ECMDB: dTDP-D-Glucose (ECMDB01328) (M2MDB000339)

Identification Taxonomy Physical Properties Biological Properties Spectra Concentrations Links References Enzymes (5)XML

Proteins (1667)

Record Information

Version

2.0

Creation Date

2012-05-31 13:49:58 -0600

Update Date

2015-09-13 15:15:22 -0600

Secondary Accession Numbers

ECMDB01328

Identification

Name:

dTDP-D-Glucose

Description

dTDP-D-glucose is a member of the chemical class known as Pyrimidine Nucleotide Sugars. These are pyrimidine nucleotides bound to a saccharide derivative through the terminal phosphate group. dTDP-D-glucose is a key metabolite in prokaryotes as a precursor for a large number of modified deoxysugars, and these deoxysugars are a major part of various antibiotics, ranging from glycosides to macrolides. (PMID 18051285)

Structure

MOL SDF PDB SMILES InChI

Synonyms:

DTDP-D-Glucose
DTDP-delta-glucose
DTDP-Glc
DTDP-Glucose
dTDP-δ-Glucose
DTDPglucose
Mono-a-D-glucopyranosyl ester
mono-a-delta-Glucopyranosyl ester
mono-a-δ-Glucopyranosyl ester
Mono-alpha-D-glucopyranosyl ester
Mono-alpha-delta-glucopyranosyl ester
mono-α-D-Glucopyranosyl ester
mono-α-δ-Glucopyranosyl ester
P-a-D-Glucopyranosyl ester
P-alpha-D-Glucopyranosyl ester
P-α-D-Glucopyranosyl ester
TDP-D-Glucose
TDP-delta-glucose
TDP-Glc
TDP-Glucose
TDP-δ-Glucose
TDPG
Thymidine 5-(trihydrogen diphosphate)
Thymidine 5-(trihydrogen diphosphoric acid)
Thymidine 5-diphosphate-D-Glucose
Thymidine 5-diphosphate-delta-Glucose
Thymidine 5-diphosphate-δ-glucose
Thymidine 5-diphosphoric acid-D-glucose
Thymidine 5-diphosphoric acid-delta-glucose
Thymidine 5-diphosphoric acid-δ-glucose

Chemical Formula:

C₁₆H₂₆N₂O₁₆P₂

Weight:

Average: 564.329
Monoisotopic: 564.075755818

InChI Key:

YSYKRGRSMLTJNL-KFQCIAAJSA-N

InChI:

InChI=1S/C16H26N2O16P2/c1-6-3-18(16(25)17-14(6)24)10-2-7(20)9(31-10)5-30-35(26,27)34-36(28,29)33-15-13(23)12(22)11(21)8(4-19)32-15/h3,7-13,15,19-23H,2,4-5H2,1H3,(H,26,27)(H,28,29)(H,17,24,25)/t7-,8+,9+,10+,11+,12-,13+,15?/m0/s1

CAS number:

2196-62-5

IUPAC Name:

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

Traditional IUPAC Name:

dtdp-D-glucose

SMILES:

CC1=CN([C@H]2C[C@H](O)[C@@H](COP(O)(=O)OP(O)(=O)OC3O[C@H](CO)[C@@H](O)[C@H](O)[C@H]3O)O2)C(=O)NC1=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
Monosaccharide phosphate
Organic pyrophosphate
Monoalkyl phosphate
Pyrimidone
Hydropyrimidine
Phosphoric acid ester
Monosaccharide
Organic phosphoric acid derivative
Oxane
Alkyl phosphate
Pyrimidine
Heteroaromatic compound
Vinylogous amide
Tetrahydrofuran
Urea
Lactam
Secondary alcohol
Oxacycle
Azacycle
Organoheterocyclic compound
Polyol
Organooxygen compound
Organonitrogen compound
Alcohol
Hydrocarbon derivative
Organic oxide
Organopnictogen compound
Organic nitrogen compound
Primary alcohol
Organic oxygen compound
Aromatic heteromonocyclic compound

Molecular Framework

Aromatic heteromonocyclic compounds

External Descriptors

dTDP-alpha-D-glucose (CHEBI:35248 )

Physical Properties

State:

Not Available

Charge:

-2

Melting point:

Not Available

Experimental Properties:

Property	Value	Source
LogP:	-5.568	PhysProp

Predicted Properties

Property	Value	Source
Water Solubility	11.2 g/L	ALOGPS
logP	-1.2	ALOGPS
logP	-3.7	ChemAxon
logS	-1.7	ALOGPS
pKa (Strongest Acidic)	1.73	ChemAxon
pKa (Strongest Basic)	-3	ChemAxon
Physiological Charge	-2	ChemAxon
Hydrogen Acceptor Count	13	ChemAxon
Hydrogen Donor Count	8	ChemAxon
Polar Surface Area	271.31 Å²	ChemAxon
Rotatable Bond Count	9	ChemAxon
Refractivity	109.3 m³·mol⁻¹	ChemAxon
Polarizability	46.61 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:

Thymidine 5'-triphosphate + Glucose 1-phosphate + Hydrogen ion <> dTDP-D-Glucose + Pyrophosphate
dTDP-D-Glucose <> 4,6-Dideoxy-4-oxo-dTDP-D-glucose + Water
Thymidine 5'-triphosphate + Glucose 1-phosphate <> Pyrophosphate + dTDP-D-Glucose
dTDP-D-Glucose <> dTDP-D-Galactose
dTDP-D-Glucose > dTDP-4-dehydro-6-deoxy-D-glucose + Water
Thymidine 5'-triphosphate + Hydrogen ion + Glucose 1-phosphate > Pyrophosphate + dTDP-D-Glucose
Alpha-D-glucose 1-phosphate + Thymidine 5'-triphosphate + Hydrogen ion > Pyrophosphate + dTDP-D-Glucose
dTDP-D-Glucose > Water + 4,6-Dideoxy-4-oxo-dTDP-D-glucose
α-D-glucose 1-phosphate + Thymidine 5'-triphosphate + Hydrogen ion > dTDP-D-Glucose + Pyrophosphate
dTDP-D-Glucose <> dTDP-D-Galactose
dTDP-D-Glucose <>4 4,6-Dideoxy-4-oxo-dTDP-D-glucose + Water
Thymidine 5'-triphosphate + Glucose 1-phosphate + Hydrogen ion <> dTDP-D-Glucose + Pyrophosphate

SMPDB Pathways:

O-antigen building blocks biosynthesis	PW002089
Secondary Metabolites: enterobacterial common antigen biosynthesis	PW000959
Secondary Metabolites: enterobacterial common antigen biosynthesis 2	PW002045
Starch and sucrose metabolism	PW000941

KEGG Pathways:

Biosynthesis of vancomycin group antibiotics ec01055
Metabolic pathways eco01100
Polyketide sugar unit biosynthesis ec00523
Starch and sucrose metabolism ec00500
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	splash10-054p-7920560000-231b6626719eee6c053e	View in MoNA
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (1 TMS) - 70eV, Positive	splash10-0600-9411517000-1aaf284fc97b157c78d4	View in MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Positive	splash10-004i-0900000000-312a08522e3cb22b111b	View in MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Positive	splash10-004i-2921000000-d3da9a944bb5a8c62cfb	View in MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Positive	splash10-004i-4900000000-415f5eced8f6fd67d535	View in MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Negative	splash10-0ik9-1403290000-6b2a8c7a42ac2eaa39c3	View in MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Negative	splash10-0fbc-4905010000-8e6b9db92566b846a800	View in MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Negative	splash10-0a6u-4901000000-4c65036f67c107c3bdf5	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:

Han, J. M., Kim, S. M., Lee, H. J., Yoo, J. C. (2007). "Cloning and expression of glucose-1-phosphate thymidylyltransferase gene (schS6) from Streptomyces sp. SCC-2136." J Microbiol Biotechnol 17:685-690. Pubmed: 18051285
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:

Goncalves, Ruth J. Thymidine diphosphate glucose and biosynthesis of glucosides in wheat germ. I. Enzymologia (1963), 26(5), 287-93.

Material Safety Data Sheet (MSDS)

Not Available

Links

External Links:

Resource	Link
CHEBI ID	15700
HMDB ID	HMDB01328
Pubchem Compound ID	439324
Kegg ID	C00842
ChemSpider ID	388455
Wikipedia ID	Not Available
BioCyc ID	DTDP-D-GLUCOSE
EcoCyc ID	DTDP-D-GLUCOSE

Enzymes

Protein Details

1. UDP-glucose 4-epimerase

General function:: Involved in catalytic activity
Specific function:: UDP-glucose = UDP-galactose
Gene Name:: galE
Uniprot ID:: P09147
Molecular weight:: 37265

Reactions

UDP-glucose = UDP-galactose.

Protein Details

2. 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

3. Glucose-1-phosphate thymidylyltransferase 1

General function:: Involved in glucose-1-phosphate thymidylyltransferase activity
Specific function:: Catalyzes the formation of dTDP-glucose, from dTTP and glucose 1-phosphate, as well as its pyrophosphorolysis
Gene Name:: rmlA1
Uniprot ID:: P37744
Molecular weight:: 32693

Reactions

dTTP + alpha-D-glucose 1-phosphate = diphosphate + dTDP-glucose.

Protein Details

4. 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

5. Glucose-1-phosphate thymidylyltransferase 2

General function:: Involved in glucose-1-phosphate thymidylyltransferase activity
Specific function:: Catalyzes the formation of dTDP-glucose, from dTTP and glucose 1-phosphate, as well as its pyrophosphorolysis
Gene Name:: rmlA2
Uniprot ID:: P61887
Molecular weight:: 32734

Reactions

dTTP + alpha-D-glucose 1-phosphate = diphosphate + dTDP-glucose.

dTDP-D-Glucose (ECMDB01328) (M2MDB000339)

Structure for #<Compound:0xaa93d604>

Enzymes

Reactions

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