(heptosyl)2-Kdo2-lipid A (ECMDB24219) (M2MDB006336)

IdentificationTaxonomyPhysical PropertiesBiological PropertiesSpectraConcentrationsLinksReferencesEnzymes (2)XML
Proteins (2)
Record Information
Version2.0
Creation Date2015-09-08 17:50:08 -0600
Update Date2015-09-14 16:46:12 -0600
Secondary Accession Numbers
  • ECMDB24219
Identification
Name:(heptosyl)2-Kdo2-lipid A
Description(Heptosyl)2-Kdo2-lipid A is a component of lipopolysaccharide. Bacterial lipopolysaccharides (LPS) typically consist of a hydrophobic domain inserted into the outer membrane known as lipid A (or endotoxin), a phosphorylated "core" oligosaccharide and a distal polysaccharide (or O antigen). The core oligosaccharides are conceptually divided into two regions: inner core and outer core. The inner core is highly conserved, comprises three deoxy-D-manno-octulosonic acid (KDO) and L-glycero-D-manno-heptose (Hep) and is often phosphorylated. The inner core oligosaccharide plays a critical role in essential barrier function of the outer membrane. The outer core comprises a tri-hexose backbone modified with varying side-branch substitutions of hexose and acetamidohexose residues. The outer core provides an attachment site for O-antigen. The completed lipid A-KDO2 serves as the acceptor on which the core oligosaccharide chains are assembled by sequential glycosyl transfer from nucleotide sugar precursors. This process involves a co-ordinated complex of membrane-associated glycosyltransferases acting at the cytoplasmic face of the plasma membrane.
Structure
Thumb
MOLSDFPDBSMILESInChI
Synonyms:Not Available
Chemical Formula:C126H225N2O49P2
Weight:Average: 2614.101
Monoisotopic: 2612.467863529
InChI Key:DBFYJNVGWVVVGJ-UHFFFAOYSA-I
InChI:InChI=1S/C126H230N2O49P2/c1-9-15-21-27-33-39-40-46-52-58-64-70-99(143)164-87(68-62-56-50-44-37-31-25-19-13-5)74-101(145)168-118-103(128-97(141)73-86(67-61-55-49-43-36-30-24-18-12-4)163-98(142)69-63-57-51-45-38-32-26-20-14-6)120(161-81-94-105(147)117(167-100(144)72-85(134)66-60-54-48-42-35-29-23-17-11-3)102(121(165-94)177-179(158,159)160)127-96(140)71-84(133)65-59-53-47-41-34-28-22-16-10-2)166-95(116(118)176-178(155,156)157)82-162-126(124(153)154)76-93(173-125(83(7)8)75-88(135)104(146)113(174-125)91(138)79-131)115(114(175-126)92(139)80-132)171-123-110(152)119(109(151)112(170-123)90(137)78-130)172-122-108(150)106(148)107(149)111(169-122)89(136)77-129/h84-95,102-123,129-139,146-152H,7,9-82H2,1-6,8H3,(H,127,140)(H,128,141)(H,153,154)(H2,155,156,157)(H2,158,159,160)/p-5
CAS number:Not Available
IUPAC Name:6-(1,2-dihydroxyethyl)-4-{[6-(1,2-dihydroxyethyl)-4,5-dihydroxy-2-(prop-1-en-2-yl)oxan-2-yl]oxy}-5-{[6-(1,2-dihydroxyethyl)-4-{[6-(1,2-dihydroxyethyl)-3,4,5-trihydroxyoxan-2-yl]oxy}-3,5-dihydroxyoxan-2-yl]oxy}-2-({5-[3-(dodecanoyloxy)tetradecanamido]-6-{[3-hydroxy-5-(3-hydroxytetradecanamido)-4-[(3-hydroxytetradecanoyl)oxy]-6-(phosphonatooxy)oxan-2-yl]methoxy}-3-(phosphonatooxy)-4-{[3-(tetradecanoyloxy)tetradecanoyl]oxy}oxan-2-yl}methoxy)oxane-2-carboxylate
Traditional IUPAC Name:6-(1,2-dihydroxyethyl)-4-{[6-(1,2-dihydroxyethyl)-4,5-dihydroxy-2-(prop-1-en-2-yl)oxan-2-yl]oxy}-5-{[6-(1,2-dihydroxyethyl)-4-{[6-(1,2-dihydroxyethyl)-3,4,5-trihydroxyoxan-2-yl]oxy}-3,5-dihydroxyoxan-2-yl]oxy}-2-({5-[3-(dodecanoyloxy)tetradecanamido]-6-{[3-hydroxy-5-(3-hydroxytetradecanamido)-4-[(3-hydroxytetradecanoyl)oxy]-6-(phosphonatooxy)oxan-2-yl]methoxy}-3-(phosphonatooxy)-4-{[3-(tetradecanoyloxy)tetradecanoyl]oxy}oxan-2-yl}methoxy)oxane-2-carboxylate
SMILES:CCCCCCCCCCCCCC(=O)OC(CCCCCCCCCCC)CC(=O)OC1C(NC(=O)CC(CCCCCCCCCCC)OC(=O)CCCCCCCCCCC)C(OCC2OC(OP([O-])([O-])=O)C(NC(=O)CC(O)CCCCCCCCCCC)C(OC(=O)CC(O)CCCCCCCCCCC)C2O)OC(COC2(CC(OC3(CC(O)C(O)C(O3)C(O)CO)C(C)=C)C(OC3OC(C(O)CO)C(O)C(OC4OC(C(O)CO)C(O)C(O)C4O)C3O)C(O2)C(O)CO)C([O-])=O)C1OP([O-])([O-])=O
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.
KingdomOrganic compounds
Super ClassLipids and lipid-like molecules
ClassSaccharolipids
Sub ClassNot Available
Direct ParentSaccharolipids
Alternative Parents
Substituents
  • Oligosaccharide phosphate
  • Oligosaccharide
  • Saccharolipid
  • Pentacarboxylic acid or derivatives
  • Hexose phosphate
  • N-acyl-alpha-hexosamine
  • Fatty acyl glycoside
  • C-glucuronide
  • Alkyl glycoside
  • O-glycosyl compound
  • Glycosyl compound
  • C-glycosyl compound
  • Ketal
  • Monoalkyl phosphate
  • Fatty acid ester
  • Beta-hydroxy acid
  • Fatty acyl
  • Alkyl phosphate
  • Pyran
  • Phosphoric acid ester
  • Oxane
  • Organic phosphoric acid derivative
  • Hydroxy acid
  • Secondary alcohol
  • Carboxylic acid ester
  • Oxacycle
  • Organoheterocyclic compound
  • 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 alcohol
  • Organooxygen compound
  • Organonitrogen compound
  • Carbonyl group
  • Alcohol
  • Organic anion
  • Aliphatic heteromonocyclic compound
Molecular FrameworkAliphatic heteromonocyclic compounds
External DescriptorsNot Available
Physical Properties
State:Not Available
Charge:-5
Melting point:Not Available
Experimental Properties:
PropertyValueSource
Predicted Properties
PropertyValueSource
Water Solubility0.087 g/LALOGPS
logP3.67ALOGPS
logP17.39ChemAxon
logS-4.5ALOGPS
pKa (Strongest Acidic)0.6ChemAxon
pKa (Strongest Basic)-4ChemAxon
Physiological Charge-5ChemAxon
Hydrogen Acceptor Count43ChemAxon
Hydrogen Donor Count20ChemAxon
Polar Surface Area814.04 ŲChemAxon
Rotatable Bond Count106ChemAxon
Refractivity653.91 m³·mol⁻¹ChemAxon
Polarizability288.61 ųChemAxon
Number of Rings6ChemAxon
Bioavailability0ChemAxon
Rule of FiveYesChemAxon
Ghose FilterYesChemAxon
Veber's RuleYesChemAxon
MDDR-like RuleYesChemAxon
Biological Properties
Cellular Locations:Membrane
Reactions:
heptosyl-Kdo2-lipid A + ADP-L-glycero-beta-D-manno-heptose + Heptosyl-KDO2-lipid A > Adenosine diphosphate + Hydrogen ion + (heptosyl)2-Kdo2-lipid A + ADP
(heptosyl)2-Kdo2-lipid A + UDP-Glucose > Uridine 5'-diphosphate + Hydrogen ion + glucosyl-(heptosyl)2-Kdo2-lipid A
SMPDB Pathways:
Lipopolysaccharide biosynthesisPW000831 ThumbThumb?image type=greyscaleThumb?image type=simple
lipopolysaccharide biosynthesis IIPW001905 ThumbThumb?image type=greyscaleThumb?image type=simple
lipopolysaccharide biosynthesis IIIPW002059 ThumbThumb?image type=greyscaleThumb?image type=simple
KEGG Pathways:
  • Lipopolysaccharide biosynthesis ec00540
EcoCyc Pathways:Not Available
Concentrations
Not Available
Spectra
Spectra:Not Available
References
References:Not Available
Synthesis Reference:Not Available
Material Safety Data Sheet (MSDS)Not Available
External Links:
ResourceLink
CHEBI IDNot Available
HMDB IDNot Available
Pubchem Compound IDNot Available
Kegg IDNot Available
ChemSpider IDNot Available
Wikipedia IDNot Available
BioCyc IDNot Available

Enzymes

Protein Details
1. Lipopolysaccharide core biosynthesis protein rfaG
General function:
Involved in biosynthetic process
Specific function:
Involved in the addition of the first glucose residue to the lipopolysaccharide core
Gene Name:
rfaG
Uniprot ID:
P25740
Molecular weight:
42284
Protein Details
2. ADP-heptose--LPS heptosyltransferase 2
General function:
Involved in transferase activity, transferring glycosyl groups
Specific function:
Specific function unknown
Gene Name:
rfaF
Uniprot ID:
P37692
Molecular weight:
39042