Showing metabocard for LPS with O-antigen (LMDB00631)

IdentificationTaxonomyOntologyPhysical propertiesSpectraBiological propertiesConcentrationsLinksReferencesXML
Record Information
Version1.0
Creation Date2016-07-13 19:54:14 UTC
Update Date2016-07-19 23:24:13 UTC
LmdbLMDB00631
Secondary Accession NumbersNone
Metabolite Identification
Common NameLPS with O-antigen
DescriptionLipopolysaccharides (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 is the major component of the outer membrane of Gram-negative bacteria, contributing greatly to the structural integrity of the bacteria, and protecting the membrane from certain kinds of chemical attack. LPS also increases the negative charge of the cell membrane and helps stabilize the overall membrane structure. It is of crucial importance to gram negative bacteria, whose death results if it is mutated or removed. LPS is an endotoxin, and induces a strong response from normal animal immune systems. LPS acts as the prototypical endotoxin because it binds the CD14/TLR4/MD2 receptor complex, which promotes the secretion of pro-inflammatory cytokines in many cell types, but especially in macrophages. In Immunology, the term "LPS challenge" refers to the process of exposing a subject to an LPS which may act as a toxin. LPS is also an exogenous pyrogen (external fever-inducing substance). Being of crucial importance to gram negative bacteria, these molecules make candidate targets for new antimicrobial agents. LPS comprises three parts: 1. O antigen (or O polysaccharide). 2. Core polysaccharide. 3. Lipid A. The making of LPS can be modified in order to present a specific sugar structure. Those can be recognised by either other LPS (which enables to inhibit LPS toxins) or glycosyltransferases which use those sugar structure to add more specific sugars. It has recently been shown that a specific enzyme in the intestine (alkaline phosphatase) can detoxify LPS by removing the two phosphate groups found on LPS carbohydrates [6]. This may function as an adaptive mechanism to help the host manage potentially toxic effects of gram-negative bacteria normally found in the small intestine. (from wiki). This card shows the example of LPS in E. coli with one o-antigen unit.
Structure
Thumb
MOLSDFPDBSMILESInChI
Synonyms
ValueSource
EndotoxinHMDB
Endotoxin lipopolysaccharideHMDB
Endotoxin LPSHMDB
LipopolysaccharideHMDB
Lipopolysaccharide with O-antigenHMDB
LPSHMDB
Chemical FormulaC211H376N8O126P6
Average Molecular Weight5227.0637
Monoisotopic Molecular Weight5224.168615516
IUPAC Name(2R,4R,5S,6R)-5-{[(3S,4R,5R,6R)-5-[({[(2-aminoethoxy)(hydroxy)phosphoryl]oxy}(hydroxy)phosphoryl)oxy]-6-[(1S)-1,2-dihydroxyethyl]-4-{[(3S,4S,5R,6R)-6-[(1S)-2-{[(3S,4R,5S,6R)-6-[(1S)-1,2-dihydroxyethyl]-3,4-dihydroxy-5-(phosphonooxy)oxan-2-yl]oxy}-1-hydroxyethyl]-4-{[(3R,4S,5R,6R)-4-{[(2R,3R,4S,5R,6R)-3-{[(3R,4S,5R,6R)-3-{[(2S,3R,4R,5S,6R)-3-acetamido-4,5-dihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}-4-{[(2S,3R,4R,5R,6R)-3-acetamido-6-({[(2R,3R,4R,5S,6R)-3-acetamido-4,5-dihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}methyl)-4-{[(2R,3R,4R,5R,6R)-3-acetamido-5-hydroxy-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}-5-hydroxyoxan-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}-3,5-dihydroxyoxan-2-yl]oxy}-3-hydroxyoxan-2-yl]oxy}-4-{[(2R,4R,5S,6R)-4-{[(2R,4R,5R,6R)-4-{[(2-aminoethoxy)(hydroxy)phosphoryl]oxy}-2-carboxy-6-[(1S)-1,2-dihydroxyethyl]-5-hydroxyoxan-2-yl]oxy}-2-carboxy-6-[(1S)-1,2-dihydroxyethyl]-5-hydroxyoxan-2-yl]oxy}-6-[(1S)-1,2-dihydroxyethyl]-2-{[(2R,3S,4R,5R,6R)-5-[(3R)-3-(dodecanoyloxy)tetradecanamido]-6-{[(2R,3S,4R,5R,6R)-3-hydroxy-5-[(3R)-3-hydroxytetradecanamido]-4-{[(3R)-3-hydroxytetradecanoyl]oxy}-6-(phosphonooxy)oxan-2-yl]methoxy}-3-(phosphonooxy)-4-{[(3R)-3-(tetradecanoyloxy)tetradecanoyl]oxy}oxan-2-yl]methoxy}oxane-2-carboxylic acid
Traditional Name(2R,4R,5S,6R)-5-{[(3S,4R,5R,6R)-5-({[2-aminoethoxy(hydroxy)phosphoryl]oxy(hydroxy)phosphoryl}oxy)-6-[(1S)-1,2-dihydroxyethyl]-4-{[(3S,4S,5R,6R)-6-[(1S)-2-{[(3S,4R,5S,6R)-6-[(1S)-1,2-dihydroxyethyl]-3,4-dihydroxy-5-(phosphonooxy)oxan-2-yl]oxy}-1-hydroxyethyl]-4-{[(3R,4S,5R,6R)-4-{[(2R,3R,4S,5R,6R)-3-{[(3R,4S,5R,6R)-3-{[(2S,3R,4R,5S,6R)-3-acetamido-4,5-dihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}-4-{[(2S,3R,4R,5R,6R)-3-acetamido-6-({[(2R,3R,4R,5S,6R)-3-acetamido-4,5-dihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}methyl)-4-{[(2R,3R,4R,5R,6R)-3-acetamido-5-hydroxy-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}-5-hydroxyoxan-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}-3,5-dihydroxyoxan-2-yl]oxy}-3-hydroxyoxan-2-yl]oxy}-4-{[(2R,4R,5S,6R)-4-{[(2R,4R,5R,6R)-4-{[2-aminoethoxy(hydroxy)phosphoryl]oxy}-2-carboxy-6-[(1S)-1,2-dihydroxyethyl]-5-hydroxyoxan-2-yl]oxy}-2-carboxy-6-[(1S)-1,2-dihydroxyethyl]-5-hydroxyoxan-2-yl]oxy}-6-[(1S)-1,2-dihydroxyethyl]-2-{[(2R,3S,4R,5R,6R)-5-[(3R)-3-(dodecanoyloxy)tetradecanamido]-6-{[(2R,3S,4R,5R,6R)-3-hydroxy-5-[(3R)-3-hydroxytetradecanamido]-4-{[(3R)-3-hydroxytetradecanoyl]oxy}-6-(phosphonooxy)oxan-2-yl]methoxy}-3-(phosphonooxy)-4-{[(3R)-3-(tetradecanoyloxy)tetradecanoyl]oxy}oxan-2-yl]methoxy}oxane-2-carboxylic acid
CAS Registry NumberNot Available
SMILES
CCCCCCCCCCCCCC(=O)O[C@H](CCCCCCCCCCC)CC(=O)O[C@@H]1[C@@H](NC(=O)C[C@@H](CCCCCCCCCCC)OC(=O)CCCCCCCCCCC)[C@H](OC[C@H]2O[C@H](OP(O)(O)=O)[C@H](NC(=O)C[C@H](O)CCCCCCCCCCC)[C@@H](OC(=O)C[C@H](O)CCCCCCCCCCC)[C@@H]2O)O[C@H](CO[C@@]2(C[C@@H](O[C@@]3(C[C@@H](O[C@@]4(C[C@@H](OP(O)(=O)OCCN)[C@H](O)[C@H](O4)[C@@H](O)CO)C(O)=O)[C@H](O)[C@H](O3)[C@@H](O)CO)C(O)=O)[C@H](OC3O[C@H]([C@@H](O)CO)[C@@H](OP(O)(=O)OP(O)(=O)OCCN)[C@H](OC4O[C@H]([C@@H](O)COC5O[C@H]([C@@H](O)CO)[C@@H](OP(O)(O)=O)[C@H](O)[C@@H]5O)[C@@H](O)[C@H](OC5O[C@H](CO[C@H]6O[C@H](CO)[C@H](O)[C@H](O)[C@H]6O)[C@@H](O)[C@H](O[C@H]6O[C@H](CO)[C@H](O)[C@H](O)[C@H]6OC6O[C@H](CO)[C@@H](O)[C@H](O[C@@H]7O[C@H](CO[C@@H]8O[C@H](CO)[C@@H](O)[C@H](O)[C@H]8NC(C)=O)[C@H](O)[C@H](O[C@@H]8O[C@H](CO)[C@H](O)[C@H](O[C@H]9O[C@H](CO[C@H]%10O[C@H](CO)[C@H](O)[C@H](O)[C@H]%10O)[C@H](O)[C@H](O)[C@H]9O)[C@H]8NC(C)=O)[C@H]7NC(C)=O)[C@H]6O[C@@H]6O[C@H](CO)[C@@H](O)[C@H](O)[C@H]6NC(C)=O)[C@H]5O)[C@@H]4O)[C@@H]3O)[C@H](O2)[C@@H](O)CO)C(O)=O)[C@H]1OP(O)(O)=O
InChI Identifier
InChI=1S/C211H376N8O126P6/c1-11-17-23-29-35-41-42-48-54-60-66-72-134(247)308-109(70-64-58-52-46-39-33-27-21-15-5)80-136(249)322-182-142(219-132(245)79-108(69-63-57-51-45-38-32-26-20-14-4)307-133(246)71-65-59-53-47-40-34-28-22-16-6)192(301-99-128-153(260)179(321-135(248)78-107(237)68-62-56-50-44-37-31-25-19-13-3)141(196(317-128)344-348(290,291)292)218-131(244)77-106(236)67-61-55-49-43-36-30-24-18-12-2)320-130(178(182)341-346(284,285)286)101-304-209(206(278)279)83-118(336-210(207(280)281)81-116(149(256)172(337-210)110(238)84-220)335-211(208(282)283)82-117(340-349(293,294)305-75-73-212)150(257)173(338-211)111(239)85-221)177(176(339-209)114(242)88-224)326-203-170(277)186(189(175(325-203)113(241)87-223)343-351(297,298)345-350(295,296)306-76-74-213)332-202-169(276)184(167(274)171(323-202)115(243)96-299-199-166(273)162(269)187(342-347(287,288)289)174(324-199)112(240)86-222)329-201-168(275)183(155(262)129(319-201)100-303-198-164(271)159(266)146(253)122(92-228)313-198)330-204-188(161(268)147(254)123(93-229)314-204)333-205-190(334-193-138(215-103(8)233)157(264)144(251)120(90-226)310-193)185(152(259)125(95-231)315-205)331-195-140(217-105(10)235)181(154(261)127(316-195)98-300-191-137(214-102(7)232)156(263)143(250)119(89-225)309-191)327-194-139(216-104(9)234)180(151(258)124(94-230)311-194)328-200-165(272)160(267)148(255)126(318-200)97-302-197-163(270)158(265)145(252)121(91-227)312-197/h106-130,137-205,220-231,236-243,250-277H,11-101,212-213H2,1-10H3,(H,214,232)(H,215,233)(H,216,234)(H,217,235)(H,218,244)(H,219,245)(H,278,279)(H,280,281)(H,282,283)(H,293,294)(H,295,296)(H,297,298)(H2,284,285,286)(H2,287,288,289)(H2,290,291,292)/t106-,107-,108-,109-,110+,111+,112+,113+,114+,115+,116-,117-,118-,119-,120-,121-,122-,123-,124-,125-,126-,127-,128-,129-,130-,137-,138-,139-,140-,141-,142-,143-,144-,145+,146+,147+,148+,149+,150+,151+,152-,153-,154+,155-,156-,157-,158+,159+,160+,161+,162-,163-,164-,165-,166+,167-,168-,169+,170+,171-,172-,173-,174-,175-,176-,177+,178-,179-,180-,181-,182-,183+,184+,185+,186-,187+,188-,189-,190-,191-,192-,193+,194+,195+,196-,197+,198+,199?,200-,201?,202?,203?,204-,205?,209-,210-,211-/m1/s1
InChI KeyBFVQTKQTUCQRPI-YYEZTRBPSA-N
Chemical Taxonomy
Description belongs to the class of organic compounds known as acylaminosugars. These are organic compounds containing a sugar linked to a chain through N-acyl group.
KingdomOrganic compounds
Super ClassOrganic oxygen compounds
ClassOrganooxygen compounds
Sub ClassCarbohydrates and carbohydrate conjugates
Direct ParentAcylaminosugars
Alternative Parents
Substituents
  • Polysaccharide
  • Acylaminosugar
  • Saccharolipid
  • Hexose phosphate
  • Fatty acyl glycoside
  • N-acyl-alpha-hexosamine
  • C-glucuronide
  • Alkyl glycoside
  • C-glycosyl compound
  • Glycosyl compound
  • O-glycosyl compound
  • Organic pyrophosphate
  • Phosphoethanolamine
  • Beta-hydroxy acid
  • Ketal
  • Fatty acid ester
  • Dialkyl phosphate
  • Monoalkyl phosphate
  • Alkyl phosphate
  • Pyran
  • Fatty amide
  • Hydroxy acid
  • N-acyl-amine
  • Fatty acyl
  • Organic phosphoric acid derivative
  • Oxane
  • Phosphoric acid ester
  • Acetamide
  • Secondary carboxylic acid amide
  • Amino acid or derivatives
  • Secondary alcohol
  • Amino acid
  • Carboxamide group
  • Carboxylic acid ester
  • Polyol
  • Acetal
  • Organoheterocyclic compound
  • Oxacycle
  • Carboxylic acid
  • Carboxylic acid derivative
  • Primary alcohol
  • Alcohol
  • Carbonyl group
  • Organic oxide
  • Hydrocarbon derivative
  • Primary aliphatic amine
  • Organonitrogen compound
  • Primary amine
  • Organic nitrogen compound
  • Amine
  • Organopnictogen compound
  • Aliphatic heteromonocyclic compound
Molecular FrameworkAliphatic heteromonocyclic compounds
External DescriptorsNot Available
Ontology
StatusDetected and Quantified
OriginNot Available
BiofunctionNot Available
ApplicationNot Available
Cellular locationsNot Available
Physical Properties
StateNot Available
Experimental Properties
PropertyValueReference
Melting PointNot AvailableNot Available
Boiling PointNot AvailableNot Available
Water SolubilityNot AvailableNot Available
LogPNot AvailableNot Available
Predicted Properties
PropertyValueSource
logP-8.2ChemAxon
pKa (Strongest Acidic)0.4ChemAxon
Physiological Charge-10ChemAxon
Hydrogen Acceptor Count116ChemAxon
Hydrogen Donor Count68ChemAxon
Polar Surface Area2096.16 ŲChemAxon
Rotatable Bond Count163ChemAxon
Refractivity1158.82 m³·mol⁻¹ChemAxon
Polarizability521.6 ųChemAxon
Number of Rings18ChemAxon
BioavailabilityYesChemAxon
Rule of FiveYesChemAxon
Ghose FilterYesChemAxon
Veber's RuleYesChemAxon
MDDR-like RuleYesChemAxon
Spectra
Spectra
Spectrum TypeDescriptionSplash KeyView
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Positivesplash10-0a6r-3290000014-5b598407e93fb55bf094Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Positivesplash10-0fba-3680100109-186d0a18d234b570c2cbSpectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Positivesplash10-004i-3950000000-821494a5093cc979f8d2Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Negativesplash10-00di-1590000003-131cd3d40a4d833f88ffSpectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Negativesplash10-00fr-3890000102-c4d4e0ded026f95dd34aSpectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Negativesplash10-00di-5890000010-beaaa06da4b2613e5b1bSpectrum
Biological Properties
Cellular LocationsNot Available
Biofluid Locations and Tissue Locations
  • Ruminal Fluid
Concentrations
BiofluidStatusValueConditionSpeciesReferenceDetails
Ruminal FluidDetected and Quantified5316 EU/mlNot AvailableCaprine details
Ruminal FluidDetected and Quantified21075 EU/mlNot AvailableCaprine details
Ruminal FluidDetected and Quantified35116 EU/mlNot AvailableCaprine details
Ruminal FluidDetected and Quantified128.179 +/- 32.523 uMNot AvailableBovine
    • Saleem F, Bouatra...
 details
Ruminal FluidDetected and Quantified147.310 +/- 40.176 uMNot AvailableBovine
    • Saleem F, Bouatra...
 details
DrugBank IDNot Available
HMDB IDHMDB0013470
FooDB IDNot Available
Phenol Explorer IDNot Available
KNApSAcK IDNot Available
BiGG IDNot Available
BioCyc IDCPD0-2294
METLIN IDNot Available
PDB IDNot Available
Wikipedia LinkNot Available
Chemspider IDNot Available
ChEBI ID16412
PubChem Compound ID53481793
Kegg Compound IDC00338
YMDB IDNot Available
ECMDB IDNot Available
References
Synthesis ReferenceNot Available
Material Safety Data Sheet (MSDS)Not Available
General ReferencesNot Available