P. aeruginosa Metabolome Database: Heptosyl2-KDO2-lipid A (PAMDB001335)

Identification Taxonomy Physical Properties Biological Properties Spectra Concentrations Links References Enzymes Transporters

Proteins (3280)

Record Information

Version

1.0

Update Date

1/22/2018 12:54:54 PM

Metabolite ID

PAMDB001335

Identification

Name:

Heptosyl2-KDO2-lipid A

Description:

Heptosyl2-kdo2-lipid A is a component of lipopolysaccharide. Bacterial lipopolysaccharides (LPS) typically consist of a hydrophobic domain inserted into the outer membrane known as lipid A (or endotoxin), a phosphorylated "core" oligosaccharide and a distal polysaccharide (or O antigen). The core oligosaccharides are conceptually divided into two regions: inner core and outer core. The inner core is highly conserved, comprises three deoxy-D-manno-octulosonic acid (KDO) and L-glycero-D-manno-heptose (Hep) and is often phosphorylated. The inner core oligosaccharide plays a critical role in essential barrier function of the outer membrane. The outer core comprises a tri-hexose backbone modified with varying side-branch substitutions of hexose and acetamidohexose residues. The outer core provides an attachment site for O-antigen. The completed lipid A-KDO2 serves as the acceptor on which the core oligosaccharide chains are assembled by sequential glycosyl transfer from nucleotide sugar precursors. This process involves a co-ordinated complex of membrane-associated glycosyltransferases acting at the cytoplasmic face of the plasma membrane.

Structure

🔍MOL SDF PDB SMILES InChI View Structure

Synonyms:

(heptosyl)2-(KDO)2-lipid A
Heptosyl-heptosyl-kdo2-lipidA
Heptosyl2-KDO2-lipid A

Chemical Formula:

C₁₂₄H₂₂₈N₂O₅₁P₂

Average Molecular Weight:

2625.0674

Monoisotopic Molecular Weight:

2623.478424052

InChI Key:

MVLFKXQHQYOOOH-JMRRDJIDSA-N

InChI:

InChI=1S/C124H228N2O51P2/c1-7-13-19-25-31-37-38-44-50-56-62-68-96(141)164-84(66-60-54-48-42-35-29-23-17-11-5)72-98(143)168-115-100(126-94(139)71-83(65-59-53-47-41-34-28-22-16-10-4)163-95(140)67-61-55-49-43-36-30-24-18-12-6)117(161-79-91-102(145)114(167-97(142)70-82(132)64-58-52-46-40-33-27-21-15-9-3)99(118(165-91)177-179(158,159)160)125-93(138)69-81(131)63-57-51-45-39-32-26-20-14-8-2)166-92(113(115)176-178(155,156)157)80-162-123(121(151)152)74-90(173-124(122(153)154)73-85(133)101(144)110(174-124)88(136)77-129)112(111(175-123)89(137)78-130)171-120-107(150)116(106(149)109(170-120)87(135)76-128)172-119-105(148)103(146)104(147)108(169-119)86(134)75-127/h81-92,99-120,122,127-137,144-150,153-154H,7-80H2,1-6H3,(H,125,138)(H,126,139)(H,151,152)(H2,155,156,157)(H2,158,159,160)/t81-,82-,83-,84-,85?,86+,87+,88?,89-,90-,91-,92-,99-,100-,101?,102-,103+,104+,105+,106-,107+,108?,109?,110?,111-,112-,113-,114-,115-,116+,117-,118-,119?,120?,123-,124?/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,5S)-6-[(1S)-1,2-dihydroxyethyl]-3,4,5-trihydroxyoxan-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:

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])(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

Taxonomy Description

This compound belongs to the class of organic compounds known as n-acyl-alpha-hexosamines. These are carbohydrate derivatives containing a hexose moiety in which the oxygen atom is replaced by an n-acyl group.

Kingdom

Organic compounds

Super Class

Organooxygen compounds

Class

Carbohydrates and carbohydrate conjugates

Sub Class

Aminosaccharides

Direct Parent

N-acyl-alpha-hexosamines

Alternative Parents

Substituents

Oligosaccharide phosphate
Oligosaccharide
Saccharolipid
Fatty acyl glycoside
Pentacarboxylic acid or derivatives
N-acyl-alpha-hexosamine
C-glucuronide
Glucosamine
Alkyl glycoside
O-glycosyl compound
Glycosyl compound
C-glycosyl compound
Pyran carboxylic acid
Pyran carboxylic acid or derivatives
Monoalkyl phosphate
Fatty acid ester
Beta-hydroxy acid
Fatty acyl
Alkyl phosphate
Pyran
Phosphoric acid ester
Oxane
Organic phosphoric acid derivative
Organic phosphate
Hydroxy acid
Secondary alcohol
Polyol
Carboxylic acid ester
1,2-diol
Oxacycle
Organoheterocyclic compound
1,1-diol
Organic 1,3-dipolar compound
Propargyl-type 1,3-dipolar organic compound
Carboxylic acid
Carboxylic acid derivative
Carboximidic acid derivative
Carboximidic acid
Carbonyl hydrate
Acetal
Hydrocarbon derivative
Primary alcohol
Organonitrogen compound
Carbonyl group
Alcohol
Aliphatic heteromonocyclic compound

Molecular Framework

Aliphatic heteromonocyclic compounds

External Descriptors

Not Available

Physical Properties

State:

Not Available

Charge:

-4

Melting point:

Not Available

Experimental Properties:

Property	Value	Source

Predicted Properties

Property	Value	Source
Water Solubility	0.18 mg/mL	ALOGPS
logP	3.3	ALOGPS
logP	17	ChemAxon
logS	-4.2	ALOGPS
pKa (Strongest Acidic)	0.55	ChemAxon
pKa (Strongest Basic)	-4.7	ChemAxon
Physiological Charge	-4	ChemAxon
Hydrogen Acceptor Count	47	ChemAxon
Hydrogen Donor Count	27	ChemAxon
Polar Surface Area	847.33 Å²	ChemAxon
Rotatable Bond Count	106	ChemAxon
Refractivity	642.48 m³·mol^-1	ChemAxon
Polarizability	290.97 Å³	ChemAxon
Number of Rings	6	ChemAxon
Bioavailability	0	ChemAxon
Rule of Five	Yes	ChemAxon
Ghose Filter	Yes	ChemAxon
Veber's Rule	Yes	ChemAxon
MDDR-like Rule	Yes	ChemAxon

Biological Properties

Cellular Locations:

Membrane

Reactions:

Heptosyl-KDO2-lipid A + ADP-L-Glycero-D-manno-heptose > Hydrogen ion + Heptosyl2-KDO2-lipid A + ADP
UDP-Glucose + Heptosyl2-KDO2-lipid A > Hydrogen ion + Glucosyl-heptosyl2-KDO2-lipid A + Uridine 5'-diphosphate

Pathways:

Lipopolysaccharide biosynthesis pae00540

Spectra

Spectra:

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

Links

External Links:

Resource	Link
CHEBI ID	Not Available
HMDB ID	Not Available
Pubchem Compound ID	25202915
Kegg ID	Not Available
ChemSpider ID	Not Available
Wikipedia ID	Not Available
BioCyc ID	CPD0-930
EcoCyc ID	CPD0-930

Enzymes

Protein Details

• 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
Locus Tag:: PA5010
Molecular weight:: 42.2 kDa

Heptosyl2-KDO2-lipid A (PAMDB001335)

Structure for Heptosyl2-KDO2-lipid A (PAMDB001335)

Enzymes