Glucosyl-heptosyl2-KDO2-lipid A-phosphate (PAMDB001337)

IdentificationTaxonomyPhysical PropertiesBiological PropertiesSpectraConcentrationsLinksReferencesEnzymes Transporters
Proteins (3280)
Record Information
Version 1.0
Update Date 1/22/2018 11:54:54 AM
Metabolite IDPAMDB001337
Identification
Name: Glucosyl-heptosyl2-KDO2-lipid A-phosphate
Description:Glucosyl-heptosyl2-kdo2-lipid A-phosphate is a component of LPS. Bacterial lipopolysaccharides (LPS) typically consist of a hydrophobic domain inserted into the outer membrane known as lipid A (or endotoxin), a phosphorylated "core" oligosaccharide and a distal polysaccharide (or O antigen). The core oligosaccharides are conceptually divided into two regions: inner core and outer core. The inner core is highly conserved, comprises three deoxy-D-manno-octulosonic acid (KDO) and L-glycero-D-manno-heptose (Hep) and is often phosphorylated. The inner core oligosaccharide plays a critical role in essential barrier function of the outer membrane. The outer core comprises a tri-hexose backbone modified with varying side-branch substitutions of hexose and acetamidohexose residues. The outer core provides an attachment site for O-antigen. The completed lipid A-KDO2 serves as the acceptor on which the core oligosaccharide chains are assembled by sequential glycosyl transfer from nucleotide sugar precursors. This process involves a co-ordinated complex of membrane-associated glycosyltransferases acting at the cytoplasmic face of the plasma membrane.
Structure
Thumb
🔍MOLSDFPDBSMILESInChIView Structure
Synonyms:
  • Glucosyl-heptosyl2-kdo2-lipid a-phosphoric acid
Chemical Formula: C130H240N2O59P3
Average Molecular Weight: 2868.1959
Monoisotopic Molecular Weight: 2866.505402924
InChI Key: DMDZBOUBYURDEM-YEJINIFKSA-O
InChI:InChI=1S/C130H239N2O59P3/c1-7-13-19-25-31-37-38-44-50-56-62-68-98(148)175-85(66-60-54-48-42-35-29-23-17-11-5)72-100(150)180-118-102(132-96(146)71-84(65-59-53-47-41-34-28-22-16-10-4)174-97(147)67-61-55-49-43-36-30-24-18-12-6)122(172-80-93-105(153)117(179-99(149)70-83(139)64-58-52-46-40-33-27-21-15-9-3)101(123(177-93)191-194(169,170)171)131-95(145)69-82(138)63-57-51-45-39-32-26-20-14-8-2)178-94(116(118)189-192(163,164)165)81-173-129(127(159)160)74-91(186-130(128(161)162)73-86(140)103(151)112(187-130)88(142)76-134)115(114(188-129)90(144)78-136)183-126-110(158)120(121(190-193(166,167)168)113(182-126)89(143)77-135)185-125-109(157)119(108(156)111(181-125)87(141)75-133)184-124-107(155)106(154)104(152)92(79-137)176-124/h82-94,101-126,128,133-144,151-158,161-162,166-168H,7-81H2,1-6H3,(H6-,131,132,145,146,159,160,163,164,165,169,170,171)/p+1/t82-,83-,84-,85-,86?,87+,88?,89?,90-,91-,92?,93-,94-,101-,102-,103?,104?,105-,106?,107?,108-,109+,110+,111?,112?,113?,114-,115-,116-,117-,118-,119+,120-,121-,122-,123-,124?,125?,126?,129-,130?/m1/s1
CAS number: Not Available
IUPAC Name:{[(3R,4R,5S)-6-{[(2R,3R,4R,6R)-6-carboxy-4-{[6-(1,2-dihydroxyethyl)-2-(dihydroxymethyl)-4,5-dihydroxyoxan-2-yl]oxy}-2-[(1R)-1,2-dihydroxyethyl]-6-{[(2R,3S,4R,5R,6R)-6-{[(2R,3S,4R,5R,6R)-5-{[(3R)-1,3-dihydroxytetradecylidene]amino}-3-hydroxy-4-{[(3R)-3-hydroxytetradecanoyl]oxy}-6-(phosphonooxy)oxan-2-yl]methoxy}-5-{[(3R)-3-(dodecanoyloxy)-1-hydroxytetradecylidene]amino}-3-(phosphonooxy)-4-{[(3R)-3-(tetradecanoyloxy)tetradecanoyl]oxy}oxan-2-yl]methoxy}oxan-3-yl]oxy}-2-(1,2-dihydroxyethyl)-4-{[(3S,4S,5R)-6-[(1S)-1,2-dihydroxyethyl]-3,5-dihydroxy-4-{[3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}oxan-2-yl]oxy}-5-hydroxyoxan-3-yl]oxy}trihydroxyphosphanium
Traditional IUPAC Name: {[(3R,4R,5S)-6-{[(2R,3R,4R,6R)-6-carboxy-4-{[6-(1,2-dihydroxyethyl)-2-(dihydroxymethyl)-4,5-dihydroxyoxan-2-yl]oxy}-2-[(1R)-1,2-dihydroxyethyl]-6-{[(2R,3S,4R,5R,6R)-6-{[(2R,3S,4R,5R,6R)-5-{[(3R)-1,3-dihydroxytetradecylidene]amino}-3-hydroxy-4-{[(3R)-3-hydroxytetradecanoyl]oxy}-6-(phosphonooxy)oxan-2-yl]methoxy}-5-{[(3R)-3-(dodecanoyloxy)-1-hydroxytetradecylidene]amino}-3-(phosphonooxy)-4-{[(3R)-3-(tetradecanoyloxy)tetradecanoyl]oxy}oxan-2-yl]methoxy}oxan-3-yl]oxy}-2-(1,2-dihydroxyethyl)-4-{[(3S,4S,5R)-6-[(1S)-1,2-dihydroxyethyl]-3,5-dihydroxy-4-{[3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}oxan-2-yl]oxy}-5-hydroxyoxan-3-yl]oxy}trihydroxyphosphanium
SMILES:[H][C@@](O)(CCCCCCCCCCC)CC(=O)O[C@@]1([H])[C@]([H])(O)[C@@]([H])(CO[C@]2([H])O[C@]([H])(CO[C@@]3(C[C@@]([H])(OC4(CC([H])(O)C([H])(O)C([H])(O4)C([H])(O)CO)C(O)O)[C@@]([H])(OC4([H])OC([H])(C([H])(O)CO)[C@@]([H])(O[P+](O)(O)O)[C@]([H])(OC5([H])OC([H])([C@@]([H])(O)CO)[C@@]([H])(O)[C@]([H])(OC6([H])OC([H])(CO)C([H])(O)C([H])(O)C6([H])O)[C@]5([H])O)[C@]4([H])O)[C@]([H])(O3)[C@]([H])(O)CO)C(O)=O)[C@@]([H])(OP(O)(O)=O)[C@]([H])(OC(=O)C[C@@]([H])(CCCCCCCCCCC)OC(=O)CCCCCCCCCCCCC)[C@@]2([H])N=C(O)C[C@@]([H])(CCCCCCCCCCC)OC(=O)CCCCCCCCCCC)O[C@]([H])(OP(O)(O)=O)[C@]1([H])N=C(O)C[C@]([H])(O)CCCCCCCCCCC
Chemical Taxonomy
Taxonomy DescriptionThis compound belongs to the class of organic compounds known as n-acyl-alpha-hexosamines. These are carbohydrate derivatives containing a hexose moiety in which the oxygen atom is replaced by an n-acyl group.
Kingdom Organic compounds
Super ClassOrganooxygen compounds
Class Carbohydrates and carbohydrate conjugates
Sub ClassAminosaccharides
Direct Parent N-acyl-alpha-hexosamines
Alternative Parents
Substituents
  • Oligosaccharide phosphate
  • Oligosaccharide
  • Saccharolipid
  • Fatty acyl glycoside
  • Pentacarboxylic acid or derivatives
  • N-acyl-alpha-hexosamine
  • C-glucuronide
  • Glucosamine
  • Alkyl glycoside
  • O-glycosyl compound
  • Glycosyl compound
  • C-glycosyl compound
  • Pyran carboxylic acid
  • Pyran carboxylic acid or derivatives
  • Monoalkyl phosphate
  • Fatty acid ester
  • Beta-hydroxy acid
  • Fatty acyl
  • Alkyl phosphate
  • Pyran
  • Phosphoric acid ester
  • Oxane
  • Organic phosphoric acid derivative
  • Organic phosphate
  • Hydroxy acid
  • Secondary alcohol
  • Polyol
  • Carboxylic acid ester
  • 1,2-diol
  • Oxacycle
  • Organoheterocyclic compound
  • 1,1-diol
  • Carboxylic acid
  • Carboxylic acid derivative
  • Carboximidic acid derivative
  • Carboximidic acid
  • Carbonyl hydrate
  • Acetal
  • Hydrocarbon derivative
  • Primary alcohol
  • Organonitrogen compound
  • Carbonyl group
  • Alcohol
  • Organic cation
  • Aliphatic heteromonocyclic compound
Molecular Framework Aliphatic heteromonocyclic compounds
External Descriptors Not Available
Physical Properties
State: Not Available
Charge:-3
Melting point: Not Available
Experimental Properties:
PropertyValueSource
Predicted Properties
PropertyValueSource
Water Solubility0.22 mg/mLALOGPS
logP3.06ALOGPS
logP14.68ChemAxon
logS-4.1ALOGPS
pKa (Strongest Acidic)0.55ChemAxon
pKa (Strongest Basic)-4.7ChemAxon
Physiological Charge-3ChemAxon
Hydrogen Acceptor Count55ChemAxon
Hydrogen Donor Count32ChemAxon
Polar Surface Area976.17 Å2ChemAxon
Rotatable Bond Count111ChemAxon
Refractivity686.88 m3·mol-1ChemAxon
Polarizability311.53 Å3ChemAxon
Number of Rings7ChemAxon
Bioavailability0ChemAxon
Rule of FiveYesChemAxon
Ghose FilterYesChemAxon
Veber's RuleYesChemAxon
MDDR-like RuleYesChemAxon
Biological Properties
Cellular Locations: Membrane
Reactions:
Glucosyl-heptosyl2-KDO2-lipid A + Adenosine triphosphate > Hydrogen ion + Glucosyl-heptosyl2-KDO2-lipid A-phosphate + ADP
Glucosyl-heptosyl2-KDO2-lipid A-phosphate + ADP-L-Glycero-D-manno-heptose > Hydrogen ion + Glucosyl-heptosyl3-KDO2-lipid A-phosphate + ADP
Pathways:
Spectra
Spectra:
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
Synthesis Reference: Not Available
Material Safety Data Sheet (MSDS) Not Available
External Links:
ResourceLink
CHEBI IDNot Available
HMDB IDNot Available
Pubchem Compound ID25200956
Kegg IDNot Available
ChemSpider IDNot Available
Wikipedia IDNot Available
BioCyc IDCPD0-933
EcoCyc IDCPD0-933

Enzymes

Protein Details
• Lipopolysaccharide core heptose(I) kinase rfaP
General function:
Involved in transferase activity, transferring phosphorus-containing groups
Specific function:
Catalyzes the phosphorylation of heptose(I) of the outer membrane lipopolysaccharide core
Gene Name:
rfaP
Locus Tag:
PA5009
Molecular weight:
31.3 kDa