(KDO)2-lipid A (ECMDB24179) (M2MDB006296)

IdentificationTaxonomyPhysical PropertiesBiological PropertiesSpectraConcentrationsLinksReferencesEnzymes (3)XML
Proteins (3)
Record Information
Version2.0
Creation Date2015-09-08 17:49:55 -0600
Update Date2015-09-14 16:46:12 -0600
Secondary Accession Numbers
  • ECMDB24179
Identification
Name:(KDO)2-lipid A
Description(KDO)2-lipid A is an intermediate in the synthesis of LPS. It has two 3-deoxy-D-manno-octulosonic acid (KDO) sugar residues in place of the core, and has no O-antigen.
Structure
Thumb
MOLSDFPDBSMILESInChI
Synonyms:
  • (Kdo)2-lipid A, cold adapted
Chemical Formula:C110H196N2O39P2
Weight:Average: 2232.704
Monoisotopic: 2231.292339975
InChI Key:DIXUKJUHGLIZGU-OIPVZEHTSA-H
InChI:InChI=1S/C110H202N2O39P2/c1-7-13-19-25-31-37-38-44-50-56-62-68-92(123)142-82(66-60-54-48-42-35-29-23-17-11-5)72-94(125)146-104-96(112-90(121)71-81(65-59-53-47-41-34-28-22-16-10-4)141-91(122)67-61-55-49-43-36-30-24-18-12-6)105(144-88(102(104)150-152(133,134)135)78-140-109(107(129)130)74-86(98(127)101(148-109)85(119)76-114)147-110(108(131)132)73-83(117)97(126)100(149-110)84(118)75-113)139-77-87-99(128)103(145-93(124)70-80(116)64-58-52-46-40-33-27-21-15-9-3)95(106(143-87)151-153(136,137)138)111-89(120)69-79(115)63-57-51-45-39-32-26-20-14-8-2/h79-88,95-106,113-119,126-128H,7-78H2,1-6H3,(H,111,120)(H,112,121)(H,129,130)(H,131,132)(H2,133,134,135)(H2,136,137,138)/p-6/t79-,80-,81-,82-,83-,84-,85-,86-,87-,88-,95-,96-,97-,98-,99-,100-,101-,102-,103-,104-,105-,106-,109-,110-/m1/s1
CAS number:Not Available
IUPAC Name:(2R,4R,5R,6R)-2-{[(2R,4R,5R,6R)-2-carboxylato-6-[(1R)-1,2-dihydroxyethyl]-2-{[(2R,3S,4R,5R,6R)-5-{[(3R)-3-(dodecanoyloxy)-1-oxidotetradecylidene]amino}-6-{[(2R,3S,4R,5R,6R)-3-hydroxy-5-{[(3R)-3-hydroxy-1-oxidotetradecylidene]amino}-4-{[(3R)-3-hydroxytetradecanoyl]oxy}-6-(phosphonooxy)oxan-2-yl]methoxy}-3-(phosphonatooxy)-4-{[(3R)-3-(tetradecanoyloxy)tetradecanoyl]oxy}oxan-2-yl]methoxy}-5-hydroxyoxan-4-yl]oxy}-6-[(1R)-1,2-dihydroxyethyl]-4,5-dihydroxyoxane-2-carboxylate
Traditional IUPAC Name:(2R,4R,5R,6R)-2-{[(2R,4R,5R,6R)-2-carboxylato-6-[(1R)-1,2-dihydroxyethyl]-2-{[(2R,3S,4R,5R,6R)-5-{[(3R)-3-(dodecanoyloxy)-1-oxidotetradecylidene]amino}-6-{[(2R,3S,4R,5R,6R)-3-hydroxy-5-{[(3R)-3-hydroxy-1-oxidotetradecylidene]amino}-4-{[(3R)-3-hydroxytetradecanoyl]oxy}-6-(phosphonooxy)oxan-2-yl]methoxy}-3-(phosphonatooxy)-4-{[(3R)-3-(tetradecanoyloxy)tetradecanoyl]oxy}oxan-2-yl]methoxy}-5-hydroxyoxan-4-yl]oxy}-6-[(1R)-1,2-dihydroxyethyl]-4,5-dihydroxyoxane-2-carboxylate
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(C[C@@]([H])(O[C@@]4(C[C@@]([H])(O)[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])(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 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
  • Oligosaccharide phosphate
  • Oligosaccharide
  • Hexacarboxylic acid or derivatives
  • Acylaminosugar
  • Saccharolipid
  • Hexose phosphate
  • N-acyl-alpha-hexosamine
  • C-glucuronide
  • C-glycosyl compound
  • Glycosyl compound
  • O-glycosyl compound
  • Beta-hydroxy acid
  • Ketal
  • Fatty acid ester
  • Fatty amide
  • Fatty acyl
  • Hydroxy acid
  • N-acyl-amine
  • Alkyl phosphate
  • Pyran
  • Organic phosphoric acid derivative
  • Oxane
  • Phosphoric acid ester
  • Carboxamide group
  • Secondary alcohol
  • Secondary carboxylic acid amide
  • Carboxylic acid ester
  • Carboxylic acid derivative
  • Organoheterocyclic compound
  • Carboxylic acid
  • Oxacycle
  • Acetal
  • Primary alcohol
  • Organopnictogen compound
  • Alcohol
  • Organic oxide
  • Carbonyl group
  • Organonitrogen compound
  • Hydrocarbon derivative
  • Organic nitrogen compound
  • Organic anion
  • Aliphatic heteromonocyclic compound
Molecular FrameworkAliphatic heteromonocyclic compounds
External Descriptors
Physical Properties
State:Not Available
Charge:-6
Melting point:Not Available
Experimental Properties:
PropertyValueSource
Predicted Properties
PropertyValueSource
Water Solubility0.026 g/LALOGPS
logP5.01ALOGPS
logP22.64ChemAxon
logS-5ALOGPS
pKa (Strongest Acidic)0.55ChemAxon
Physiological Charge-6ChemAxon
Hydrogen Acceptor Count35ChemAxon
Hydrogen Donor Count12ChemAxon
Polar Surface Area662.39 ŲChemAxon
Rotatable Bond Count98ChemAxon
Refractivity605.17 m³·mol⁻¹ChemAxon
Polarizability249.52 ųChemAxon
Number of Rings4ChemAxon
Bioavailability0ChemAxon
Rule of FiveYesChemAxon
Ghose FilterYesChemAxon
Veber's RuleYesChemAxon
MDDR-like RuleYesChemAxon
Biological Properties
Cellular Locations:Membrane
Reactions:
Lauroyl-KDO2-lipid IV(A) + myristoyl-[acp] > a holo-[acyl-carrier protein] + (KDO)2-lipid A
(KDO)2-lipid A + ADP-L-glycero-beta-D-manno-heptose > Hydrogen ion + Adenosine diphosphate + heptosyl-Kdo2-lipid A + ADP + Heptosyl-KDO2-lipid A
2 4-Amino-4-deoxy-alpha-L-arabinopyranosyl di-trans,octa-cis-undecaprenyl phosphate + (KDO)2-lipid A >2 di-trans,octa-cis-undecaprenyl diphosphate + L-Ara4N-modified 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
polymyxin resistancePW002052 ThumbThumb?image type=greyscaleThumb?image type=simple
KEGG Pathways:
  • Lipopolysaccharide biosynthesis ec00540
EcoCyc Pathways:Not Available
Concentrations
Not Available
Spectra
Spectra:
Spectrum TypeDescriptionSplash Key
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Positivesplash10-000x-1290000000-11ae518f9b6e3d1febecView in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Positivesplash10-00dl-2290000000-1fe35c45b114339ac9d3View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Positivesplash10-052f-8961100000-83ffd298ca91aa9bb219View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Negativesplash10-001r-3190000000-ca0d72bf7d698f820ffaView in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Negativesplash10-0umi-9742000000-c7f89f307f213742d992View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Negativesplash10-06vi-9320000000-fe409eb62d6fb5c8e661View in MoNA
References
References:Not Available
Synthesis Reference:Not Available
Material Safety Data Sheet (MSDS)Not Available
External Links:
ResourceLink
CHEBI ID58540
HMDB IDNot Available
Pubchem Compound ID25244473
Kegg IDNot Available
ChemSpider IDNot Available
Wikipedia IDNot Available
BioCyc IDNot Available

Enzymes

Protein Details
1. Lipid A biosynthesis (KDO)2-(lauroyl)-lipid IVA acyltransferase
General function:
Involved in transferase activity, transferring acyl groups
Specific function:
Transfers myristate or laurate, activated on ACP, to the lipid IVA moiety of (KDO)2-(lauroyl)-lipid IVA. Decanoyl, palmitoyl, palmitoleoyl, and (R)-3-hydroxymyristoyl-ACP are poor acyl donors. Functions optimally after laurate incorporation by htrB has taken place. Acylates (KDO)2-(lauroyl)-lipid IVA about 100 times faster than (KDO)2-lipid IVA. Displays a preference for myristoyl-ACP over lauroyl-ACP
Gene Name:
msbB
Uniprot ID:
P24205
Molecular weight:
37410
Protein Details
2. Undecaprenyl phosphate-alpha-4-amino-4-deoxy-L-arabinose arabinosyl transferase
General function:
Involved in transferase activity, transferring pentosyl groups
Specific function:
Catalyzes the transfer of the L-Ara4N moiety of the glycolipid undecaprenyl phosphate-alpha-L-Ara4N to lipid A. The modified arabinose is attached to lipid A and is required for resistance to polymyxin and cationic antimicrobial peptides
Gene Name:
arnT
Uniprot ID:
P76473
Molecular weight:
62542
Reactions
4-amino-4-deoxy-alpha-L-arabinopyranosyl di-trans,octa-cis-undecaprenyl phosphate + lipid IV(A) = lipid II(A) + di-trans,octa-cis-undecaprenyl phosphate.
Protein Details
3. Lipopolysaccharide heptosyltransferase 1
General function:
Involved in transferase activity, transferring glycosyl groups
Specific function:
Heptose transfer to the lipopolysaccharide core. It transfers the innnermost heptose to [4'-P](3-deoxy-D-manno- octulosonic acid)2-IVA
Gene Name:
rfaC
Uniprot ID:
P24173
Molecular weight:
35544