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Record Information
Version	2.0
Creation Date	2012-05-31 14:58:20 -0600
Update Date	2015-06-03 17:20:37 -0600
Secondary Accession Numbers	ECMDB21090
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, E. coli 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	MOLSDFPDBSMILESInChI × Structure for #<Compound:0xaec636b8> Close
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
Weight:	Average: 4330.3543 Monoisotopic: 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
Description	belongs to the class of organic compounds known as saccharolipids. Saccharolipids are compounds in which fatty acids are linked directly to a sugar backbone, forming structures that are compatible with membrane bilayers. In the saccharolipids, a sugar substitutes for the glycerol backbone that is present in glycerolipids and glycerophospholipids. The most familiar saccharolipids contain an acylated glucosamine. In contrast to others glycolipids, the fatty acid is not glycosidically linked to the sugar moiety.
Kingdom	Organic compounds
Super Class	Lipids and lipid-like molecules
Class	Saccharolipids
Sub Class	Not Available
Direct Parent	Saccharolipids
Alternative Parents	Polysaccharides Hexose phosphates N-acyl-alpha-hexosamines C-glucuronides Alkyl glycosides O-glycosyl compounds C-glycosyl compounds Organic pyrophosphates Phosphoethanolamines Monoalkyl phosphates Ketals Fatty acid esters Dialkyl phosphates Beta hydroxy acids and derivatives Pyrans Oxanes Secondary alcohols Isoureas Carboxylic acid esters Amino acids Propargyl-type 1,3-dipolar organic compounds Polyols Oxacyclic compounds Carboxylic acids Carboximidamides Primary alcohols Organopnictogen compounds Organic oxides Monoalkylamines Imines Hydrocarbon derivatives Carbonyl compounds
Substituents	Polysaccharide Saccharolipid Hexose phosphate N-acyl-alpha-hexosamine Fatty acyl glycoside C-glucuronide Glucuronic acid or derivatives Alkyl glycoside O-glycosyl compound Glycosyl compound C-glycosyl compound Organic pyrophosphate Phosphoethanolamine Ketal Dialkyl phosphate Monoalkyl phosphate Fatty acid ester Beta-hydroxy acid Fatty acyl Alkyl phosphate Pyran Phosphoric acid ester Oxane Organic phosphoric acid derivative Hydroxy acid Amino acid Secondary alcohol Isourea Carboxylic acid ester Amino acid or derivatives Oxacycle Organoheterocyclic compound Organic 1,3-dipolar compound Propargyl-type 1,3-dipolar organic compound Carboximidamide Polyol Carboxylic acid Carboxylic acid derivative Carboximidic acid derivative Carboximidic acid Acetal Organic nitrogen compound Organic oxygen compound Organopnictogen compound Organic oxide 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:	-8
Melting point:	Not Available
Experimental Properties:	Property Value Source LogP: 5.5247 PhysProp
Predicted Properties	Property Value Source logP 8.09 ChemAxon pKa (Strongest Acidic) 0.38 ChemAxon Physiological Charge -8 ChemAxon Hydrogen Acceptor Count 92 ChemAxon Hydrogen Donor Count 52 ChemAxon Polar Surface Area 1647.1 Ų ChemAxon Rotatable Bond Count 145 ChemAxon Refractivity 998.56 m³·mol⁻¹ ChemAxon Number of Rings 13 ChemAxon Bioavailability 0 ChemAxon Rule of Five Yes ChemAxon Ghose Filter Yes ChemAxon Veber's Rule Yes ChemAxon MDDR-like Rule Yes ChemAxon
Biological Properties
Cellular Locations:	Membrane
Reactions:
SMPDB Pathways:	Lipopolysaccharide biosynthesis PW000831
KEGG Pathways:	ABC transporters ec02010 Lipopolysaccharide biosynthesis ec00540
EcoCyc Pathways:	superpathway of lipopolysaccharide biosynthesis LPSSYN-PWY
Concentrations
	Not Available
Spectra
Spectra:	Not Available
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
Links
External Links:	Resource Link CHEBI ID 16412 HMDB ID HMDB13471 Pubchem Compound ID 11970143 Kegg ID C00338 ChemSpider ID Not Available Wikipedia Lipopolysaccharide BioCyc ID Not Available

Enzymes

Transporters