KDO2-(palmitoleoyl)-lipid IVA (ECMDB20572) (M2MDB001375)

IdentificationTaxonomyPhysical PropertiesBiological PropertiesSpectraConcentrationsLinksReferencesEnzymes (3)XML
Proteins (3)
Record Information
Version2.0
Creation Date2012-05-31 14:51:16 -0600
Update Date2015-06-03 17:20:19 -0600
Secondary Accession Numbers
  • ECMDB20572
Identification
Name:KDO2-(palmitoleoyl)-lipid IVA
DescriptionKdo2-(palmitoleoyl)-lipid iva is a member of the chemical class known as Polysaccharide Phosphates. These are polysaccharides in which a phosphate group is bound to at least one carbohydrate unit. (inferred from compound structure)
Structure
Thumb
MOLSDFPDBSMILESInChI
Synonyms:Not Available
Chemical Formula:C100H182N2O38P2
Weight:Average: 2082.4532
Monoisotopic: 2081.184582494
InChI Key:GUGOELZTMNFFOJ-RLUYZOBBSA-N
InChI:InChI=1S/C100H182N2O38P2/c1-6-11-16-21-26-31-32-33-34-39-44-49-54-59-82(113)131-73(58-53-48-43-38-30-25-20-15-10-5)63-81(112)102-86-94(135-84(115)62-72(107)57-52-47-42-37-29-24-19-14-9-4)92(139-141(123,124)125)79(69-130-99(97(119)120)65-77(88(117)91(137-99)76(110)67-104)136-100(98(121)122)64-74(108)87(116)90(138-100)75(109)66-103)133-95(86)129-68-78-89(118)93(134-83(114)61-71(106)56-51-46-41-36-28-23-18-13-8-3)85(96(132-78)140-142(126,127)128)101-80(111)60-70(105)55-50-45-40-35-27-22-17-12-7-2/h31-32,70-79,85-96,103-110,116-118H,6-30,33-69H2,1-5H3,(H,101,111)(H,102,112)(H,119,120)(H,121,122)(H2,123,124,125)(H2,126,127,128)/t70-,71-,72-,73-,74-,75-,76-,77-,78-,79-,85-,86-,87-,88-,89-,90-,91-,92-,93-,94-,95-,96-,99-,100-/m1/s1
CAS number:Not Available
IUPAC Name:(2R,4R,5R,6R)-4-{[(2R,4R,5R,6R)-2-carboxy-6-[(1R)-1,2-dihydroxyethyl]-4,5-dihydroxyoxan-2-yl]oxy}-6-[(1R)-1,2-dihydroxyethyl]-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-(hexadec-9-enoyloxy)-1-hydroxytetradecylidene]amino}-4-{[(3R)-3-hydroxytetradecanoyl]oxy}-3-(phosphonooxy)oxan-2-yl]methoxy}-5-hydroxyoxane-2-carboxylic acid
Traditional IUPAC Name:(2R,4R,5R,6R)-4-{[(2R,4R,5R,6R)-2-carboxy-6-[(1R)-1,2-dihydroxyethyl]-4,5-dihydroxyoxan-2-yl]oxy}-6-[(1R)-1,2-dihydroxyethyl]-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-(hexadec-9-enoyloxy)-1-hydroxytetradecylidene]amino}-4-{[(3R)-3-hydroxytetradecanoyl]oxy}-3-(phosphonooxy)oxan-2-yl]methoxy}-5-hydroxyoxane-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(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])(O)CCCCCCCCCCC)[C@@]2([H])N=C(O)C[C@@]([H])(CCCCCCCCCCC)OC(=O)CCCCCCCC=CCCCCCC)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.
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
  • C-glucuronide
  • 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
  • Organic 1,3-dipolar compound
  • Propargyl-type 1,3-dipolar organic compound
  • 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
  • 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 Solubility0.037 g/LALOGPS
logP3.82ALOGPS
logP18.03ChemAxon
logS-4.8ALOGPS
pKa (Strongest Acidic)0.55ChemAxon
Physiological Charge-5ChemAxon
Hydrogen Acceptor Count35ChemAxon
Hydrogen Donor Count19ChemAxon
Polar Surface Area639.34 ŲChemAxon
Rotatable Bond Count87ChemAxon
Refractivity519.77 m³·mol⁻¹ChemAxon
Polarizability229.88 ųChemAxon
Number of Rings4ChemAxon
Bioavailability0ChemAxon
Rule of FiveYesChemAxon
Ghose FilterYesChemAxon
Veber's RuleYesChemAxon
MDDR-like RuleYesChemAxon
Biological Properties
Cellular Locations:Membrane
Reactions:
a-Kdo-(2->4)-a-Kdo-(2->6)-lipid IVA + a palmitoleoyl-[acp]  > KDO2-(palmitoleoyl)-lipid IVA + a holo-[acyl-carrier protein]
KDO2-(palmitoleoyl)-lipid IVA + myristoyl-[acp] > KDO2-lipid A, cold adapted + a holo-[acyl-carrier protein]
SMPDB Pathways:
lipopolysaccharide biosynthesis IIIPW002059 ThumbThumb?image type=greyscaleThumb?image type=simple
KEGG Pathways:Not Available
EcoCyc Pathways:
Concentrations
Not Available
Spectra
Spectra:
Spectrum TypeDescriptionSplash Key
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, PositiveNot AvailableView in JSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, PositiveNot AvailableView in JSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, PositiveNot AvailableView in JSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, NegativeNot AvailableView in JSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, NegativeNot AvailableView in JSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, NegativeNot AvailableView in JSpectraViewer
References
References:
  • 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
  • van der Werf, M. J., Overkamp, K. M., Muilwijk, B., Coulier, L., Hankemeier, T. (2007). "Microbial metabolomics: toward a platform with full metabolome coverage." Anal Biochem 370:17-25. Pubmed: 17765195
  • Winder, C. L., Dunn, W. B., Schuler, S., Broadhurst, D., Jarvis, R., Stephens, G. M., Goodacre, R. (2008). "Global metabolic profiling of Escherichia coli cultures: an evaluation of methods for quenching and extraction of intracellular metabolites." Anal Chem 80:2939-2948. Pubmed: 18331064
Synthesis Reference:Not Available
Material Safety Data Sheet (MSDS)Not Available
External Links:
ResourceLink
CHEBI IDNot Available
HMDB IDNot Available
Pubchem Compound ID25203723
Kegg IDNot Available
ChemSpider IDNot Available
Wikipedia IDNot Available
BioCyc IDKDO2-PALMITOLEOYL-LIPID-IVA
EcoCyc IDKDO2-PALMITOLEOYL-LIPID-IVA

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. Protein ddg
General function:
Involved in transferase activity, transferring acyl groups
Specific function:
Specific function unknown
Gene Name:
ddg
Uniprot ID:
P0ACV2
Molecular weight:
35493
Protein Details
3. Protein crcA
General function:
Not Available
Specific function:
Not known; overproduction leads to camphor resistance and chromosome condensation
Gene Name:
crcA
Uniprot ID:
P37001
Molecular weight:
21770