LPS (1-O-antigen) (PAMDB001504)

IdentificationTaxonomyPhysical PropertiesBiological PropertiesSpectraConcentrationsLinksReferencesEnzymes Transporters
Proteins (3280)
Record Information
Version 1.0
Update Date 1/22/2018 12:54:54 PM
Metabolite IDPAMDB001504
Identification
Name: LPS (1-O-antigen)
Description:Lipopolysaccharides (LPS), also known as lipoglycans, are large molecules consisting of a lipid and a polysaccharide joined by a covalent bond; they are found in the outer membrane of Gram-negative bacteria, act as endotoxins and elicit strong immune responses in animals. LPS consists of three parts: O antigen (or O polysaccharide), core polysaccharide and lipid A.When LPS contains a repetitive glycan polymer this is referred to as the O antigen, O polysaccharide, or O side chain of the bacteria. LPS (1-o-antigen) contains only one unit of O antigen. The O antigen is attached to the core oligosaccharide, and comprises the outermost domain of the LPS molecule. The composition of the O chain varies from strain to strain, for example there are over 160 different O antigen structures produced by different Pseudomonas aeruginosa strains. The presence or absence of O chains determine whether the LPS is considered rough or smooth. Full length O-chains would render the LPS smooth while the absence or reduction of O-chains would make the LPS rough. Bacteria with rough LPS usually have more penetrable cell membranes to hydrophobic antibiotics since a rough LPS is more hydrophobic. O antigen is exposed on the very outer surface of the bacterial cell, and as a consequence, is a target for recognition by host antibodies.
Structure
Thumb
🔍MOLSDFPDBSMILESInChIView Structure
Synonyms:
  • Lipopolysaccharide
Chemical Formula: C215H386N10O123P6
Average Molecular Weight: 5265.2011
Monoisotopic Molecular Weight: 5262.26826998
InChI Key: CWWMHIJTLCZEJI-UHFFFAOYSA-N
InChI:InChI=1S/C215H386N10O123P6/c1-15-21-27-33-39-45-46-52-58-64-70-76-130(245)311-114(74-68-62-56-50-43-37-31-25-19-5)84-132(247)325-177-138(223-128(243)83-113(73-67-61-55-49-42-36-30-24-18-4)310-129(244)75-69-63-57-51-44-38-32-26-20-6)194(304-100-124-147(256)174(324-131(246)82-112(241)72-66-60-54-48-41-35-29-23-17-3)137(198(320-124)347-351(293,294)295)222-127(242)81-111(240)71-65-59-53-47-40-34-28-22-16-2)323-126(173(177)343-349(287,288)289)102-307-213(208(279)280)192(278)188(342-214(209(281)282)190(276)183(162(271)168(338-214)103(7)85-226)341-215(210(283)284)191(277)184(345-352(296,297)308-79-77-216)163(272)169(339-215)104(8)86-227)186(172(340-213)107(11)89-230)336-205-166(275)181(187(171(328-205)106(10)88-229)346-354(300,301)348-353(298,299)309-80-78-217)334-204-165(274)179(161(270)167(326-204)108(12)97-302-201-160(269)156(265)182(344-350(290,291)292)170(327-201)105(9)87-228)331-203-164(273)178(149(258)125(322-203)101-306-200-158(267)153(262)142(251)118(93-234)316-200)332-206-185(155(264)143(252)119(94-235)317-206)335-207-189(337-195-134(225-212(219)286)151(260)140(249)116(91-232)313-195)180(146(255)121(96-237)318-207)333-197-136(221-110(14)239)176(148(257)123(319-197)99-303-193-133(224-211(218)285)150(259)139(248)115(90-231)312-193)329-196-135(220-109(13)238)175(145(254)120(95-236)314-196)330-202-159(268)154(263)144(253)122(321-202)98-305-199-157(266)152(261)141(250)117(92-233)315-199/h103-108,111-126,133-207,226-237,240-241,248-278H,15-102,216-217H2,1-14H3,(H,220,238)(H,221,239)(H,222,242)(H,223,243)(H,279,280)(H,281,282)(H,283,284)(H,296,297)(H,298,299)(H,300,301)(H3,218,224,285)(H3,219,225,286)(H2,287,288,289)(H2,290,291,292)(H2,293,294,295)
CAS number: Not Available
IUPAC Name:(2R,3S,4R,5R,6R)-5-{[(3S,4R,5R,6R)-5-[({[(2-aminoethoxy)(hydroxy)phosphoryl]oxy}(hydroxy)phosphoryl)oxy]-4-{[(3S,4S,5R,6R)-4-{[(3R,4S,5R,6R)-4-{[(2R,3R,4S,5R,6R)-3-{[(3R,4S,5R,6R)-3-{[(2S,3R,4R,5S,6R)-4,5-dihydroxy-3-[(C-hydroxycarbonimidoyl)amino]-6-(hydroxymethyl)oxan-2-yl]oxy}-4-{[(2S,3R,4R,5R,6R)-6-({[(2R,3R,4R,5S,6R)-4,5-dihydroxy-3-[(C-hydroxycarbonimidoyl)amino]-6-(hydroxymethyl)oxan-2-yl]oxy}methyl)-5-hydroxy-4-{[(2R,3R,4R,5R,6R)-5-hydroxy-3-[(1-hydroxyethylidene)amino]-6-(hydroxymethyl)-4-{[(2S,3R,4S,5R,6R)-3,4,5-trihydroxy-6-({[(2S,3R,4S,5R,6R)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}methyl)oxan-2-yl]oxy}oxan-2-yl]oxy}-3-[(1-hydroxyethylidene)amino]oxan-2-yl]oxy}-5-hydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}-4,5-dihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}-3,5-dihydroxy-6-({[(2S,3R,4S,5R,6R)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}methyl)oxan-2-yl]oxy}-6-[(2S)-1-{[(3S,4R,5S,6R)-3,4-dihydroxy-6-[(2S)-1-hydroxypropan-2-yl]-5-(phosphonooxy)oxan-2-yl]oxy}propan-2-yl]-3,5-dihydroxyoxan-2-yl]oxy}-3-hydroxy-6-[(2S)-1-hydroxypropan-2-yl]oxan-2-yl]oxy}-4-{[(2S,3S,4S,5R,6R)-4-{[(2S,3S,4S,5R,6R)-4-{[(2-aminoethoxy)(hydroxy)phosphoryl]oxy}-2-carboxy-3,5-dihydroxy-6-[(2S)-1-hydroxypropan-2-yl]oxan-2-yl]oxy}-2-carboxy-3,5-dihydroxy-6-[(2S)-1-hydroxypropan-2-yl]oxan-2-yl]oxy}-2-{[(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}-3-hydroxy-6-[(2S)-1-hydroxypropan-2-yl]oxane-2-carboxylic acid
Traditional IUPAC Name: (2R,3S,4R,5R,6R)-5-{[(3S,4R,5R,6R)-5-({[2-aminoethoxy(hydroxy)phosphoryl]oxy(hydroxy)phosphoryl}oxy)-4-{[(3S,4S,5R,6R)-4-{[(3R,4S,5R,6R)-4-{[(2R,3R,4S,5R,6R)-3-{[(3R,4S,5R,6R)-3-{[(2S,3R,4R,5S,6R)-4,5-dihydroxy-3-(C-hydroxycarbonimidoylamino)-6-(hydroxymethyl)oxan-2-yl]oxy}-4-{[(2S,3R,4R,5R,6R)-6-({[(2R,3R,4R,5S,6R)-4,5-dihydroxy-3-(C-hydroxycarbonimidoylamino)-6-(hydroxymethyl)oxan-2-yl]oxy}methyl)-5-hydroxy-4-{[(2R,3R,4R,5R,6R)-5-hydroxy-3-[(1-hydroxyethylidene)amino]-6-(hydroxymethyl)-4-{[(2S,3R,4S,5R,6R)-3,4,5-trihydroxy-6-({[(2S,3R,4S,5R,6R)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}methyl)oxan-2-yl]oxy}oxan-2-yl]oxy}-3-[(1-hydroxyethylidene)amino]oxan-2-yl]oxy}-5-hydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}-4,5-dihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}-3,5-dihydroxy-6-({[(2S,3R,4S,5R,6R)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}methyl)oxan-2-yl]oxy}-6-[(2S)-1-{[(3S,4R,5S,6R)-3,4-dihydroxy-6-[(2S)-1-hydroxypropan-2-yl]-5-(phosphonooxy)oxan-2-yl]oxy}propan-2-yl]-3,5-dihydroxyoxan-2-yl]oxy}-3-hydroxy-6-[(2S)-1-hydroxypropan-2-yl]oxan-2-yl]oxy}-4-{[(2S,3S,4S,5R,6R)-4-{[(2S,3S,4S,5R,6R)-4-{[2-aminoethoxy(hydroxy)phosphoryl]oxy}-2-carboxy-3,5-dihydroxy-6-[(2S)-1-hydroxypropan-2-yl]oxan-2-yl]oxy}-2-carboxy-3,5-dihydroxy-6-[(2S)-1-hydroxypropan-2-yl]oxan-2-yl]oxy}-2-{[(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}-3-hydroxy-6-[(2S)-1-hydroxypropan-2-yl]oxane-2-carboxylic acid
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(O[C@]([H])([C@@]([H])(C)CO)[C@@]([H])(OC4([H])O[C@]([H])([C@@]([H])(C)CO)[C@@]([H])(OP(O)(=O)OP(O)(=O)OCCN)[C@]([H])(OC5([H])O[C@]([H])([C@@]([H])(C)COC6([H])O[C@]([H])([C@@]([H])(C)CO)[C@@]([H])(OP(O)(O)=O)[C@]([H])(O)[C@]6([H])O)[C@@]([H])(O)[C@]([H])(OC6([H])O[C@]([H])(CO[C@@]7([H])O[C@]([H])(CO)[C@]([H])(O)[C@]([H])(O)[C@@]7([H])O)[C@@]([H])(O)[C@]([H])(O[C@@]7([H])O[C@]([H])(CO)[C@]([H])(O)[C@]([H])(O)[C@@]7([H])OC7([H])O[C@]([H])(CO)[C@@]([H])(O)[C@]([H])(O[C@]8([H])O[C@]([H])(CO[C@]9([H])O[C@]([H])(CO)[C@@]([H])(O)[C@]([H])(O)[C@@]9([H])NC(O)=N)[C@]([H])(O)[C@]([H])(O[C@]9([H])O[C@]([H])(CO)[C@]([H])(O)[C@]([H])(O[C@@]%10([H])O[C@]([H])(CO[C@@]%11([H])O[C@]([H])(CO)[C@]([H])(O)[C@]([H])(O)[C@@]%11([H])O)[C@]([H])(O)[C@]([H])(O)[C@@]%10([H])O)[C@@]9([H])N=C(C)O)[C@@]8([H])N=C(C)O)[C@@]7([H])O[C@]7([H])O[C@]([H])(CO)[C@@]([H])(O)[C@]([H])(O)[C@@]7([H])NC(O)=N)[C@@]6([H])O)[C@]5([H])O)[C@]4([H])O)[C@]([H])(O[C@]4(O[C@]([H])([C@@]([H])(C)CO)[C@@]([H])(O)[C@]([H])(O[C@]5(O[C@]([H])([C@@]([H])(C)CO)[C@@]([H])(O)[C@]([H])(OP(O)(=O)OCCN)[C@]5([H])O)C(O)=O)[C@]4([H])O)C(O)=O)[C@]3([H])O)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
  • Fatty acyl glycoside
  • N-acyl-alpha-hexosamine
  • C-glucuronide
  • Glucuronic acid or derivatives
  • Glucosamine
  • Alkyl glycoside
  • O-glycosyl compound
  • Glycosyl compound
  • C-glycosyl compound
  • Organic pyrophosphate
  • Pyran carboxylic acid
  • Pyran carboxylic acid or derivatives
  • Phosphoethanolamine
  • Dialkyl phosphate
  • Monoalkyl phosphate
  • Amino saccharide
  • 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
  • Isourea
  • Carboxylic acid ester
  • 1,2-diol
  • Oxacycle
  • Organoheterocyclic compound
  • Organic 1,3-dipolar compound
  • Propargyl-type 1,3-dipolar organic compound
  • Carboximidamide
  • Carboxylic acid
  • Carboxylic acid derivative
  • Carboximidic acid derivative
  • Carboximidic acid
  • Acetal
  • Hydrocarbon derivative
  • Primary amine
  • Primary alcohol
  • Organooxygen compound
  • Organonitrogen compound
  • Primary aliphatic amine
  • Imine
  • Carbonyl group
  • Amine
  • Alcohol
  • Aliphatic heteromonocyclic compound
Molecular Framework Aliphatic heteromonocyclic compounds
External Descriptors Not Available
Physical Properties
State: Solid
Charge:-3
Melting point: Not Available
Experimental Properties:
PropertyValueSource
LogP:0.6127PhysProp
Predicted Properties
PropertyValueSource
logP0.61ChemAxon
pKa (Strongest Acidic)0.38ChemAxon
Physiological Charge-3ChemAxon
Hydrogen Acceptor Count121ChemAxon
Hydrogen Donor Count69ChemAxon
Polar Surface Area2103.45 Å2ChemAxon
Rotatable Bond Count163ChemAxon
Refractivity1204.58 m3·mol-1ChemAxon
Number of Rings18ChemAxon
Bioavailability0ChemAxon
Rule of FiveYesChemAxon
Ghose FilterYesChemAxon
Veber's RuleYesChemAxon
MDDR-like RuleYesChemAxon
Biological Properties
Cellular Locations: Cytoplasm
Reactions:
UDP-Glucose + LPS (1-O-antigen) <> Uridine 5'-diphosphate + D-Glucosyllipopolysaccharide
Uridine diphosphategalactose + LPS (1-O-antigen) > Uridine 5'-diphosphate + 3-alpha-D-galactosyl-[lipopolysaccharide glucose]
UDP-Glucose + LPS (1-O-antigen) > Uridine 5'-diphosphate + D-glucosyl-lipopolysaccharide
Uridine diphosphate-N-acetylglucosamine + LPS (1-O-antigen) > Uridine 5'-diphosphate + N-acetyl-D-glucosaminyllipopolysaccharide
Uridine diphosphate-N-acetylglucosamine + LPS (1-O-antigen) <> Uridine 5'-diphosphate
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 ID16412
HMDB IDNot Available
Pubchem Compound ID11970143
Kegg IDC00338
ChemSpider IDNot Available
Wikipedia IDNot Available
BioCyc IDNot Available

Enzymes

Protein Details
• Lipopolysaccharide export system permease protein lptG
General function:
Involved in lipopolysaccharide transport
Specific function:
Part of the ABC transporter complex lptBFG involved in the translocation of lipopolysaccharide (LPS) from the inner membrane to the outer membrane
Gene Name:
lptG
Locus Tag:
PA3827
Molecular weight:
39.2 kDa
Protein Details
• Lipopolysaccharide export system permease protein lptF
General function:
Involved in lipopolysaccharide-transporting ATPase acti
Specific function:
Part of the ABC transporter complex lptBFG involved in the translocation of lipopolysaccharide (LPS) from the inner membrane to the outer membrane
Gene Name:
lptF
Locus Tag:
PA3828
Molecular weight:
41.3 kDa

Transporters

Protein Details
• Lipopolysaccharide export system permease protein lptG
General function:
Involved in lipopolysaccharide transport
Specific function:
Part of the ABC transporter complex lptBFG involved in the translocation of lipopolysaccharide (LPS) from the inner membrane to the outer membrane
Gene Name:
lptG
Locus Tag:
PA3827
Molecular weight:
39.2 kDa
Protein Details
• Lipopolysaccharide export system permease protein lptF
General function:
Involved in lipopolysaccharide-transporting ATPase acti
Specific function:
Part of the ABC transporter complex lptBFG involved in the translocation of lipopolysaccharide (LPS) from the inner membrane to the outer membrane
Gene Name:
lptF
Locus Tag:
PA3828
Molecular weight:
41.3 kDa