ECMDB: GDP-4-Dehydro-6-deoxy-D-mannose (ECMDB01346) (M2MDB000347)

Identification Taxonomy Physical Properties Biological Properties Spectra Concentrations Links References Enzymes (2)XML

Proteins (408)

Record Information

Version

2.0

Creation Date

2012-05-31 13:50:24 -0600

Update Date

2015-06-03 15:53:56 -0600

Secondary Accession Numbers

ECMDB01346

Identification

Name:

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

Description

GDP-4-Dehydro-6-deoxy-D-mannose is an intermediate in fructose and mannose metabolism. GDP-4-Dehydro-6-deoxy-D-mannose is generated by GDP-D-mannose-4,6-dehydratase (GMD). This compound is then converted by the FX protein (GDP-4-keto-6-D-deoxymannose epimerase/GDP-4-keto-6-L-galactose reductase) to GDP-L-fucose. (PMID: 11698403). It is also involved in amino sugar and nucleotide sugar metabolism. (KEGG)

Structure

MOL SDF PDB SMILES InChI

Synonyms:

GDP-4-Dehydro-6-deoxy-D-mannose
GDP-4-Dehydro-6-deoxy-D-talose
GDP-4-Dehydro-D-rhamnose
GDP-4-Keto-6-D-deoxymannose
GDP-4-keto-6-deoxy-α-D-mannose
GDP-4-keto-6-Deoxy-a-D-mannose
GDP-4-Keto-6-deoxy-alpha-D-mannose
GDP-4-Keto-6-deoxy-D-mannose
GDP-4-keto-6-Deoxy-α-D-mannose
GDP-4-Keto-6-deoxymannose
GDP-4-Oxo-6-deoxy-D-mannose
GDP-4-Oxo-6-deoxymannose
Guanosine diphosphate-4-keto-6-deoxy-D-mannose
Guanosine diphosphoric acid-4-keto-6-deoxy-D-mannose

Chemical Formula:

C₁₆H₂₃N₅O₁₅P₂

Weight:

Average: 587.3258
Monoisotopic: 587.066588115

InChI Key:

PNHLMHWWFOPQLK-BKUUWRAGSA-N

InChI:

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

CAS number:

18186-48-6

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 IUPAC Name:

gdp-4-keto-6-deoxymannose

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

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 )

Physical Properties

State:

Solid

Charge:

-2

Melting point:

Not Available

Experimental Properties:

Property	Value	Source

Predicted Properties

Property	Value	Source
Water Solubility	6.35 g/L	ALOGPS
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	0	ChemAxon
Rule of Five	Yes	ChemAxon
Ghose Filter	Yes	ChemAxon
Veber's Rule	Yes	ChemAxon
MDDR-like Rule	Yes	ChemAxon

Biological Properties

Cellular Locations:

Cytoplasm

Reactions:

GDP-4-Dehydro-6-deoxy-D-mannose > GDP-4-Oxo-L-fucose
Guanosine diphosphate mannose <> GDP-4-Dehydro-6-deoxy-D-mannose + Water
GDP-L-Fucose + NADP <> GDP-4-Dehydro-6-deoxy-D-mannose + NADPH + Hydrogen ion
GDP-L-Fucose + NADP < Hydrogen ion + NADPH + GDP-4-Dehydro-6-deoxy-D-mannose
Guanosine diphosphate mannose > Water + GDP-4-Dehydro-6-deoxy-D-mannose
GDP-L-Fucose + NADP > GDP-4-Dehydro-6-deoxy-D-mannose + NADPH
GDP-4-Dehydro-6-deoxy-D-mannose + NADPH + Hydrogen ion + NADPH > GDP-L-Fucose + NADP
Guanosine diphosphate mannose <> GDP-4-Dehydro-6-deoxy-D-mannose + Water
Guanosine diphosphate mannose <> GDP-4-Dehydro-6-deoxy-D-mannose + Water

SMPDB Pathways:

Mannose Metabolism	PW000822
colanic acid building blocks biosynthesis	PW000951

KEGG Pathways:

Amino sugar and nucleotide sugar metabolism ec00520
Fructose and mannose metabolism ec00051
Metabolic pathways eco01100

EcoCyc Pathways:

GDP-L-fucose biosynthesis I (from GDP-D-mannose) PWY-66

Concentrations

Not Available

Spectra

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	Not Available	View in JSpectraViewer
1D NMR	13C NMR Spectrum	Not Available	View in JSpectraViewer
1D NMR	1H NMR Spectrum	Not Available	View in JSpectraViewer
1D NMR	13C NMR Spectrum	Not Available	View in JSpectraViewer
1D NMR	1H NMR Spectrum	Not Available	View in JSpectraViewer
1D NMR	13C NMR Spectrum	Not Available	View in JSpectraViewer
1D NMR	1H NMR Spectrum	Not Available	View in JSpectraViewer
1D NMR	13C NMR Spectrum	Not Available	View in JSpectraViewer
1D NMR	1H NMR Spectrum	Not Available	View in JSpectraViewer
1D NMR	13C NMR Spectrum	Not Available	View in JSpectraViewer
1D NMR	1H NMR Spectrum	Not Available	View in JSpectraViewer
1D NMR	13C NMR Spectrum	Not Available	View in JSpectraViewer
1D NMR	1H NMR Spectrum	Not Available	View in JSpectraViewer
1D NMR	13C NMR Spectrum	Not Available	View in JSpectraViewer
1D NMR	1H NMR Spectrum	Not Available	View in JSpectraViewer
1D NMR	13C NMR Spectrum	Not Available	View in JSpectraViewer
1D NMR	1H NMR Spectrum	Not Available	View in JSpectraViewer
1D NMR	13C NMR Spectrum	Not Available	View in JSpectraViewer
1D NMR	1H NMR Spectrum	Not Available	View in JSpectraViewer
1D NMR	13C NMR Spectrum	Not Available	View in JSpectraViewer

References

References:

Kanehisa, M., Goto, S., Sato, Y., Furumichi, M., Tanabe, M. (2012). "KEGG for integration and interpretation of large-scale molecular data sets." Nucleic Acids Res 40:D109-D114. Pubmed: 22080510
Keseler, I. M., Collado-Vides, J., Santos-Zavaleta, A., Peralta-Gil, M., Gama-Castro, S., Muniz-Rascado, L., Bonavides-Martinez, C., Paley, S., Krummenacker, M., Altman, T., Kaipa, P., Spaulding, A., Pacheco, J., Latendresse, M., Fulcher, C., Sarker, M., Shearer, A. G., Mackie, A., Paulsen, I., Gunsalus, R. P., Karp, P. D. (2011). "EcoCyc: a comprehensive database of Escherichia coli biology." Nucleic Acids Res 39:D583-D590. Pubmed: 21097882
Roos, C., Kolmer, M., Mattila, P., Renkonen, R. (2002). "Composition of Drosophila melanogaster proteome involved in fucosylated glycan metabolism." J Biol Chem 277:3168-3175. Pubmed: 11698403
van der Werf, M. J., Overkamp, K. M., Muilwijk, B., Coulier, L., Hankemeier, T. (2007). "Microbial metabolomics: toward a platform with full metabolome coverage." Anal Biochem 370:17-25. Pubmed: 17765195
Winder, C. L., Dunn, W. B., Schuler, S., Broadhurst, D., Jarvis, R., Stephens, G. M., Goodacre, R. (2008). "Global metabolic profiling of Escherichia coli cultures: an evaluation of methods for quenching and extraction of intracellular metabolites." Anal Chem 80:2939-2948. Pubmed: 18331064

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

Links

External Links:

Resource	Link
CHEBI ID	16955
HMDB ID	HMDB01346
Pubchem Compound ID	439446
Kegg ID	C01222
ChemSpider ID	388554
Wikipedia ID	Not Available
BioCyc ID	GDP-4-DEHYDRO-6-DEOXY-D-MANNOSE
EcoCyc ID	GDP-4-DEHYDRO-6-DEOXY-D-MANNOSE

Enzymes

Protein Details

1. GDP-mannose 4,6-dehydratase

General function:: Involved in catalytic activity
Specific function:: GDP-mannose = GDP-4-dehydro-6-deoxy-D-mannose + H(2)O
Gene Name:: gmd
Uniprot ID:: P0AC88
Molecular weight:: 42047

Reactions

GDP-mannose = GDP-4-dehydro-6-deoxy-D-mannose + H(2)O.

Protein 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:: fcl
Uniprot ID:: P32055
Molecular weight:: 36141

Reactions

GDP-L-fucose + NADP(+) = GDP-4-dehydro-6-deoxy-D-mannose + NADPH.

GDP-4-Dehydro-6-deoxy-D-mannose (ECMDB01346) (M2MDB000347)

Structure for #<Compound:0xabd84400>

Enzymes

Reactions

Reactions