ECMDB: TDP-Fuc4NAc (ECMDB23181) (M2MDB003571)

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

Proteins (2)

Record Information

Version

2.0

Creation Date

2012-10-10 12:20:52 -0600

Update Date

2015-06-03 17:26:06 -0600

Secondary Accession Numbers

ECMDB23181

Identification

Name:

TDP-Fuc4NAc

Description

TDP-Fuc4NAc is an intermediate in LPS biosynthesis. It is a substrate for 4-alpha-L-fucosyltransferase which catalyzes the reaction TDP-Fuc4NAc + Und-PP-GlcNAc-ManNAcA = TDP + Und-PP-GlcNAc-ManNAcA-Fuc4NAc. It is part of the reaction that synthesizes lipid III, the third lipid-linked intermediate in enterobacterial common antigen (ECA) or LPS biosynthesis.

Structure

MOL SDF PDB SMILES InChI

Synonyms:

Not Available

Chemical Formula:

C₁₈H₂₉N₃O₁₅P₂

Weight:

Average: 589.3815
Monoisotopic: 589.107390297

InChI Key:

YHXQWYBLXUELDA-QVDZPGAXSA-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:

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

Traditional IUPAC Name:

{[(2R,3R,4S,5R,6R)-5-acetamido-3,4-dihydroxy-6-methyloxan-2-yl]oxy(hydroxy)phosphoryl}oxy[3-hydroxy-5-(5-methyl-2,4-dioxo-3H-pyrimidin-1-yl)oxolan-2-yl]methoxyphosphinic acid

SMILES:

[H]OC1([H])C([H])([H])C([H])(OC1([H])C([H])([H])OP(=O)(O[H])OP(=O)(O[H])O[C@@]1([H])O[C@]([H])(C([H])([H])[H])[C@]([H])(N([H])C(=O)C([H])([H])[H])[C@]([H])(O[H])[C@@]1([H])O[H])N1C([H])=C(C(=O)N([H])C1=O)C([H])([H])[H]

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
Pentose phosphate
Organic pyrophosphate
Monosaccharide phosphate
Hydroxypyrimidine
Monoalkyl phosphate
Pyrimidone
Alkyl phosphate
Pyrimidine
Phosphoric acid ester
Oxane
Organic phosphoric acid derivative
Monosaccharide
Hydropyrimidine
Heteroaromatic compound
Tetrahydrofuran
Secondary alcohol
Oxacycle
Azacycle
Organoheterocyclic compound
Organic 1,3-dipolar compound
Propargyl-type 1,3-dipolar organic compound
Carboximidic acid derivative
Carboximidic acid
Organic nitrogen compound
Organic oxygen compound
Organopnictogen compound
Organic oxide
Hydrocarbon derivative
Organooxygen compound
Organonitrogen compound
Alcohol
Aromatic heteromonocyclic compound

Molecular Framework

Aromatic heteromonocyclic compounds

External Descriptors

Not Available

Physical Properties

State:

Not Available

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	50.35 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:

TDP-Fuc4NAc + Und-PP-GlcNAc-ManNAcA > Thiamine pyrophosphate + Und-PP-GlcNAc-ManNAcA-Fuc4NAc
Undecaprenyl N-acetyl-glucosaminyl-N-acetyl-mannosaminuronate pyrophosphate + TDP-Fuc4NAc + Undecaprenyl-diphospho-N-acetylglucosamine-N-acetylmannosaminuronate > Hydrogen ion + dTDP + Undecaprenyl N-acetyl-glucosaminyl-N-acetyl-mannosaminuronate-4-acetamido-4,6-dideoxy-D-galactose pyrophosphate + Undecaprenyl-diphospho N-acetylglucosamine-N-acetylmannosaminuronate-N-acetamido-4,6-dideoxy-D-galactose
Acetyl-CoA + dTDP-thomosamine > TDP-Fuc4NAc + Coenzyme A + Hydrogen ion

SMPDB Pathways:

Secondary Metabolites: enterobacterial common antigen biosynthesis	PW000959
Secondary Metabolites: enterobacterial common antigen biosynthesis 2	PW002045

KEGG Pathways:

Not Available

EcoCyc Pathways:

Not Available

Concentrations

Not Available

Spectra

Spectra:

Spectrum Type	Description	Splash Key
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_4_5) - 70eV, Positive	Not Available	View in JSpectraViewer
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Positive	splash10-004i-0900000000-6226f678c77544327a87	View in MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Positive	splash10-004i-2911000000-594e03df4f12b67e6b9d	View in MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Positive	splash10-004i-3900000000-3bb72823a69187b08f98	View in MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Negative	splash10-004r-3902370000-0311e3fb2b28f4dff725	View in MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Negative	splash10-0kdl-5903010000-abe5b359927843431d6f	View in MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Negative	splash10-0bvl-4900000000-eb48c67ed731e58d8872	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:

Not Available

Synthesis Reference:

Not Available

Material Safety Data Sheet (MSDS)

Not Available

Links

External Links:

Resource	Link
CHEBI ID	Not Available
HMDB ID	Not Available
Pubchem Compound ID	25202247
Kegg ID	Not Available
ChemSpider ID	Not Available
Wikipedia ID	Not Available
BioCyc ID	Not Available

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

TDP-Fuc4NAc (ECMDB23181) (M2MDB003571)

Structure for #<Compound:0xa3f42718>

Enzymes

Reactions