Glucosyl-heptosyl2-KDO2-lipid A (ECMDB20528) (M2MDB001336)

IdentificationTaxonomyPhysical PropertiesBiological PropertiesSpectraConcentrationsLinksReferencesEnzymes (2)XML
Proteins (2)
Record Information
Version2.0
Creation Date2012-05-31 14:49:09 -0600
Update Date2015-06-03 17:20:09 -0600
Secondary Accession Numbers
  • ECMDB20528
Identification
Name:Glucosyl-heptosyl2-KDO2-lipid A
DescriptionGlucosyl-heptosyl2-kdo2-lipid a belongs to the class of Hexose Oligosaccharides. These are oligosaccharides in which the saccharide units are hexoses. (inferred from compound structure)
Structure
Thumb
MOLSDFPDBSMILESInChI
Synonyms:
ValueSource
(2R,4R,5R,6R)-4-{[6-(1,2-dihydroxyethyl)-2-(dihydroxymethyl)-4,5-dihydroxyoxan-2-yl]oxy}-6-[(1R)-1,2-dihydroxyethyl]-5-{[(3S,4S,5R)-6-[(1S)-1,2-dihydroxyethyl]-4-{[(3S,4S,5R)-6-[(1S)-1,2-dihydroxyethyl]-3,5-dihydroxy-4-{[3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}oxan-2-yl]oxy}-3,5-dihydroxyoxan-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}oxane-2-carboxylateGenerator
Chemical Formula:C130H238N2O56P2
Weight:Average: 2787.208
Monoisotopic: 2785.531247482
InChI Key:HDKHSFRFZFJRSI-MVTQOQRPSA-N
InChI:InChI=1S/C130H238N2O56P2/c1-7-13-19-25-31-37-38-44-50-56-62-68-98(148)173-85(66-60-54-48-42-35-29-23-17-11-5)72-100(150)178-119-102(132-96(146)71-84(65-59-53-47-41-34-28-22-16-10-4)172-97(147)67-61-55-49-43-36-30-24-18-12-6)122(170-80-93-105(153)118(177-99(149)70-83(139)64-58-52-46-40-33-27-21-15-9-3)101(123(175-93)188-190(167,168)169)131-95(145)69-82(138)63-57-51-45-39-32-26-20-14-8-2)176-94(117(119)187-189(164,165)166)81-171-129(127(160)161)74-91(184-130(128(162)163)73-86(140)103(151)114(185-130)89(143)77-135)116(115(186-129)90(144)78-136)181-125-110(158)121(109(157)112(179-125)87(141)75-133)183-126-111(159)120(108(156)113(180-126)88(142)76-134)182-124-107(155)106(154)104(152)92(79-137)174-124/h82-94,101-126,128,133-144,151-159,162-163H,7-81H2,1-6H3,(H,131,145)(H,132,146)(H,160,161)(H2,164,165,166)(H2,167,168,169)/t82-,83-,84-,85-,86?,87+,88+,89?,90-,91-,92?,93-,94-,101-,102-,103?,104?,105-,106?,107?,108-,109-,110+,111+,112?,113?,114?,115-,116-,117-,118-,119-,120+,121+,122-,123-,124?,125?,126?,129-,130?/m1/s1
CAS number:Not Available
IUPAC Name:(2R,4R,5R,6R)-4-{[6-(1,2-dihydroxyethyl)-2-(dihydroxymethyl)-4,5-dihydroxyoxan-2-yl]oxy}-6-[(1R)-1,2-dihydroxyethyl]-5-{[(3S,4S,5R)-6-[(1S)-1,2-dihydroxyethyl]-4-{[(3S,4S,5R)-6-[(1S)-1,2-dihydroxyethyl]-3,5-dihydroxy-4-{[3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}oxan-2-yl]oxy}-3,5-dihydroxyoxan-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}oxane-2-carboxylic acid
Traditional IUPAC Name:(2R,4R,5R,6R)-4-{[6-(1,2-dihydroxyethyl)-2-(dihydroxymethyl)-4,5-dihydroxyoxan-2-yl]oxy}-6-[(1R)-1,2-dihydroxyethyl]-5-{[(3S,4S,5R)-6-[(1S)-1,2-dihydroxyethyl]-4-{[(3S,4S,5R)-6-[(1S)-1,2-dihydroxyethyl]-3,5-dihydroxy-4-{[3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}oxan-2-yl]oxy}-3,5-dihydroxyoxan-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}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(C[C@@]([H])(OC4(CC([H])(O)C([H])(O)C([H])(O4)C([H])(O)CO)C(O)O)[C@@]([H])(OC4([H])OC([H])([C@@]([H])(O)CO)[C@@]([H])(O)[C@]([H])(OC5([H])OC([H])([C@@]([H])(O)CO)[C@@]([H])(O)[C@]([H])(OC6([H])OC([H])(CO)C([H])(O)C([H])(O)C6([H])O)[C@]5([H])O)[C@]4([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 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
  • Organic 1,3-dipolar compound
  • Propargyl-type 1,3-dipolar organic compound
  • Polyol
  • Carboxylic acid
  • Carboxylic acid derivative
  • Carboximidic acid derivative
  • Carboximidic acid
  • Carbonyl hydrate
  • 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:-4
Melting point:Not Available
Experimental Properties:
PropertyValueSource
Predicted Properties
PropertyValueSource
Water Solubility0.22 g/LALOGPS
logP3ALOGPS
logP15.23ChemAxon
logS-4.1ALOGPS
pKa (Strongest Acidic)0.55ChemAxon
pKa (Strongest Basic)-4.7ChemAxon
Physiological Charge-4ChemAxon
Hydrogen Acceptor Count52ChemAxon
Hydrogen Donor Count30ChemAxon
Polar Surface Area926.48 ŲChemAxon
Rotatable Bond Count109ChemAxon
Refractivity674.89 m³·mol⁻¹ChemAxon
Polarizability306.84 ųChemAxon
Number of Rings7ChemAxon
Bioavailability0ChemAxon
Rule of FiveYesChemAxon
Ghose FilterYesChemAxon
Veber's RuleYesChemAxon
MDDR-like RuleYesChemAxon
Biological Properties
Cellular Locations:Membrane
Reactions:
UDP-Glucose + Heptosyl2-KDO2-lipid A > Hydrogen ion + Glucosyl-heptosyl2-KDO2-lipid A + Uridine 5'-diphosphate
Glucosyl-heptosyl2-KDO2-lipid A + Adenosine triphosphate > Hydrogen ion + Glucosyl-heptosyl2-KDO2-lipid A-phosphate + ADP
SMPDB Pathways:
Lipopolysaccharide biosynthesisPW000831 ThumbThumb?image type=greyscaleThumb?image type=simple
KEGG Pathways:
  • Lipopolysaccharide biosynthesis ec00540
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:
  • 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
Synthesis Reference:Not Available
Material Safety Data Sheet (MSDS)Not Available
External Links:
ResourceLink
CHEBI IDNot Available
HMDB IDNot Available
Pubchem Compound ID25202907
Kegg IDNot Available
ChemSpider IDNot Available
Wikipedia IDNot Available
BioCyc IDCPD0-932
EcoCyc IDCPD0-932

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. Lipopolysaccharide core heptose(I) kinase rfaP
General function:
Involved in transferase activity, transferring phosphorus-containing groups
Specific function:
Catalyzes the phosphorylation of heptose(I) of the outer membrane lipopolysaccharide core
Gene Name:
rfaP
Uniprot ID:
P25741
Molecular weight:
30872