ECMDB: UDP-3-O-(3-Hydroxymyristoyl)-N-acetylglucosamine (ECMDB04164) (M2MDB000644)

Identification Taxonomy Physical Properties Biological Properties Spectra Concentrations Links References Enzymes (3)XML

Proteins (491)

Record Information

Version

2.0

Creation Date

2012-05-31 14:06:55 -0600

Update Date

2015-06-03 15:54:49 -0600

Secondary Accession Numbers

ECMDB04164

Identification

Name:

UDP-3-O-(3-Hydroxymyristoyl)-N-acetylglucosamine

Description

UDP-3-o-(3-hydroxymyristoyl)-n-acetylglucosamine 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.

Structure

MOL SDF PDB SMILES InChI

Synonyms:

UDP-3-O-(3-hydroxymyristoyl)-N-acetylglucosamine
UDP-3-O-(3-hydroxytetradecanoyl)-N-acetylglucosamine
UDP-3-O-(3-Hydroxymyristoyl)-N-acetylglucosamine
UDP-3-O-(3-Hydroxytetradecanoyl)-N-acetylglucosamine
UDP-HMyrGlcNAc
UDP-Ohmyr-acetylglucosamine

Chemical Formula:

C₃₁H₅₃N₃O₁₉P₂

Weight:

Average: 833.7087
Monoisotopic: 833.274849553

InChI Key:

TZSJGZGYQDNRRX-MPLCHSTDSA-N

InChI:

InChI=1S/C31H53N3O19P2/c1-3-4-5-6-7-8-9-10-11-12-19(37)15-23(39)51-28-24(32-18(2)36)30(50-20(16-35)26(28)41)52-55(46,47)53-54(44,45)48-17-21-25(40)27(42)29(49-21)34-14-13-22(38)33-31(34)43/h13-14,19-21,24-30,35,37,40-42H,3-12,15-17H2,1-2H3,(H,32,36)(H,44,45)(H,46,47)(H,33,38,43)/t19-,20-,21-,24-,25-,26-,27-,28-,29-,30-/m1/s1

CAS number:

108636-29-9

IUPAC Name:

N-[(2R,3R,4R,5S,6R)-2-({[({[(2R,3S,4R,5R)-3,4-dihydroxy-5-(4-hydroxy-2-oxo-1,2-dihydropyrimidin-1-yl)oxolan-2-yl]methoxy}(hydroxy)phosphoryl)oxy](hydroxy)phosphoryl}oxy)-5-hydroxy-6-(hydroxymethyl)-4-{[(3R)-3-hydroxytetradecanoyl]oxy}oxan-3-yl]ethanimidic acid

Traditional IUPAC Name:

N-[(2R,3R,4R,5S,6R)-2-[({[(2R,3S,4R,5R)-3,4-dihydroxy-5-(4-hydroxy-2-oxopyrimidin-1-yl)oxolan-2-yl]methoxy(hydroxy)phosphoryl}oxy(hydroxy)phosphoryl)oxy]-5-hydroxy-6-(hydroxymethyl)-4-{[(3R)-3-hydroxytetradecanoyl]oxy}oxan-3-yl]ethanimidic acid

SMILES:

[H][C@@](O)(CCCCCCCCCCC)CC(=O)O[C@@]1([H])[C@]([H])(O)[C@@]([H])(CO)O[C@]([H])(OP(O)(=O)OP(O)(=O)OC[C@@]2([H])O[C@@]([H])(N3C=CC(O)=NC3=O)[C@]([H])(O)[C@]2([H])O)[C@]1([H])N=C(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 ribonucleoside diphosphate
Saccharolipid
Pentose-5-phosphate
Pentose phosphate
N-acyl-alpha-hexosamine
Glycosyl compound
N-glycosyl compound
Organic pyrophosphate
Monosaccharide phosphate
Beta-hydroxy acid
Monoalkyl phosphate
Pyrimidone
Fatty acid ester
Fatty acyl
Organic phosphoric acid derivative
Alkyl phosphate
Oxane
Hydroxy acid
Hydropyrimidine
Phosphoric acid ester
Pyrimidine
Monosaccharide
Heteroaromatic compound
Acetamide
Vinylogous amide
Tetrahydrofuran
Urea
Secondary alcohol
Secondary carboxylic acid amide
Carboxamide group
Lactam
Carboxylic acid ester
Organoheterocyclic compound
Carboxylic acid derivative
Azacycle
Oxacycle
Monocarboxylic acid or derivatives
Primary alcohol
Hydrocarbon derivative
Organic oxide
Organopnictogen compound
Organic oxygen compound
Alcohol
Organic nitrogen compound
Carbonyl group
Organonitrogen compound
Organooxygen compound
Aromatic heteromonocyclic compound

Molecular Framework

Aromatic heteromonocyclic compounds

External Descriptors

UDP-amino sugar (CHEBI:61537 )

Physical Properties

State:

Not Available

Charge:

-2

Melting point:

Not Available

Experimental Properties:

Property	Value	Source

Predicted Properties

Property	Value	Source
Water Solubility	2.89 g/L	ALOGPS
logP	0.61	ALOGPS
logP	0.7	ChemAxon
logS	-2.5	ALOGPS
pKa (Strongest Acidic)	1.73	ChemAxon
pKa (Strongest Basic)	-3.7	ChemAxon
Physiological Charge	-2	ChemAxon
Hydrogen Acceptor Count	17	ChemAxon
Hydrogen Donor Count	9	ChemAxon
Polar Surface Area	333.69 Å²	ChemAxon
Rotatable Bond Count	24	ChemAxon
Refractivity	184.31 m³·mol⁻¹	ChemAxon
Polarizability	80.02 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:

Lipopolysaccharide biosynthesis

PW000831

KEGG Pathways:

Lipopolysaccharide biosynthesis ec00540

EcoCyc Pathways:

superpathway of (KDO)₂-lipid A biosynthesis NAGLIPASYN-PWY
superpathway of lipopolysaccharide biosynthesis LPSSYN-PWY

Concentrations

Not Available

Spectra

Spectra:

Spectrum Type	Description	Splash Key
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Positive	splash10-03di-0910000020-fedcabb1e352348e4b41	View in MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Positive	splash10-03di-2910010000-9c7cdad9942cd448b2e2	View in MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Positive	splash10-03di-3910000000-1906defd57b0d60b4180	View in MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Negative	splash10-0ik9-7912501340-ee6a700cf210afdb6a69	View in MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Negative	splash10-03dl-8915131020-7c28b07f154e3dacae45	View in MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Negative	splash10-052f-5922000000-e1498ccc14935f8be289	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	28131
HMDB ID	Not Available
Pubchem Compound ID	25244942
Kegg ID	C04738
ChemSpider ID	26332242
Wikipedia ID	Not Available
BioCyc ID	UDP-OHMYR-ACETYLGLUCOSAMINE
EcoCyc ID	UDP-OHMYR-ACETYLGLUCOSAMINE
Ligand Expo	U20

Enzymes

Protein Details

1. Acyl-[acyl-carrier-protein]--UDP-N-acetylglucosamine O-acyltransferase

General function:: Involved in transferase activity
Specific function:: Involved in the biosynthesis of lipid A, a phosphorylated glycolipid that anchors the lipopolysaccharide to the outer membrane of the cell
Gene Name:: lpxA
Uniprot ID:: P0A722
Molecular weight:: 28080

Reactions

(R)-3-hydroxytetradecanoyl-[acyl-carrier-protein] + UDP-N-acetylglucosamine = [acyl-carrier-protein] + UDP-3-O-(3-hydroxytetradecanoyl)-N-acetylglucosamine.

Protein Details

2. UDP-3-O-[3-hydroxymyristoyl] N-acetylglucosamine deacetylase

General function:: Involved in UDP-3-O-[3-hydroxymyristoyl] N-acetylglucosamine deacetylase activity
Specific function:: The key enzyme in the biosynthesis of lipid A, a phosphorylated glycolipid that anchors the lipopolysaccharide to the outer membrane of the cell. Degraded by FtsH; when the activity of FtsH is reduced too much lipid A and not enough phospholipids are made (both pathways use the same precursor), which is lethal
Gene Name:: lpxC
Uniprot ID:: P0A725
Molecular weight:: 33956

Reactions

UDP-3-O-(3-hydroxytetradecanoyl)-N-acetylglucosamine + H(2)O = UDP-3-O-(3-hydroxytetradecanoyl)-glucosamine + acetate.

Protein Details

3. Acyl carrier protein

General function:: Involved in fatty acid biosynthetic process
Specific function:: Carrier of the growing fatty acid chain in fatty acid biosynthesis
Gene Name:: acpP
Uniprot ID:: P0A6A8
Molecular weight:: 8640

UDP-3-O-(3-Hydroxymyristoyl)-N-acetylglucosamine (ECMDB04164) (M2MDB000644)

Structure for #<Compound:0x909b01dc>

Enzymes

Reactions

Reactions