Record Information
Version 1.0
Update Date 1/22/2018 12:54:54 PM
Metabolite IDPAMDB001343
Identification
Name: Lipid A-core
Description:Lipid a-core belongs to the class of Polyhexoses. These are polysaccharides in which the saccharide units are hexoses. (inferred from compound structure) Lipopolysaccharide (LPS) is a major component on the surface of Gram negative bacteria and is composed of lipid A-core and the O antigen polysaccharide. (PMID 20333251) WaaL is a membrane enzyme implicated in ligating undecaprenyl-diphosphate (Und-PP)-linked O antigen to lipid A-core oligosaccharide. (PMID 19019161) MsbA is an essential ATP-binding cassette half-transporter in the cytoplasmic membrane of the gram-negative Pseudomonas aeruginosa and is required for the export of lipopolysaccharides (LPS) to the outer membrane, most likely by transporting the lipid A core moiety. (PMID 16159769)
Structure
Thumb
Synonyms:Not Available
Chemical Formula: C162H296N2O89P4
Average Molecular Weight: 3819.9387
Monoisotopic Molecular Weight: 3817.764804888
InChI Key: PIKXVLIJAUWPDI-VUQADABISA-P
InChI:InChI=1S/C162H294N2O89P4/c1-7-13-19-25-31-37-38-44-50-56-62-68-108(184)229-90(66-60-54-48-42-35-29-23-17-11-5)72-110(186)237-142-112(164-106(182)71-89(65-59-53-47-41-34-28-22-16-10-4)228-107(183)67-61-55-49-43-36-30-24-18-12-6)149(224-84-102-117(191)141(236-109(185)70-88(173)64-58-52-46-40-33-27-21-15-9-3)111(150(232-102)253-257(220,221)222)163-105(181)69-87(172)63-57-51-45-39-32-26-20-14-8-2)235-104(140(142)250-254(211,212)213)86-227-161(159(207)208)74-98(247-162(160(209)210)73-91(174)113(187)135(248-162)94(177)77-167)139(138(249-161)96(179)79-169)242-156-131(205)144(147(251-255(214,215)216)136(240-156)95(178)78-168)245-157-132(206)145(148(252-256(217,218)219)137(241-157)97(180)82-223-152-127(201)121(195)124(198)133(238-152)92(175)75-165)244-155-130(204)143(118(192)103(234-155)85-225-151-126(200)119(193)114(188)99(80-170)230-151)243-158-146(123(197)115(189)100(81-171)231-158)246-154-129(203)120(194)116(190)101(233-154)83-226-153-128(202)122(196)125(199)134(239-153)93(176)76-166/h87-104,111-158,160,165-180,187-206,209-210,214-219H,7-86H2,1-6H3,(H5-2,163,164,181,182,207,208,211,212,213,220,221,222)/p+2/t87-,88-,89-,90-,91-,92+,93+,94-,95+,96-,97+,98-,99-,100-,101-,102-,103-,104-,111-,112-,113-,114+,115-,116-,117-,118-,119+,120+,121+,122+,123+,124+,125+,126-,127+,128+,129-,130-,131+,132+,133?,134?,135-,136?,137?,138-,139-,140-,141-,142-,143?,144-,145-,146?,147-,148-,149-,150-,151?,152?,153?,154?,155?,156?,157?,158?,161-,162-/m1/s1
CAS number: Not Available
IUPAC Name:{[(3R,4R,5S)-6-{[(2R,3R,4R,6R)-6-carboxy-2-[(1R)-1,2-dihydroxyethyl]-4-{[(2R,4R,5R,6R)-6-[(1R)-1,2-dihydroxyethyl]-2-(dihydroxymethyl)-4,5-dihydroxyoxan-2-yl]oxy}-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-[(1S)-1,2-dihydroxyethyl]-4-{[(3S,4R,5R)-6-[(1S)-2-{[(3S,4S,5S)-6-[(1S)-1,2-dihydroxyethyl]-3,4,5-trihydroxyoxan-2-yl]oxy}-1-hydroxyethyl]-4-{[(3R,5R,6R)-4-{[(4S,5S,6R)-3-{[(3R,4S,5S,6R)-6-({[(3S,4S,5S)-6-[(1S)-1,2-dihydroxyethyl]-3,4,5-trihydroxyoxan-2-yl]oxy}methyl)-3,4,5-trihydroxyoxan-2-yl]oxy}-4,5-dihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}-3,5-dihydroxy-6-({[(3R,4S,5R,6R)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}methyl)oxan-2-yl]oxy}-3-hydroxy-5-[(trihydroxyphosphaniumyl)oxy]oxan-2-yl]oxy}-5-hydroxyoxan-3-yl]oxy}trihydroxyphosphanium
Traditional IUPAC Name: {[(3R,4R,5S)-6-{[(2R,3R,4R,6R)-6-carboxy-2-[(1R)-1,2-dihydroxyethyl]-4-{[(2R,4R,5R,6R)-6-[(1R)-1,2-dihydroxyethyl]-2-(dihydroxymethyl)-4,5-dihydroxyoxan-2-yl]oxy}-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-[(1S)-1,2-dihydroxyethyl]-4-{[(3S,4R,5R)-6-[(1S)-2-{[(3S,4S,5S)-6-[(1S)-1,2-dihydroxyethyl]-3,4,5-trihydroxyoxan-2-yl]oxy}-1-hydroxyethyl]-4-{[(3R,5R,6R)-4-{[(4S,5S,6R)-3-{[(3R,4S,5S,6R)-6-({[(3S,4S,5S)-6-[(1S)-1,2-dihydroxyethyl]-3,4,5-trihydroxyoxan-2-yl]oxy}methyl)-3,4,5-trihydroxyoxan-2-yl]oxy}-4,5-dihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}-3,5-dihydroxy-6-({[(3R,4S,5R,6R)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}methyl)oxan-2-yl]oxy}-3-hydroxy-5-[(trihydroxyphosphaniumyl)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])(O[C@@]4(C[C@@]([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)COC6([H])OC([H])([C@@]([H])(O)CO)[C@@]([H])(O)[C@]([H])(O)[C@]6([H])O)[C@@]([H])(O[P+](O)(O)O)[C@]([H])(OC6([H])O[C@]([H])(COC7([H])O[C@]([H])(CO)[C@]([H])(O)[C@]([H])(O)[C@@]7([H])O)[C@@]([H])(O)C([H])(OC7([H])O[C@]([H])(CO)[C@@]([H])(O)[C@]([H])(O)C7([H])OC7([H])O[C@]([H])(COC8([H])OC([H])([C@@]([H])(O)CO)[C@@]([H])(O)[C@]([H])(O)[C@]8([H])O)[C@@]([H])(O)[C@]([H])(O)[C@@]7([H])O)[C@@]6([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 polysaccharides. These are compounds containing more than ten saccharide units.
Kingdom Organic compounds
Super ClassOrganic Polymers
Class Polysaccharides
Sub ClassNot Available
Direct Parent Polysaccharides
Alternative Parents
Substituents
  • Polysaccharide
  • Saccharolipid
  • Hexose phosphate
  • Pentacarboxylic acid or derivatives
  • Fatty acyl glycoside
  • N-acyl-alpha-hexosamine
  • C-glucuronide
  • Alkyl glycoside
  • O-glycosyl compound
  • C-glycosyl compound
  • Glycosyl compound
  • Pyran carboxylic acid
  • Pyran carboxylic acid or derivatives
  • Fatty acid ester
  • Monoalkyl phosphate
  • Ketal
  • Beta-hydroxy acid
  • Hydroxy acid
  • Phosphoric acid ester
  • Pyran
  • Alkyl phosphate
  • Fatty acyl
  • Organic phosphoric acid derivative
  • Organic phosphate
  • 1,2-diol
  • Carboxylic acid ester
  • Secondary alcohol
  • Polyol
  • Oxacycle
  • Organoheterocyclic compound
  • 1,1-diol
  • Carboxylic acid
  • Acetal
  • Carboxylic acid derivative
  • Carboximidic acid derivative
  • Organonitrogen compound
  • Carbonyl group
  • Organic cation
  • Alcohol
  • Hydrocarbon derivative
  • Organic oxide
  • Primary alcohol
  • Organooxygen compound
  • Aliphatic heteromonocyclic compound
Molecular Framework Aliphatic heteromonocyclic compounds
External Descriptors Not Available
Physical Properties
State: Not Available
Charge:-2
Melting point: Not Available
Experimental Properties:
PropertyValueSource
Predicted Properties
PropertyValueSource
logP4.01ChemAxon
pKa (Strongest Acidic)0.55ChemAxon
pKa (Strongest Basic)-4.7ChemAxon
Physiological Charge-2ChemAxon
Hydrogen Acceptor Count85ChemAxon
Hydrogen Donor Count51ChemAxon
Polar Surface Area1462.07 Å2ChemAxon
Rotatable Bond Count130ChemAxon
Refractivity872.87 m3·mol-1ChemAxon
Polarizability396 Å3ChemAxon
Number of Rings12ChemAxon
Bioavailability0ChemAxon
Rule of FiveYesChemAxon
Ghose FilterYesChemAxon
Veber's RuleYesChemAxon
MDDR-like RuleYesChemAxon
Biological Properties
Cellular Locations: Membrane
Reactions:
Pathways:
Spectra
Spectra:
References
References:
  • Hug, I., Couturier, M. R., Rooker, M. M., Taylor, D. E., Stein, M., Feldman, M. F. (2010). "Helicobacter pylori lipopolysaccharide is synthesized via a novel pathway with an evolutionary connection to protein N-glycosylation." PLoS Pathog 6:e1000819. Pubmed: 20333251
  • 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
  • Perez, J. M., McGarry, M. A., Marolda, C. L., Valvano, M. A. (2008). "Functional analysis of the large periplasmic loop of the Escherichia coli K-12 WaaL O-antigen ligase." Mol Microbiol 70:1424-1440. Pubmed: 19019161
  • Woebking, B., Reuter, G., Shilling, R. A., Velamakanni, S., Shahi, S., Venter, H., Balakrishnan, L., van Veen, H. W. (2005). "Drug-lipid A interactions on the Escherichia coli ABC transporter MsbA." J Bacteriol 187:6363-6369. Pubmed: 16159769
Synthesis Reference: Not Available
Material Safety Data Sheet (MSDS) Not Available
External Links:
ResourceLink
CHEBI IDNot Available
HMDB IDNot Available
Pubchem Compound ID25202953
Kegg IDNot Available
ChemSpider IDNot Available
Wikipedia IDNot Available
BioCyc IDCPD0-939
EcoCyc IDCPD0-939

Enzymes

General function:
Involved in nucleotide binding
Specific function:
Involved in lipid A export and possibly also in glycerophospholipid export and for biogenesis of the outer membrane. Transmembrane domains (TMD) form a pore in the inner membrane and the ATP-binding domain (NBD) is responsible for energy generation
Gene Name:
msbA
Locus Tag:
PA4997
Molecular weight:
66.4 kDa

Transporters

General function:
Involved in nucleotide binding
Specific function:
Involved in lipid A export and possibly also in glycerophospholipid export and for biogenesis of the outer membrane. Transmembrane domains (TMD) form a pore in the inner membrane and the ATP-binding domain (NBD) is responsible for energy generation
Gene Name:
msbA
Locus Tag:
PA4997
Molecular weight:
66.4 kDa