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Record Information

Version

2.0

Creation Date

2012-05-31 13:51:42 -0600

Update Date

2015-06-03 15:54:05 -0600

Secondary Accession Numbers

ECMDB01399

Identification

Name:

4,6-Dideoxy-4-oxo-dTDP-D-glucose

Description

4,6-Dideoxy-4-oxo-dTDP-D-glucose is a product of the enzyme TDP-glucose 4,6-dehydratase [EC:4.2.1.46] in the Nucleotide sugars metabolism (KEGG)

Structure

MOL SDF PDB SMILES InChI

Synonyms:

DTDP-4-dehydro-6-deoxy-α-D-glucopyranose
dTDP-4-dehydro-6-Deoxy-a-D-galactose
dTDP-4-dehydro-6-Deoxy-a-D-glucopyranose
dTDP-4-dehydro-6-Deoxy-a-D-glucose
DTDP-4-Dehydro-6-deoxy-alpha-D-galactose
DTDP-4-Dehydro-6-deoxy-alpha-D-glucopyranose
DTDP-4-Dehydro-6-deoxy-alpha-D-glucose
DTDP-4-Dehydro-6-deoxy-D-galactose
DTDP-4-Dehydro-6-deoxy-D-glucose
DTDP-4-dehydro-6-deoxy-L-mannose
dTDP-4-dehydro-6-Deoxy-α-D-galactose
dTDP-4-dehydro-6-Deoxy-α-D-glucopyranose
dTDP-4-dehydro-6-Deoxy-α-D-glucose
DTDP-4-dehydro-L-rhamnose
DTDP-4-oxo-6-deoxy--α-D-glucose
dTDP-4-oxo-6-Deoxy--a-D-glucose
DTDP-4-Oxo-6-deoxy--alpha-D-glucose
dTDP-4-oxo-6-Deoxy--α-D-glucose
dTDP-4-oxo-6-Deoxy-a-D-glucose
DTDP-4-Oxo-6-deoxy-alpha-D-glucose
DTDP-4-Oxo-6-deoxy-D-glucose
DTDP-4-oxo-6-deoxy-L-mannose
dTDP-4-oxo-6-Deoxy-α-D-glucose
DTDP-4-oxo-L-rhamnose
DTDP-6-deoxy-α-D-xylo-4-hexosulose
dTDP-6-Deoxy-α-D-xylo-4-hexosulose
DTDP-6-deoxy-α-D-xylohex-4-ulose
dTDP-6-Deoxy-a-D-xylo-4-hexosulose
dTDP-6-Deoxy-a-D-xylohex-4-ulose
DTDP-6-Deoxy-alpha-D-xylo-4-hexosulose
DTDP-6-Deoxy-alpha-D-xylohex-4-ulose
dTDP-6-Deoxy-α-D-xylo-4-hexosulose
dTDP-6-Deoxy-α-D-xylohex-4-ulose
DTDP-DDGlc
TDP-4-keto-6-deoxy--α-D-glucose
TDP-4-keto-6-Deoxy--a-D-glucose
TDP-4-Keto-6-deoxy--alpha-D-glucose
TDP-4-keto-6-Deoxy--α-D-glucose
TDP-4-keto-6-deoxy-D-glucose
TDP-4-oxo-6-deoxy--α-D-glucose
TDP-4-oxo-6-Deoxy--a-D-glucose
TDP-4-Oxo-6-deoxy--alpha-D-glucose
TDP-4-oxo-6-Deoxy--α-D-glucose
TDP-4-oxo-6-deoxy-D-glucose
Thymidine 5'-[3-(D-xylo-hexopyranosyl-4-ulose) dihydrogen diphosphate]
Thymidine 5'-[3-(D-xylo-hexopyranosyl-4-ulose) dihydrogen diphosphoric acid]

Chemical Formula:

C₁₆H₂₄N₂O₁₅P₂

Weight:

Average: 546.3137
Monoisotopic: 546.065191132

InChI Key:

PSXWNITXWWECNY-SRPWTXKTSA-N

InChI:

InChI=1S/C16H24N2O15P2/c1-6-4-18(16(24)17-14(6)23)10-3-8(19)9(31-10)5-29-34(25,26)33-35(27,28)32-15-13(22)12(21)11(20)7(2)30-15/h4,7-10,12-13,15,19,21-22H,3,5H2,1-2H3,(H,25,26)(H,27,28)(H,17,23,24)/t7-,8+,9-,10-,12+,13-,15?/m1/s1

CAS number:

Not Available

IUPAC Name:

{[(3R,4R,6R)-3,4-dihydroxy-6-methyl-5-oxooxan-2-yl]oxy}({[hydroxy({[(2R,3S,5R)-3-hydroxy-5-(5-methyl-2,4-dioxo-1,2,3,4-tetrahydropyrimidin-1-yl)oxolan-2-yl]methoxy})phosphoryl]oxy})phosphinic acid

Traditional IUPAC Name:

[(3R,4R,6R)-3,4-dihydroxy-6-methyl-5-oxooxan-2-yl]oxy({hydroxy[(2R,3S,5R)-3-hydroxy-5-(5-methyl-2,4-dioxo-3H-pyrimidin-1-yl)oxolan-2-yl]methoxyphosphoryl}oxy)phosphinic acid

SMILES:

C[C@H]1OC(OP(O)(=O)OP(O)(=O)OC[C@H]2O[C@H](C[C@@H]2O)N2C=C(C)C(=O)NC2=O)[C@H](O)[C@@H](O)C1=O

Chemical Taxonomy

Description

belongs to the class of organic compounds known as pyrimidine nucleotide sugars. These are pyrimidine nucleotides bound to a saccharide derivative through the terminal phosphate group.

Kingdom

Organic compounds

Super Class

Nucleosides, nucleotides, and analogues

Class

Pyrimidine nucleotides

Sub Class

Pyrimidine nucleotide sugars

Direct Parent

Pyrimidine nucleotide sugars

Alternative Parents

Substituents

Pyrimidine nucleotide sugar
Pyrimidine 2'-deoxyribonucleoside diphosphate
Pentose phosphate
Organic pyrophosphate
Pyrimidone
Monoalkyl phosphate
Hydropyrimidine
Organic phosphoric acid derivative
Pyrimidine
Oxane
Phosphoric acid ester
Alkyl phosphate
Heteroaromatic compound
Vinylogous amide
Tetrahydrofuran
Secondary alcohol
Lactam
Ketone
Urea
Cyclic ketone
Oxacycle
Azacycle
Organoheterocyclic compound
Organooxygen compound
Organonitrogen compound
Hydrocarbon derivative
Organic oxide
Organopnictogen compound
Organic oxygen compound
Organic nitrogen compound
Alcohol
Carbonyl group
Aromatic heteromonocyclic compound

Molecular Framework

Aromatic heteromonocyclic compounds

External Descriptors

TDP-sugar (CHEBI:16620 )

Physical Properties

State:

Solid

Charge:

-2

Melting point:

Not Available

Experimental Properties:

Property	Value	Source

Predicted Properties

Property	Value	Source
Water Solubility	11.3 g/L	ALOGPS
logP	-0.93	ALOGPS
logP	-2	ChemAxon
logS	-1.7	ALOGPS
pKa (Strongest Acidic)	1.73	ChemAxon
pKa (Strongest Basic)	-3.2	ChemAxon
Physiological Charge	-2	ChemAxon
Hydrogen Acceptor Count	12	ChemAxon
Hydrogen Donor Count	6	ChemAxon
Polar Surface Area	247.92 Å²	ChemAxon
Rotatable Bond Count	8	ChemAxon
Refractivity	106.99 m³·mol⁻¹	ChemAxon
Polarizability	45.19 Å³	ChemAxon
Number of Rings	3	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:

SMPDB Pathways:

Not Available

KEGG Pathways:

Biosynthesis of vancomycin group antibiotics ec01055
Metabolic pathways eco01100
Polyketide sugar unit biosynthesis ec00523
Streptomycin biosynthesis ec00521

EcoCyc Pathways:

dTDP-L-rhamnose biosynthesis I DTDPRHAMSYN-PWY
enterobacterial common antigen biosynthesis ECASYN-PWY

Concentrations

Not Available

Spectra

Spectra:

Spectrum Type	Description	Splash Key
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (Non-derivatized) - 70eV, Positive	splash10-004i-9812620000-55c82e214c8402cb2283	View in MoNA
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (2 TMS) - 70eV, Positive	splash10-00b9-9823704000-df6af03755642135c5a0	View in MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Positive	splash10-004i-0900000000-5240324bf97c105ae51d	View in MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Positive	splash10-004i-3921000000-7e9e2dfed9a99533be0a	View in MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Positive	splash10-004i-4900000000-c718341e14191248128a	View in MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Negative	splash10-0f6t-3403290000-9b28f5967f6c5a9fa675	View in MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Negative	splash10-0fbc-5904010000-e8611fa8f8e1490b7ed1	View in MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Negative	splash10-0a6u-5901000000-2158145d7f9abac6643e	View in MoNA
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
1D NMR	1H 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
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:

Not Available

Material Safety Data Sheet (MSDS)

Not Available

Links

External Links:

Resource	Link
CHEBI ID	16620
HMDB ID	HMDB01399
Pubchem Compound ID	443496
Kegg ID	C11907
ChemSpider ID	391705
Wikipedia ID	Not Available
BioCyc ID	DTDP-DEOH-DEOXY-GLUCOSE
EcoCyc ID	DTDP-DEOH-DEOXY-GLUCOSE

Enzymes

Protein Details

1. dTDP-glucose 4,6-dehydratase 2

General function:: Involved in dTDP-glucose 4,6-dehydratase activity
Specific function:: Catalyzes the dehydration of dTDP-D-glucose to form dTDP-6-deoxy-D-xylo-4-hexulose via a three-step process involving oxidation, dehydration and reduction
Gene Name:: rffG
Uniprot ID:: P27830
Molecular weight:: 39754

Reactions

dTDP-glucose = dTDP-4-dehydro-6-deoxy-D-glucose + H(2)O.

Protein Details

2. dTDP-4-dehydrorhamnose 3,5-epimerase

General function:: Involved in dTDP-4-dehydrorhamnose 3,5-epimerase activity
Specific function:: Catalyzes the epimerization of the C3' and C5'positions of dTDP-6-deoxy-D-xylo-4-hexulose, forming dTDP-6-deoxy-L-lyxo-4- hexulose
Gene Name:: rfbC
Uniprot ID:: P37745
Molecular weight:: 21270

Reactions

dTDP-4-dehydro-6-deoxy-D-glucose = dTDP-4-dehydro-6-deoxy-L-mannose.

Protein Details

3. dTDP-glucose 4,6-dehydratase 1

General function:: Involved in dTDP-glucose 4,6-dehydratase activity
Specific function:: Catalyzes the dehydration of dTDP-D-glucose to form dTDP-6-deoxy-D-xylo-4-hexulose via a three-step process involving oxidation, dehydration and reduction
Gene Name:: rfbB
Uniprot ID:: P37759
Molecular weight:: 40558

Reactions

dTDP-glucose = dTDP-4-dehydro-6-deoxy-D-glucose + H(2)O.

Protein Details

4. Lipopolysaccharide biosynthesis protein rffA

General function:: Involved in catalytic activity
Specific function:: Involved in ECA elongation
Gene Name:: rffA
Uniprot ID:: P27833
Molecular weight:: 41901

Structural search and advanced query search is temporarily unavailable. We are working to fix this issue. Thank you for your support and patience.

4,6-Dideoxy-4-oxo-dTDP-D-glucose (M2MDB000370)

Structure for #<Compound:0x9d2af434>

Enzymes

Reactions

Reactions

Reactions