Ra-LPS (PAMDB001506)

IdentificationTaxonomyPhysical PropertiesBiological PropertiesSpectraConcentrationsLinksReferencesEnzymes Transporters
Proteins (3280)
Record Information
Version 1.0
Update Date 1/22/2018 11:54:54 AM
Metabolite IDPAMDB001506
Identification
Name: Ra-LPS
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. There are 2 forms of LPS: smooth-form and rough-form. The smooth-form (S-form) LPS consists of three parts: O antigen (or O polysaccharide), core region and lipid A. The rough-form (R-form) LPS only consists of core region and lipid A. The 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). Depending on the quantity and composition of the sugars in the core region, Pseudomonas aeruginosa K-12 R-form LPS can be classified as Ra, Rb1, Rb2, Rc, Rd1, Rd2, and Re-LPS. LPS is first synthesized as KDO-lipid A or Re-LPS. Adding more sugars to the core region gives rise to Rd, Rc, Rb and Ra-LPS. (Wikipedia; PMID: 17403049; PMID: 17364071; PMDI: 20203010)
Structure
Thumb
🔍MOLSDFPDBSMILESInChIView Structure
Synonyms:
  • Core oligosaccharide
  • Core oligosaccharide lipid A
  • Endotoxin Lipopolysaccharide core
  • Endotoxin LPS core
  • Lipopolysaccharide
  • Lipopolysaccharide core endotoxin
  • Lipopolysaccharide Ra component
  • LPS core
Chemical Formula: C180H328N6O98P6
Average Molecular Weight: 4330.3543
Monoisotopic Molecular Weight: 4327.929256554
InChI Key: CQMSKDRUAIEDAN-FCHZNYOBSA-N
InChI:InChI=1S/C180H328N6O98P6/c1-13-19-25-31-37-43-44-50-56-62-68-74-116(201)255-105(72-66-60-54-48-41-35-29-23-17-5)82-118(203)264-149-121(185-114(199)81-104(71-65-59-53-47-40-34-28-22-16-4)254-115(200)73-67-61-55-49-42-36-30-24-18-6)164(249-93-110-126(208)148(263-117(202)80-103(197)70-64-58-52-46-39-33-27-21-15-3)120(166(260-110)283-287(239,240)241)184-113(198)79-102(196)69-63-57-51-45-38-32-26-20-14-2)262-112(147(149)279-285(233,234)235)95-251-178(174(226)227)163(225)160(278-179(175(228)229)161(223)154(136(218)142(274-179)96(7)83-187)277-180(176(230)231)162(224)155(281-288(242,243)252-77-75-181)137(219)143(275-180)97(8)84-188)158(146(276-178)100(11)87-191)273-171-140(222)152(159(145(267-171)99(10)86-190)282-290(246,247)284-289(244,245)253-78-76-182)270-170-139(221)151(135(217)141(265-170)101(12)92-248-168-134(216)132(214)153(280-286(236,237)238)144(266-168)98(9)85-189)268-169-138(220)150(127(209)111(261-169)94-250-167-133(215)129(211)123(205)107(89-193)257-167)269-172-157(131(213)125(207)108(90-194)258-172)272-173-156(130(212)124(206)109(91-195)259-173)271-165-119(186-177(183)232)128(210)122(204)106(88-192)256-165/h96-112,119-173,187-197,204-225H,13-95,181-182H2,1-12H3,(H,184,198)(H,185,199)(H,226,227)(H,228,229)(H,230,231)(H,242,243)(H,244,245)(H,246,247)(H3,183,186,232)(H2,233,234,235)(H2,236,237,238)(H2,239,240,241)/t96-,97-,98-,99-,100-,101-,102+,103+,104+,105+,106+,107+,108+,109+,110+,111+,112+,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+,159+,160-,161-,162-,163-,164+,165-,166+,167-,168?,169?,170?,171?,172+,173?,178+,179-,180-/m0/s1
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,5S,6R)-3-{[(2S,3R,4R,5S,6R)-4,5-dihydroxy-3-[(C-hydroxycarbonimidoyl)amino]-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}-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,5S,6R)-3-{[(2S,3R,4R,5S,6R)-4,5-dihydroxy-3-(C-hydroxycarbonimidoylamino)-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}-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@@]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
  • Hexose phosphate
  • N-acyl-alpha-hexosamine
  • Fatty acyl glycoside
  • C-glucuronide
  • Glucuronic acid or derivatives
  • Alkyl glycoside
  • O-glycosyl compound
  • C-glycosyl compound
  • Glycosyl compound
  • Organic pyrophosphate
  • Pyran carboxylic acid
  • Pyran carboxylic acid or derivatives
  • Phosphoethanolamine
  • Monoalkyl phosphate
  • Beta-hydroxy acid
  • Ketal
  • Dialkyl phosphate
  • Fatty acid ester
  • Alkyl phosphate
  • Organic phosphate
  • Organic phosphoric acid derivative
  • Pyran
  • Hydroxy acid
  • Phosphoric acid ester
  • Fatty acyl
  • 1,2-diol
  • Amino acid or derivatives
  • Amino acid
  • Carboxylic acid ester
  • Secondary alcohol
  • Isourea
  • Polyol
  • Acetal
  • Oxacycle
  • Carboximidic acid derivative
  • Carboxylic acid derivative
  • Carboxylic acid
  • Organoheterocyclic compound
  • Organic 1,3-dipolar compound
  • Propargyl-type 1,3-dipolar organic compound
  • Carboximidamide
  • Primary alcohol
  • Carbonyl group
  • Primary aliphatic amine
  • Amine
  • Organooxygen compound
  • Alcohol
  • Hydrocarbon derivative
  • Organonitrogen compound
  • Organic oxide
  • Primary amine
  • Imine
  • Aliphatic heteromonocyclic compound
Molecular Framework Aliphatic heteromonocyclic compounds
External Descriptors Not Available
Physical Properties
State: Solid
Charge:-8
Melting point: Not Available
Experimental Properties:
PropertyValueSource
LogP:5.5247PhysProp
Predicted Properties
PropertyValueSource
logP8.09ChemAxon
pKa (Strongest Acidic)0.38ChemAxon
Physiological Charge-8ChemAxon
Hydrogen Acceptor Count92ChemAxon
Hydrogen Donor Count52ChemAxon
Polar Surface Area1647.1 Å2ChemAxon
Rotatable Bond Count145ChemAxon
Refractivity998.56 m3·mol-1ChemAxon
Number of Rings13ChemAxon
Bioavailability0ChemAxon
Rule of FiveYesChemAxon
Ghose FilterYesChemAxon
Veber's RuleYesChemAxon
MDDR-like RuleYesChemAxon
Biological Properties
Cellular Locations: Membrane
Reactions:
Pathways:
Spectra
Spectra:
References
References:
  • Holst, O. (2007). "The structures of core regions from enterobacterial lipopolysaccharides - an update." FEMS Microbiol Lett 271:3-11. Pubmed: 17403049
  • 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
  • Zubova, S. V., Prokhorenko, I. R. (2006). "Use of colorimetric method for evaluation of LPS of different structure." Bull Exp Biol Med 141:765-767. Pubmed: 17364071
Synthesis Reference: Not Available
Material Safety Data Sheet (MSDS) Not Available
External Links:
ResourceLink
CHEBI ID16412
HMDB IDHMDB13471
Pubchem Compound ID11970143
Kegg IDC00338
ChemSpider IDNot Available
WikipediaLipopolysaccharide
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