Heptosyl-KDO2-lipid A (ECMDB20526) (M2MDB001334)

IdentificationTaxonomyPhysical PropertiesBiological PropertiesSpectraConcentrationsLinksReferencesEnzymes (2)XML
Proteins (2)
Record Information
Version2.0
Creation Date2012-05-31 14:49:03 -0600
Update Date2015-09-17 15:42:04 -0600
Secondary Accession Numbers
  • ECMDB20526
Identification
Name:Heptosyl-KDO2-lipid A
DescriptionHeptosyl-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:Not Available
Chemical Formula:C117H208N2O45P2
Weight:Average: 2424.871
Monoisotopic: 2423.355728081
InChI Key:HPDZKCJEWNZSML-YOZKHJKSSA-H
InChI:InChI=1S/C117H214N2O45P2/c1-7-13-19-25-31-37-38-44-50-56-62-68-94(132)153-83(66-60-54-48-42-35-29-23-17-11-5)72-96(134)157-110-98(119-92(130)71-82(65-59-53-47-41-34-28-22-16-10-4)152-93(131)67-61-55-49-43-36-30-24-18-12-6)111(150-78-89-100(136)109(156-95(133)70-81(124)64-58-52-46-40-33-27-21-15-9-3)97(112(154-89)164-166(147,148)149)118-91(129)69-80(123)63-57-51-45-39-32-26-20-14-8-2)155-90(108(110)163-165(144,145)146)79-151-116(114(140)141)74-88(160-117(115(142)143)73-84(125)99(135)105(161-117)86(127)76-121)107(106(162-116)87(128)77-122)159-113-103(139)101(137)102(138)104(158-113)85(126)75-120/h80-90,97-113,120-128,135-139H,7-79H2,1-6H3,(H,118,129)(H,119,130)(H,140,141)(H,142,143)(H2,144,145,146)(H2,147,148,149)/p-6/t80-,81-,82-,83-,84-,85+,86-,87-,88-,89-,90-,97-,98-,99-,100-,101+,102+,103+,104-,105-,106-,107-,108-,109-,110-,111-,112-,113-,116-,117-/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,5S)-6-[(1S)-1,2-dihydroxyethyl]-3,4,5-trihydroxyoxan-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,5S)-6-[(1S)-1,2-dihydroxyethyl]-3,4,5-trihydroxyoxan-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@@]1(O[C@@](C[C@@H](O)[C@H]1O)(O[C@@H]1C[C@@](OC[C@H]2O[C@@H](OC[C@H]3O[C@H](OP([O-])([O-])=O)[C@H](NC(=O)C[C@H](O)CCCCCCCCCCC)[C@@H](OC(=O)C[C@H](O)CCCCCCCCCCC)[C@@H]3O)[C@H](NC(=O)C[C@@H](CCCCCCCCCCC)OC(=O)CCCCCCCCCCC)[C@@H](OC(=O)C[C@@H](CCCCCCCCCCC)OC(=O)CCCCCCCCCCCCC)[C@@H]2OP([O-])([O-])=O)(O[C@]([H])([C@H](O)CO)[C@@H]1O[C@H]1O[C@H]([C@@H](O)CO)[C@@H](O)[C@H](O)[C@@H]1O)C([O-])=O)C([O-])=O)[C@H](O)CO
Chemical Taxonomy
Description belongs to the class of organic compounds known as purine nucleosides. Purine nucleosides are compounds comprising a purine base attached to a ribosyl or deoxyribosyl moiety.
KingdomOrganic compounds
Super ClassNucleosides, nucleotides, and analogues
ClassPurine nucleosides
Sub ClassNot Available
Direct ParentPurine nucleosides
Alternative Parents
Substituents
  • Purine nucleoside
  • N-glycosyl compound
  • Glycosyl compound
  • Beta amino acid or derivatives
  • Pentose monosaccharide
  • 6-aminopurine
  • Purine
  • Imidazopyrimidine
  • Aminopyrimidine
  • Imidolactam
  • Pyrimidine
  • N-substituted imidazole
  • Monosaccharide
  • Heteroaromatic compound
  • Tetrahydrofuran
  • Organic sulfuric acid or derivatives
  • Imidazole
  • Azole
  • Amino acid
  • Secondary alcohol
  • Amino acid or derivatives
  • 1,2-diol
  • Oxacycle
  • Azacycle
  • Organoheterocyclic compound
  • Monocarboxylic acid or derivatives
  • Carboxylic acid
  • Carboxylic acid derivative
  • Organic nitrogen compound
  • Organic oxygen compound
  • Organopnictogen compound
  • Organic oxide
  • Hydrocarbon derivative
  • Primary amine
  • Organooxygen compound
  • Organonitrogen compound
  • Primary aliphatic amine
  • Carbonyl group
  • Amine
  • Alcohol
  • Organic anion
  • Aromatic heteropolycyclic compound
Molecular FrameworkAromatic heteropolycyclic compounds
External DescriptorsNot Available
Physical Properties
State:Not Available
Charge:-4
Melting point:Not Available
Experimental Properties:
PropertyValueSource
Predicted Properties
PropertyValueSource
Water Solubility0.076 g/LALOGPS
logP3.86ALOGPS
logP19.4ChemAxon
logS-4.5ALOGPS
pKa (Strongest Acidic)0.55ChemAxon
pKa (Strongest Basic)-4.7ChemAxon
Physiological Charge-4ChemAxon
Hydrogen Acceptor Count41ChemAxon
Hydrogen Donor Count23ChemAxon
Polar Surface Area747.95 ŲChemAxon
Rotatable Bond Count102ChemAxon
Refractivity604.1 m³·mol⁻¹ChemAxon
Polarizability272.27 ųChemAxon
Number of Rings5ChemAxon
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-D-manno-heptose > Hydrogen ion + Heptosyl2-KDO2-lipid A + ADP
Hydrogen ion + KDO2-Lipid A + ADP-L-Glycero-D-manno-heptose > Heptosyl-KDO2-lipid A + ADP
(KDO)2-lipid A + ADP-L-glycero-beta-D-manno-heptose > Hydrogen ion + Adenosine diphosphate + heptosyl-Kdo2-lipid A + ADP + Heptosyl-KDO2-lipid A
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
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:
Concentrations
Not Available
Spectra
Spectra:
Spectrum TypeDescriptionSplash Key
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Positivesplash10-03di-2282900001-0073f635f7daf31db22eView in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Positivesplash10-00l7-7750200903-0fce7bedd4915013696dView in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Positivesplash10-01x0-7862901615-754eefe62da988a243a1View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Negativesplash10-0jdi-6079803010-a2099f63797fe10637f3View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Negativesplash10-004i-9141100000-0975079ce641649dcb75View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Negativesplash10-004i-9100000000-8b25fc14a284800e5c63View in MoNA
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 ID25203480
Kegg IDNot Available
ChemSpider IDNot Available
Wikipedia IDNot Available
BioCyc IDCPD0-929
EcoCyc IDCPD0-929

Enzymes

Protein Details
1. 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
Protein Details
2. 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