a-Kdo-(2->4)-a-Kdo-(2->6)-lipid IVA (ECMDB24178) (M2MDB006295)

IdentificationTaxonomyPhysical PropertiesBiological PropertiesSpectraConcentrationsLinksReferencesEnzymes (4)XML
Proteins (4)
Record Information
Version2.0
Creation Date2015-09-08 17:49:54 -0600
Update Date2015-09-14 16:46:29 -0600
Secondary Accession Numbers
  • ECMDB24178
Identification
Name:a-Kdo-(2->4)-a-Kdo-(2->6)-lipid IVA
Descriptionalpha-Kdo-(2->4)-alpha-Kdo-(2->6)-lipid IVA is an intermediate in (Kdo)2-lipid A biosynthesis I pathway in E.coli. It is a substrate for the enzyme lauroyl acyltransferase which catalyzes the reaction a dodecanoyl-[acp] + alpha-Kdo-(2->4)-alpha-Kdo-(2->6)-lipid IVA -> alpha-Kdo-(2->4)-alpha-Kdo-(2->6)-(lauroyl)-lipid IVA + a holo-[acyl-carrier protein]. It is also a intermediate in superpathway of (Kdo)2-lipid A biosynthesis (BioCyc compound: KDO2-LIPID-IVA) .
Structure
Thumb
MOLSDFPDBSMILESInChI
Synonyms:Not Available
Chemical Formula:C84H148N2O37P2
Weight:Average: 1840.036
Monoisotopic: 1838.926909189
InChI Key:XAOLJGCZESYRFT-UHFFFAOYSA-H
InChI:InChI=1S/C84H154N2O37P2/c1-5-9-13-17-21-25-29-33-37-41-55(89)45-65(96)85-69-77(117-67(98)47-57(91)43-39-35-31-27-23-19-15-11-7-3)73(102)63(115-80(69)123-125(110,111)112)53-113-79-70(86-66(97)46-56(90)42-38-34-30-26-22-18-14-10-6-2)78(118-68(99)48-58(92)44-40-36-32-28-24-20-16-12-8-4)76(122-124(107,108)109)64(116-79)54-114-83(81(103)104)50-62(72(101)75(120-83)61(95)52-88)119-84(82(105)106)49-59(93)71(100)74(121-84)60(94)51-87/h55-64,69-80,87-95,100-102H,5-54H2,1-4H3,(H,85,96)(H,86,97)(H,103,104)(H,105,106)(H2,107,108,109)(H2,110,111,112)/p-6
CAS number:Not Available
IUPAC Name:4-{[2-carboxylato-6-(1,2-dihydroxyethyl)-4,5-dihydroxyoxan-2-yl]oxy}-6-(1,2-dihydroxyethyl)-5-hydroxy-2-[(6-{[3-hydroxy-5-(3-hydroxytetradecanamido)-4-[(3-hydroxytetradecanoyl)oxy]-6-(phosphonatooxy)oxan-2-yl]methoxy}-5-(3-hydroxytetradecanamido)-4-[(3-hydroxytetradecanoyl)oxy]-3-(phosphonatooxy)oxan-2-yl)methoxy]oxane-2-carboxylate
Traditional IUPAC Name:4-{[2-carboxylato-6-(1,2-dihydroxyethyl)-4,5-dihydroxyoxan-2-yl]oxy}-6-(1,2-dihydroxyethyl)-5-hydroxy-2-[(6-{[3-hydroxy-5-(3-hydroxytetradecanamido)-4-[(3-hydroxytetradecanoyl)oxy]-6-(phosphonatooxy)oxan-2-yl]methoxy}-5-(3-hydroxytetradecanamido)-4-[(3-hydroxytetradecanoyl)oxy]-3-(phosphonatooxy)oxan-2-yl)methoxy]oxane-2-carboxylate
SMILES:CCCCCCCCCCCC(O)CC(=O)NC1C(OP([O-])([O-])=O)OC(COC2OC(COC3(CC(OC4(CC(O)C(O)C(O4)C(O)CO)C([O-])=O)C(O)C(O3)C(O)CO)C([O-])=O)C(OP([O-])([O-])=O)C(OC(=O)CC(O)CCCCCCCCCCC)C2NC(=O)CC(O)CCCCCCCCCCC)C(O)C1OC(=O)CC(O)CCCCCCCCCCC
Chemical Taxonomy
Description belongs to the class of organic compounds known as 6-alkylaminopurines. 6-alkylaminopurines are compounds that contain an alkylamine group attached at the 6-position of a purine. Purine is a bicyclic aromatic compound made up of a pyrimidine ring fused to an imidazole ring.
KingdomOrganic compounds
Super ClassOrganoheterocyclic compounds
ClassImidazopyrimidines
Sub ClassPurines and purine derivatives
Direct Parent6-alkylaminopurines
Alternative Parents
Substituents
  • 6-alkylaminopurine
  • Benzylamine
  • Aminopyrimidine
  • Secondary aliphatic/aromatic amine
  • Monocyclic benzene moiety
  • Pyrimidine
  • Benzenoid
  • Imidolactam
  • Imidazole
  • Heteroaromatic compound
  • Azole
  • Secondary amine
  • Azacycle
  • Hydrocarbon derivative
  • Organic nitrogen compound
  • Organonitrogen compound
  • Organopnictogen compound
  • Amine
  • Aromatic heteropolycyclic compound
Molecular FrameworkAromatic heteropolycyclic compounds
External Descriptors
Physical Properties
State:Not Available
Charge:-6
Melting point:Not Available
Experimental Properties:
PropertyValueSource
Predicted Properties
PropertyValueSource
Water Solubility0.093 g/LALOGPS
logP3.17ALOGPS
logP9.83ChemAxon
logS-4.3ALOGPS
pKa (Strongest Acidic)0.6ChemAxon
Physiological Charge-6ChemAxon
Hydrogen Acceptor Count33ChemAxon
Hydrogen Donor Count14ChemAxon
Polar Surface Area643.27 ŲChemAxon
Rotatable Bond Count72ChemAxon
Refractivity461.2 m³·mol⁻¹ChemAxon
Polarizability198.74 ųChemAxon
Number of Rings4ChemAxon
Bioavailability0ChemAxon
Rule of FiveYesChemAxon
Ghose FilterYesChemAxon
Veber's RuleYesChemAxon
MDDR-like RuleYesChemAxon
Biological Properties
Cellular Locations:Membrane
Reactions:
alpha-Kdo-(2→6)-lipid IVA + CMP-3-Deoxy-D-manno-octulosonate > Cytidine monophosphate + Hydrogen ion + a-Kdo-(2->4)-a-Kdo-(2->6)-lipid IVA + Cytidine monophosphate + a-Kdo-(2->4)-a-Kdo-(2->6)-lipid IVA
a-Kdo-(2->4)-a-Kdo-(2->6)-lipid IVA + dodecanoyl-[acp]  + a-Kdo-(2->4)-a-Kdo-(2->6)-lipid IVA > Lauroyl-KDO2-lipid IV(A) + a holo-[acyl-carrier protein]
a-Kdo-(2->4)-a-Kdo-(2->6)-lipid IVA + PE(12:0/10:0) + a-Kdo-(2->4)-a-Kdo-(2->6)-lipid IVA > 1,2-Diacyl-sn-glycerol (didodecanoyl, n-C12:0) + phosphoethanolamine-Kdo2-lipid A + Phosphoethanolamine KDO(2)-lipid (A)
PE(16:0/16:0) + a-Kdo-(2->4)-a-Kdo-(2->6)-lipid IVA + a-Kdo-(2->4)-a-Kdo-(2->6)-lipid IVA > phosphoethanolamine-Kdo2-lipid A + 1,2-dihexadecanoyl-rac-glycerol + Phosphoethanolamine KDO(2)-lipid (A)
a-Kdo-(2->4)-a-Kdo-(2->6)-lipid IVA + a palmitoleoyl-[acp]  > KDO2-(palmitoleoyl)-lipid IVA + a holo-[acyl-carrier protein]
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:
Spectrum TypeDescriptionSplash Key
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Positivesplash10-000f-0000000090-8a7d9022617b80a2b875View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Positivesplash10-004i-1100000090-797c4db9457d87df826dView in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Positivesplash10-0596-9340000120-1461aa4efbef7d039b61View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Negativesplash10-000f-3030000090-3112b8ef03d5d44a7b3aView in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Negativesplash10-0ukc-9742000030-785ce5d9cbacbe538508View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Negativesplash10-06xx-9551000000-d01bd711c23f6a8317c5View in MoNA
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 ID74414042
Kegg IDNot Available
ChemSpider IDNot Available
Wikipedia IDNot Available
BioCyc IDNot Available

Enzymes

Protein Details
1. 3-deoxy-D-manno-octulosonic-acid transferase
General function:
Involved in biosynthetic process
Specific function:
Essential step in lipopolysaccharides biosynthesis. Acts at transfer of 3-deoxy-D-mono octulonic acid (KDO) from CMP-KDO to a tetraacyldisaccharide 1,4'-bisphosphate precursor of lipid A (lipid IVA). Transfers two molecules of KDO to lipid IVA. Degraded by FtsH; therefore FtsH regulates the addition of the sugar moiety of the LPS and thus the maturation of the LPS precursor
Gene Name:
waaA
Uniprot ID:
P0AC75
Molecular weight:
47291
Protein Details
2. Lipid A biosynthesis lauroyl acyltransferase
General function:
Involved in transferase activity, transferring acyl groups
Specific function:
Acylates the intermediate (KDO)2-lipid IVA to form (KDO)2-(lauroyl)-lipid IVA. Has 10 fold selectivity for lauroyl- ACP over myristoyl-ACP
Gene Name:
htrB
Uniprot ID:
P0ACV0
Molecular weight:
35407
Protein Details
3. Phosphoethanolamine transferase eptB
General function:
Involved in catalytic activity
Specific function:
Catalyzes the addition of a phosphoethanolamine (pEtN) moiety to the outer 3-deoxy-D-manno-octulosonic acid (KDO) residue of a KDO(2)-lipid A. Phosphatidylethanolamines with one unsaturated acyl group functions as pEtN donors and the reaction releases diacylglycerol
Gene Name:
eptB
Uniprot ID:
P37661
Molecular weight:
63804
Protein Details
4. 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