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Record Information
Version4.0
StatusDetected and Quantified
Creation Date2010-05-06 13:28:02 UTC
Update Date2019-07-23 05:58:56 UTC
HMDB IDHMDB0013471
Secondary Accession Numbers
  • HMDB13471
Metabolite Identification
Common NameLPS core
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. LPS Core domain always contains an oligosaccharide component which attaches directly to lipid A and commonly contains sugars such as heptose and 3-deoxy-D-mannooctulosonic Acid (also known as KDO, keto-deoxyoctulosonate).[2] The LPS Cores of many bacteria also contain non-carbohydrate components, such as phosphate, amino acids, and ethanolamine substitutents.(from wiki). This card shows the LPS core component in E.coli. LPS core has also been found in Pseudomonas and Salmonella (PMID: 9791168 ) (Wikipedia).
Structure
Open uri20190723 12651 h0nr31?1563861536
Synonyms
ValueSource
Core oligosaccharideHMDB
Core oligosaccharide lipid aHMDB
Endotoxin lipopolysaccharide coreHMDB
Endotoxin LPS coreHMDB
Lipopolysaccharide core endotoxinHMDB
Lipopolysaccharide ra componentHMDB
Ra-LPSHMDB
Chemical FormulaC175H317N5O101P6
Average Molecular Weight4293.205
Monoisotopic Molecular Weight4290.824851063
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,5S,6R)-3-{[(2S,3R,4R,5S,6R)-3-acetamido-4,5-dihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}-4,5-dihydroxy-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,5S,6R)-3-{[(2S,3R,4R,5S,6R)-3-acetamido-4,5-dihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}-4,5-dihydroxy-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]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/C175H317N5O101P6/c1-8-14-20-26-32-38-39-45-51-57-63-69-118(202)252-98(67-61-55-49-43-36-30-24-18-12-5)77-120(204)261-152-123(180-116(200)76-97(66-60-54-48-42-35-29-23-17-11-4)251-117(201)68-62-56-50-44-37-31-25-19-13-6)160(246-91-112-130(211)151(260-119(203)75-96(192)65-59-53-47-41-34-28-22-16-10-3)122(162(257-112)280-284(236,237)238)179-115(199)74-95(191)64-58-52-46-40-33-27-21-15-9-2)259-114(150(152)277-282(230,231)232)93-248-173(170(224)225)80-107(272-174(171(226)227)78-105(128(209)144(273-174)99(193)81-181)271-175(172(228)229)79-106(276-285(239,240)249-72-70-176)129(210)145(274-175)100(194)82-182)149(148(275-173)103(197)85-185)265-167-142(223)155(159(147(264-167)102(196)84-184)279-287(243,244)281-286(241,242)250-73-71-177)268-166-141(222)154(139(220)143(262-166)104(198)90-245-164-138(219)136(217)156(278-283(233,234)235)146(263-164)101(195)83-183)266-165-140(221)153(131(212)113(258-165)92-247-163-137(218)133(214)125(206)109(87-187)254-163)267-168-158(135(216)127(208)110(88-188)255-168)270-169-157(134(215)126(207)111(89-189)256-169)269-161-121(178-94(7)190)132(213)124(205)108(86-186)253-161/h95-114,121-169,181-189,191-198,205-223H,8-93,176-177H2,1-7H3,(H,178,190)(H,179,199)(H,180,200)(H,224,225)(H,226,227)(H,228,229)(H,239,240)(H,241,242)(H,243,244)(H2,230,231,232)(H2,233,234,235)(H2,236,237,238)/t95-,96-,97-,98-,99+,100+,101+,102+,103+,104+,105-,106-,107-,108-,109-,110-,111-,112-,113-,114-,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-,159-,160-,161+,162-,163+,164?,165?,166?,167?,168-,169?,173-,174-,175-/m1/s1
InChI KeyAAXCQFOXUJMCCW-PETQGJDISA-N
Chemical Taxonomy
DescriptionThis compound 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
Disposition

Source:

Biological location:

Physical Properties
StateSolid
Experimental Properties
PropertyValueReference
Melting PointNot AvailableNot Available
Boiling PointNot AvailableNot Available
Water SolubilityNot AvailableNot Available
LogPNot AvailableNot Available
Predicted Properties
PropertyValueSource
logP1.54ChemAxon
pKa (Strongest Acidic)0.4ChemAxon
Physiological Charge-10ChemAxon
Hydrogen Acceptor Count91ChemAxon
Hydrogen Donor Count53ChemAxon
Polar Surface Area1673.8 ŲChemAxon
Rotatable Bond Count145ChemAxon
Refractivity963.45 m³·mol⁻¹ChemAxon
Number of Rings13ChemAxon
Bioavailability0ChemAxon
Rule of FiveYesChemAxon
Ghose FilterYesChemAxon
Veber's RuleYesChemAxon
MDDR-like RuleYesChemAxon
Spectra
Spectrum TypeDescriptionSplash KeyView
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Positivesplash10-00di-3190100203-6cc73cac6ee8b6f34f63JSpectraViewer | MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Positivesplash10-01zc-9271311813-15153f67fde929abb801JSpectraViewer | MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Positivesplash10-006x-9882221311-ce1866014f1c60c8f6d8JSpectraViewer | MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Negativesplash10-00b9-4091010001-e7a6007021379e3bde15JSpectraViewer | MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Negativesplash10-004i-9150000010-b9005aa390051477aed9JSpectraViewer | MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Negativesplash10-004i-9100000000-68958ff65e8f5e748306JSpectraViewer | MoNA
Biological Properties
Cellular LocationsNot Available
Biospecimen Locations
  • Blood
Tissue LocationsNot Available
Pathways
Normal Concentrations
BiospecimenStatusValueAgeSexConditionReferenceDetails
BloodDetected and Quantified0.000014 uMAdult (>18 years old)BothNormal details
BloodDetected and Quantified0.0000027 uMAdult (>18 years old)BothNormal details
Abnormal Concentrations
Not Available
Associated Disorders and Diseases
Disease ReferencesNone
Associated OMIM IDsNone
DrugBank IDNot Available
Phenol Explorer Compound IDNot Available
FoodDB IDFDB029471
KNApSAcK IDNot Available
Chemspider IDNot Available
KEGG Compound IDc0338
BioCyc IDCPD0-2271
BiGG IDNot Available
Wikipedia LinkNot Available
METLIN IDNot Available
PubChem Compound53481794
PDB IDNot Available
ChEBI ID59309
Food Biomarker OntologyNot Available
VMH IDNot Available
References
Synthesis ReferenceNot Available
Material Safety Data Sheet (MSDS)Not Available
General References
  1. Heinrichs DE, Yethon JA, Whitfield C: Molecular basis for structural diversity in the core regions of the lipopolysaccharides of Escherichia coli and Salmonella enterica. Mol Microbiol. 1998 Oct;30(2):221-32. [PubMed:9791168 ]