ECMDB: dTDP-4-Acetamido-4,6-dideoxy-D-galactose (ECMDB20613) (M2MDB001412)

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

Proteins (2)

Record Information

Version

2.0

Creation Date

2012-05-31 14:53:26 -0600

Update Date

2015-06-03 17:20:23 -0600

Secondary Accession Numbers

ECMDB20613

Identification

Name:

dTDP-4-Acetamido-4,6-dideoxy-D-galactose

Description

dTDP-4-acetamido-4,6-dideoxy-D-galactose reacts with undecaprenyl N-acetyl-glucosaminyl-N-acetyl-mannosaminuronate to produce undecaprenyl N-acetyl-glucosaminyl-N-acetyl-mannosaminuronate-4-acetamido-4,6-dideoxy-D-galactose pyrophosphate and dTDP. The reaction is catalyzed by certain members of the fucosyltransferase family of enzymes.

Structure

MOL SDF PDB SMILES InChI

Synonyms:

DTDP-4-Acetamido-4,6-dideoxy-D-glucose
TDP-4-acetamido-4,6-dideoxy-D-galactose
TDP-Fuc-4-Nac
TDP-Fuc4NAc

Chemical Formula:

C₁₈H₂₉N₃O₁₅P₂

Weight:

Average: 589.3815
Monoisotopic: 589.107390297

InChI Key:

YHXQWYBLXUELDA-ANBZSJOMSA-N

InChI:

InChI=1S/C18H29N3O15P2/c1-7-5-21(18(27)20-16(7)26)12-4-10(23)11(34-12)6-32-37(28,29)36-38(30,31)35-17-15(25)14(24)13(8(2)33-17)19-9(3)22/h5,8,10-15,17,23-25H,4,6H2,1-3H3,(H,19,22)(H,28,29)(H,30,31)(H,20,26,27)/t8-,10?,11?,12?,13?,14+,15-,17?/m1/s1

CAS number:

Not Available

IUPAC Name:

{[(3R,4S,6R)-5-acetamido-3,4-dihydroxy-6-methyloxan-2-yl]oxy}({[hydroxy({[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,4S,6R)-5-acetamido-3,4-dihydroxy-6-methyloxan-2-yl]oxy({hydroxy[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)OCC2OC(CC2O)N2C=C(C)C(=O)NC2=O)[C@H](O)[C@@H](O)C1NC(C)=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
Pyrimidone
Monoalkyl phosphate
Hydropyrimidine
Monosaccharide
Organic phosphoric acid derivative
Oxane
Phosphoric acid ester
Pyrimidine
Alkyl phosphate
Tetrahydrofuran
Heteroaromatic compound
Acetamide
Vinylogous amide
Secondary carboxylic acid amide
Secondary alcohol
Carboxamide group
Lactam
Urea
Azacycle
Organoheterocyclic compound
Carboxylic acid derivative
Oxacycle
Alcohol
Carbonyl group
Organic nitrogen compound
Organic oxygen compound
Organonitrogen compound
Organooxygen compound
Organopnictogen compound
Organic oxide
Hydrocarbon derivative
Aromatic heteromonocyclic compound

Molecular Framework

Aromatic heteromonocyclic compounds

External Descriptors

Not Available

Physical Properties

State:

Solid

Charge:

-2

Melting point:

Not Available

Experimental Properties:

Property	Value	Source

Predicted Properties

Property	Value	Source
Water Solubility	7 g/L	ALOGPS
logP	-0.98	ALOGPS
logP	-2.9	ChemAxon
logS	-1.9	ALOGPS
pKa (Strongest Acidic)	1.74	ChemAxon
pKa (Strongest Basic)	-0.38	ChemAxon
Physiological Charge	-2	ChemAxon
Hydrogen Acceptor Count	12	ChemAxon
Hydrogen Donor Count	7	ChemAxon
Polar Surface Area	259.95 Å²	ChemAxon
Rotatable Bond Count	9	ChemAxon
Refractivity	118.86 m³·mol⁻¹	ChemAxon
Polarizability	51.1 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:

Acetyl-CoA + dTDP-D-Fucosamine > Coenzyme A + dTDP-4-Acetamido-4,6-dideoxy-D-galactose + Hydrogen ion
dTDP-4-Acetamido-4,6-dideoxy-D-galactose + Undecaprenyl-diphospho-N-acetylglucosamine-N-acetylmannosaminuronate > dTDP + Hydrogen ion + Undecaprenyl-diphospho N-acetylglucosamine-N-acetylmannosaminuronate-N-acetamido-4,6-dideoxy-D-galactose
Undecaprenyl phosphate + dTDP-4-Acetamido-4,6-dideoxy-D-galactose > Hydrogen ion + undecaprenyl N-acetyl-glucosaminyl-N-acetyl-mannosaminuronate-4-acetamido-4,6-dideoxy-D-galactose pyrophosphate + dTDP

SMPDB Pathways:

Secondary Metabolites: enterobacterial common antigen biosynthesis 3

PW002046

KEGG Pathways:

Not Available

EcoCyc Pathways:

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	splash10-0fi3-2912210000-f236800b9ea7dbdbc3e3	View in MoNA
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (1 TMS) - 70eV, Positive	splash10-004l-5982503000-79125e55f9f7a2c55fc7	View in MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Positive	splash10-004i-0900000000-f7a2498425541d18be17	View in MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Positive	splash10-004i-2921000000-48f99fad61488b9aebc6	View in MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Positive	splash10-004i-3900000000-ab03069c074b9d44b24c	View in MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Negative	splash10-004r-3902360000-7ea32efc573937e26e96	View in MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Negative	splash10-0fbd-5905010000-1a60390d221fe42f6751	View in MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Negative	splash10-0bvl-4900000000-67cffdb89f0e9fb148ae	View in MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Positive	splash10-0006-0301090000-98d568ca19349700cef7	View in MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Positive	splash10-004i-4921150000-f1bbebffe5a7eb4ba3ba	View in MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Positive	splash10-00ou-3910000000-b99e9cf3521aa54e6ac7	View in MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Negative	splash10-000i-0000090000-1ac94c56ce51c1ddb59b	View in MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Negative	splash10-004i-9313240000-0b8ec16dca58c4798042	View in MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Negative	splash10-001i-3309100000-a2da5e2ab068e38735db	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
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	Not Available
HMDB ID	HMDB12222
Pubchem Compound ID	16069985
Kegg ID	C06018
ChemSpider ID	35032421
Wikipedia ID	Not Available
BioCyc ID	TDP-FUC4NAC
EcoCyc ID	TDP-FUC4NAC

Enzymes

Protein Details

1. 4-alpha-L-fucosyltransferase

General function:: Involved in fucosyltransferase activity
Specific function:: Catalyzes the synthesis of Und-PP-GlcNAc-ManNAcA-Fuc4NAc (Lipid III), the third lipid-linked intermediate involved in ECA synthesis
Gene Name:: wecF
Uniprot ID:: P56258
Molecular weight:: 40639

Reactions

TDP-Fuc4NAc + Und-PP-GlcNAc-ManNAcA = TDP + Und-PP-GlcNAc-ManNAcA-Fuc4NAc.

Protein Details

2. Lipopolysaccharide biosynthesis protein rffC

General function:: Involved in protein binding
Specific function:: Transaminase converting thymidine diphosphate(TDP)-4- keto-6-deoxy-D-glucose to TDP-4-amino-4,6-dideoxy-D-galactose, the immediate precursor of the ECA sugar TDP-Fuc4NAc
Gene Name:: rffC
Uniprot ID:: P27832
Molecular weight:: 24220

dTDP-4-Acetamido-4,6-dideoxy-D-galactose (ECMDB20613) (M2MDB001412)

Structure for #<Compound:0xb278b218>

Enzymes

Reactions