lipid II(A) (PAMDB003413)

IdentificationTaxonomyPhysical PropertiesBiological PropertiesSpectraConcentrationsLinksReferencesEnzymes Transporters
Proteins (3280)
Record Information
Version 1.0
Update Date 1/22/2018 11:54:54 AM
Metabolite IDPAMDB003413
Identification
Name: lipid II(A)
Description:Lipid II is a membrane-anchored cell-wall precursor that is essential for bacterial cell-wall biosynthesis. It is the target for at least four different classes of antibiotic, including the clinically important glycopeptide antibiotic vancomycin. Lipid II consists of one GlcNAc-MurNAc-pentapeptide subunit linked to a polyiosoprenoid anchor 11 subunits long via a pyrophosphate linker.
Structure
Thumb
🔍MOLSDFPDBSMILESInChIView Structure
Synonyms:
  • (2R,5R,8S,13R,16S,19R)-19-{(2R,3R,4R,5S,6R)-3-Acetamido-5-{(2R,3R,4R,5S,6R)-3-acetamido-4,5-dihydroxy-6-(hydroxymethyl)tetrahydro-2H-pyran-2-yloxy}-6-(hydroxymethyl)-2-({({(2Z,6Z,10Z,14Z,18Z,22Z,26Z,30Z,34E,38E)-3,7,11,15,19,23,27,31,35,39,43-undecamethyl-2,6,10,14,18,22,26,30,34,38,42-tetratetracontaundecaen-1-yloxy}phosphinato)oxyphosphinato}oxy)tetrahydro-2H-pyran-4-yloxy}-8-(4R)-4-ammonio-4-carboxylatobutyl-13-carboxylato-2,5,16-trimethyl-4,7,10,15,18-pentaoxo-3,6,9,14,17-pentaazaicosan-1-
  • (2R,6S)-6-(4R)-4-(2S)-2-(2R)-2-(2R,3S,4R,5R,6R)-5-acetamido-3-(2R,3R,4R,5S,6R)-3-acetamido-4,5-dihydroxy-6-(hydroxymethyl)oxan-2-yloxy-2-(hydroxymethyl)-6-oxido-oxido-(2Z,6Z,10Z,14Z,18Z,22Z,26Z,30Z,34E,38E)-3,7,11,15,19,23,27,31,35,39,43-undecamethyltetratetraconta-2,6,10,14,18,22,26,30,34,38,42-undecaenoxyphosphoryloxyphosphoryloxyoxan-4-yloxypropanoylaminopropanoylamino-4-carboxylatobutanoylamino-2-azaniumyl-7-(2R)-1-(1R)-1-carboxylatoethylamino-1-oxopropan-2-ylamino-7-oxoheptanoate
  • (2R,6S)-6-(4R)-4-(2S)-2-(2R)-2-(2R,3S,4R,5R,6R)-5-acetamido-3-(2R,3R,4R,5S,6R)-3-acetamido-4,5-Dihydroxy-6-(hydroxymethyl)oxan-2-yloxy-2-(hydroxymethyl)-6-oxido-oxido-(2Z,6Z,10Z,14Z,18Z,22Z,26Z,30Z,34E,38E)-3,7,11,15,19,23,27,31,35,39,43-undecamethyltetratetraconta-2,6,10,14,18,22,26,30,34,38,42-undecaenoxyphosphoryloxyphosphoryloxyoxan-4-yloxypropanoylaminopropanoylamino-4-carboxylatobutanoylamino-2-azaniumyl-7-(2R)-1-(1R)-1-carboxylatoethylamino-1-oxopropan-2-ylamino-7-oxoheptanoic acid
  • N-acetylmuramoyl-L-alanyl-D-glutamyl-meso-2,6-diaminopimelyl-D-alanyl-D-alanine-diphosphoundecaprenyl-N-acetylglucosamine
Chemical Formula: C95H152N8O28P2
Average Molecular Weight: 1916.2077
Monoisotopic Molecular Weight: 1915.019129344
InChI Key: OXJNZXDFVLDLEI-DYDCPVFNSA-J
InChI:InChI=1S/C95H156N8O28P2/c1-58(2)30-19-31-59(3)32-20-33-60(4)34-21-35-61(5)36-22-37-62(6)38-23-39-63(7)40-24-41-64(8)42-25-43-65(9)44-26-45-66(10)46-27-47-67(11)48-28-49-68(12)54-55-125-132(121,122)131-133(123,124)130-95-82(101-74(18)107)86(85(79(57-105)128-95)129-94-81(100-73(17)106)84(110)83(109)78(56-104)127-94)126-72(16)89(113)97-70(14)88(112)103-77(93(119)120)52-53-80(108)102-76(51-29-50-75(96)92(117)118)90(114)98-69(13)87(111)99-71(15)91(115)116/h30,32,34,36,38,40,42,44,46,48,54,69-72,75-79,81-86,94-95,104-105,109-110H,19-29,31,33,35,37,39,41,43,45,47,49-53,55-57,96H2,1-18H3,(H,97,113)(H,98,114)(H,99,111)(H,100,106)(H,101,107)(H,102,108)(H,103,112)(H,115,116)(H,117,118)(H,119,120)(H,121,122)(H,123,124)/p-4/b59-32+,60-34+,61-36-,62-38-,63-40-,64-42-,65-44-,66-46-,67-48-,68-54-/t69-,70+,71-,72-,75-,76+,77-,78-,79-,81-,82-,83-,84-,85-,86-,94-,95-/m1/s1
CAS number: Not Available
IUPAC Name:(4R)-N-[(1S,5R)-5-amino-5-carboxy-1-{[(1R)-1-{[(1R)-1-carboxyethyl]carboximidato}ethyl]-C-hydroxycarbonimidoyl}pentyl]-4-carboxy-4-{[(2S)-2-{[(2R)-2-{[(2R,3S,4R,5R,6R)-3-{[(2R,3R,4R,5S,6R)-4,5-dihydroxy-6-(hydroxymethyl)-3-[(1-oxidoethylidene)amino]oxan-2-yl]oxy}-6-{[hydroxy({[hydroxy({[(2Z,6Z,10Z,14Z,18Z,22Z,26Z,30Z,34E,38E)-3,7,11,15,19,23,27,31,35,39,43-undecamethyltetratetraconta-2,6,10,14,18,22,26,30,34,38,42-undecaen-1-yl]oxy})phosphoryl]oxy})phosphoryl]oxy}-2-(hydroxymethyl)-5-[(1-oxidoethylidene)amino]oxan-4-yl]oxy}-1-hydroxypropylidene]amino}-1-hydroxypropylidene]amino}butanecarboximidate
Traditional IUPAC Name: (4R)-N-[(1S,5R)-5-amino-5-carboxy-1-{[(1R)-1-{[(1R)-1-carboxyethyl]carboximidato}ethyl]-C-hydroxycarbonimidoyl}pentyl]-4-carboxy-4-{[(2S)-2-{[(2R)-2-{[(2R,3S,4R,5R,6R)-3-{[(2R,3R,4R,5S,6R)-4,5-dihydroxy-6-(hydroxymethyl)-3-[(1-oxidoethylidene)amino]oxan-2-yl]oxy}-6-{[hydroxy({hydroxy[(2Z,6Z,10Z,14Z,18Z,22Z,26Z,30Z,34E,38E)-3,7,11,15,19,23,27,31,35,39,43-undecamethyltetratetraconta-2,6,10,14,18,22,26,30,34,38,42-undecaen-1-yl]oxyphosphoryl}oxy)phosphoryl]oxy}-2-(hydroxymethyl)-5-[(1-oxidoethylidene)amino]oxan-4-yl]oxy}-1-hydroxypropylidene]amino}-1-hydroxypropylidene]amino}butanecarboximidate
SMILES:OC[C@@]1([H])O[C@]([H])(O[C@]2([H])[C@@]([H])(CO)O[C@]([H])(OP(O)(=O)OP(O)(=O)OC\C([H])=C(\C)CC\C([H])=C(\C)CC\C([H])=C(\C)CC\C([H])=C(\C)CC\C([H])=C(\C)CC\C([H])=C(\C)CC\C([H])=C(\C)CC\C([H])=C(\C)CC\C([H])=C(/C)CC\C([H])=C(/C)CCC=C(C)C)[C@]([H])(N=C(C)[O-])[C@@]2([H])O[C@@](C)([H])C(O)=N[C@](C)([H])C(O)=N[C@]([H])(CCC([O-])=N[C@@]([H])(CCC[C@](N)([H])C(=O)O)C(O)=N[C@@](C)([H])C([O-])=N[C@@](C)([H])C(=O)O)C(=O)O)[C@]([H])(N=C(C)[O-])[C@](O)([H])[C@@]1(O)[H]
Chemical Taxonomy
Taxonomy DescriptionThis compound belongs to the class of organic compounds known as polyprenyl phospho carbohydrates. These are polyprenyl phosphates with a carbohydrate moiety attached to it.
Kingdom Organic compounds
Super ClassLipids and lipid-like molecules
Class Prenol lipids
Sub ClassPolyprenols
Direct Parent Polyprenyl phospho carbohydrates
Alternative Parents
Substituents
  • Polyterpenoid
  • Bactoprenol diphosphate
  • Polyprenyl phospho carbohydrate
  • Alpha peptide
  • Saccharolipid
  • N-acyl-alpha-hexosamine
  • Disaccharide phosphate
  • N-acyl-aliphatic-alpha amino acid
  • N-acyl-alpha amino acid or derivatives
  • N-acyl-alpha-amino acid
  • Glucosamine
  • Amino sugar
  • O-glycosyl compound
  • Glycosyl compound
  • Disaccharide
  • L-alpha-amino acid
  • Organic pyrophosphate
  • Isoprenoid phosphate
  • Alpha-amino acid or derivatives
  • Alpha-amino acid
  • Tricarboxylic acid or derivatives
  • Monoalkyl phosphate
  • Amino saccharide
  • Amino fatty acid
  • Fatty acyl
  • Alkyl phosphate
  • Phosphoric acid ester
  • Oxane
  • Organic phosphoric acid derivative
  • Organic phosphate
  • Saccharide
  • Secondary alcohol
  • 1,2-diol
  • Oxacycle
  • Organoheterocyclic compound
  • Ether
  • Dialkyl ether
  • Carboxylic acid
  • Carboxylic acid derivative
  • Carboximidic acid derivative
  • Carboximidic acid
  • Acetal
  • Hydrocarbon derivative
  • Primary amine
  • Primary alcohol
  • Organooxygen compound
  • Organonitrogen compound
  • Primary aliphatic amine
  • Carbonyl group
  • Amine
  • Alcohol
  • Organic anion
  • Aliphatic heteromonocyclic compound
Molecular Framework Aliphatic heteromonocyclic compounds
External Descriptors Not Available
Physical Properties
State: Not Available
Charge:-3
Melting point: Not Available
Experimental Properties:
PropertyValueSource
Predicted Properties
PropertyValueSource
Water Solubility0.00349 mg/mLALOGPS
logP3.36ALOGPS
logP15.46ChemAxon
logS-5.8ALOGPS
pKa (Strongest Acidic)1.72ChemAxon
Physiological Charge-3ChemAxon
Hydrogen Acceptor Count33ChemAxon
Hydrogen Donor Count13ChemAxon
Polar Surface Area597.5 Å2ChemAxon
Rotatable Bond Count64ChemAxon
Refractivity555.51 m3·mol-1ChemAxon
Polarizability202.88 Å3ChemAxon
Number of Rings2ChemAxon
Bioavailability0ChemAxon
Rule of FiveYesChemAxon
Ghose FilterYesChemAxon
Veber's RuleYesChemAxon
MDDR-like RuleYesChemAxon
Biological Properties
Cellular Locations: Membrane
Reactions:
Undecaprenyl-diphospho-N-acetylmuramoyl-L-alanyl-D-glutamyl-meso-2,6-diaminopimeloyl-D-alanyl-D-alanine + Uridine diphosphate-N-acetylglucosamine + Undecaprenyl-diphospho-N-acetylmuramoyl-L-alanyl-D-glutamyl-meso-2,6-diaminopimeloyl-D-alanyl-D-alanine > Uridine 5'-diphosphate + Hydrogen ion + lipid II(A) + Uridine 5'-diphosphate
2 lipid II(A) > Undecaprenyl diphosphate + Hydrogen ion + a peptidoglycan dimer (meso-diaminopimelate containing)
Pathways: Not Available
Spectra
Spectra:
Spectrum TypeDescriptionSplash Key
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Positivesplash10-014j-0000000009-c8eacfb35aadf342f26dView in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Positivesplash10-0f7k-0000000009-6e76699821fa092d5934View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Positivesplash10-0007-9000000414-b8677c5b58dfaab4b0d4View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Negativesplash10-03km-6760000009-290090c6e3aef9477812View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Negativesplash10-0adi-7790000002-fc4b27f567f5f8462e5fView in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Negativesplash10-08pi-9410000000-d4bba6def638801601c9View 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 IDNot Available
Kegg IDNot Available
ChemSpider ID26332214
Wikipedia IDNot Available
BioCyc IDNot Available

Enzymes

Protein Details
• Penicillin-binding protein 1B
General function:
Involved in catalytic activity
Specific function:
Cell wall formation. Synthesis of cross-linked peptidoglycan from the lipid intermediates. The enzyme has a penicillin-insensitive transglycosylase N-terminal domain (formation of linear glycan strands) and a penicillin-sensitive transpeptidase C-terminal domain (cross-linking of the peptide subunits)
Gene Name:
mrcB
Locus Tag:
PA4700
Molecular weight:
85.5 kDa
Reactions
(GlcNAc-(1->4)-Mur2Ac(oyl-L-Ala-gamma-D-Glu-L-Lys-D-Ala-D-Ala))(n)-diphosphoundecaprenol + GlcNAc-(1->4)-Mur2Ac(oyl-L-Ala-gamma-D-Glu-L-Lys-D-Ala-D-Ala)-diphosphoundecaprenol = (GlcNAc-(1->4)-Mur2Ac(oyl-L-Ala-gamma-D-Glu-L-Lys-D-Ala-D-Ala))(n+1)-diphosphoundecaprenol + undecaprenyl diphosphate.
Protein Details
• UDP-N-acetylglucosamine--N-acetylmuramyl-(pentapeptide) pyrophosphoryl-undecaprenol N-acetylglucosamine transferase
General function:
Involved in undecaprenyldiphospho-muramoylpentapeptide beta-N-acetylglucosaminyltransferase activity
Specific function:
Cell wall formation. Catalyzes the transfer of a GlcNAc subunit on undecaprenyl-pyrophosphoryl-MurNAc-pentapeptide (lipid intermediate I) to form undecaprenyl-pyrophosphoryl-MurNAc- (pentapeptide)GlcNAc (lipid intermediate II)
Gene Name:
murG
Locus Tag:
PA4412
Molecular weight:
37.8 kDa
Reactions
UDP-N-acetylglucosamine + Mur2Ac(oyl-L-Ala-gamma-D-Glu-L-Lys-D-Ala-D-Ala)-diphosphoundecaprenol = UDP + GlcNAc-(1->4)-Mur2Ac(oyl-L-Ala-gamma-D-Glu-L-Lys-D-Ala-D-Ala)-diphosphoundecaprenol.
Protein Details
• Undecaprenyl phosphate-alpha-4-amino-4-deoxy-L-arabinose arabinosyl transferase
General function:
Involved in transferase activity, transferring pentosyl groups
Specific function:
Catalyzes the transfer of the L-Ara4N moiety of the glycolipid undecaprenyl phosphate-alpha-L-Ara4N to lipid A. The modified arabinose is attached to lipid A and is required for resistance to polymyxin and cationic antimicrobial peptides
Gene Name:
arnT
Locus Tag:
PA3556
Molecular weight:
61.7 kDa
Reactions
4-amino-4-deoxy-alpha-L-arabinopyranosyl di-trans,octa-cis-undecaprenyl phosphate + lipid IV(A) = lipid II(A) + di-trans,octa-cis-undecaprenyl phosphate.
Protein Details
• Penicillin-binding protein 1C
General function:
Involved in catalytic activity
Specific function:
Cell wall formation. The enzyme has a penicillin- insensitive transglycosylase N-terminal domain (formation of linear glycan strands) and a transpeptidase C-terminal domain which may not be functional
Gene Name:
pbpC
Locus Tag:
PA2272
Molecular weight:
61.1 kDa