	Not Available	View in JSpectraViewer
1D NMR	¹³C NMR Spectrum (1D, 700 MHz, D₂O, predicted)	Not Available	View in JSpectraViewer
1D NMR	¹H NMR Spectrum (1D, 800 MHz, D₂O, predicted)	Not Available	View in JSpectraViewer
1D NMR	¹³C NMR Spectrum (1D, 800 MHz, D₂O, predicted)	Not Available	View in JSpectraViewer
1D NMR	¹H NMR Spectrum (1D, 900 MHz, D₂O, predicted)	Not Available	View in JSpectraViewer
1D NMR	¹³C NMR Spectrum (1D, 900 MHz, D₂O, predicted)	Not Available	View in JSpectraViewer
1D NMR	¹H NMR Spectrum (1D, 1000 MHz, D₂O, predicted)	Not Available	View in JSpectraViewer
1D NMR	¹³C NMR Spectrum (1D, 1000 MHz, D₂O, predicted)	Not Available	View in JSpectraViewer

Biological Properties

Cellular Locations

Cytoplasm

Biospecimen Locations

Not Available

Pathways

Name	SMPDB/Pathwhiz	KEGG
Fructose and Mannose Degradation		Not Available

Normal Concentrations

Not Available

Abnormal Concentrations

Not Available

External Links

HMDB ID

HMDB0001346

DrugBank ID

Not Available

Phenol Explorer Compound ID

Not Available

FooDB 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

Synthesis Reference

Oths, Philip J.; Mayer, Robert M.; Floss, Heinz G. Stereochemistry and mechanism of the GDP-mannose dehydratase reaction. Carbohydrate Research (1990), 198(1), 91-100.

Material Safety Data Sheet (MSDS)

Not Available

General References

Not Available

Enzymes

Enzyme Details

1. dTDP-D-glucose 4,6-dehydratase

General function:: Cell wall/membrane/envelope biogenesis
Specific function:: Not Available
Gene Name:: TGDS
Uniprot ID:: A6QLW2
Molecular weight:: 40666.0

Reactions

Guanosine diphosphate mannose → GDP-4-Dehydro-6-deoxy-D-mannose + Water	details

Enzyme Details

2. 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-4-Dehydro-6-deoxy-D-mannose (BMDB0001346)

Structure for BMDB0001346 (GDP-4-Dehydro-6-deoxy-D-mannose)

Enzymes

Reactions

Reactions