N-acetyl-D-glucosaminyldiphosphodolichol (YMDB00934)

Identification
YMDB IDYMDB00934
NameN-acetyl-D-glucosaminyldiphosphodolichol
SpeciesSaccharomyces cerevisiae
StrainBaker's yeast
DescriptionN-acetyl-D-glucosaminyldiphosphodolichol belongs to the class of organic compounds known as polyprenyl phospho carbohydrates. These are polyprenyl phosphates with a carbohydrate moiety attached to it. N-acetyl-D-glucosaminyldiphosphodolichol is an extremely weak basic (essentially neutral) compound (based on its pKa).
Structure
Thumb
MOLSDFPDBSMILESInChI
Synonyms
  • N-Acetyl-D-glucosaminyl-diphosphodolichol
CAS numberNot Available
WeightAverage: 1745.5239
Monoisotopic: 1744.290253221
InChI KeyNCKLCSDHQCYXQT-NFNHYLGRSA-N
InChIInChI=1S/C108H179NO12P2/c1-83(2)42-23-43-84(3)44-24-45-85(4)46-25-47-86(5)48-26-49-87(6)50-27-51-88(7)52-28-53-89(8)54-29-55-90(9)56-30-57-91(10)58-31-59-92(11)60-32-61-93(12)62-33-63-94(13)64-34-65-95(14)66-35-67-96(15)68-36-69-97(16)70-37-71-98(17)72-38-73-99(18)74-39-75-100(19)76-40-77-101(20)78-41-79-102(21)80-81-118-122(114,115)121-123(116,117)120-108-105(109-103(22)111)107(113)106(112)104(82-110)119-108/h42,44,46,48,50,52,54,56,58,60,62,64,66,68,70,72,74,76,78,102,104-108,110,112-113H,23-41,43,45,47,49,51,53,55,57,59,61,63,65,67,69,71,73,75,77,79-82H2,1-22H3,(H,109,111)(H,114,115)(H,116,117)/b84-44+,85-46+,86-48+,87-50+,88-52-,89-54+,90-56+,91-58+,92-60+,93-62+,94-64+,95-66+,96-68+,97-70-,98-72+,99-74+,100-76+,101-78+/t102?,104-,105-,106-,107-,108-/m1/s1
IUPAC Name{[(2R,3R,4R,5S,6R)-3-acetamido-4,5-dihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}({[hydroxy({[(6E,10E,14E,18E,22Z,26E,30E,34E,38E,42E,46E,50E,54E,58Z,62E,66E,70E,74E)-3,7,11,15,19,23,27,31,35,39,43,47,51,55,59,63,67,71,75,79-icosamethyloctaconta-6,10,14,18,22,26,30,34,38,42,46,50,54,58,62,66,70,74,78-nonadecaen-1-yl]oxy})phosphoryl]oxy})phosphinic acid
Traditional IUPAC Name[(2R,3R,4R,5S,6R)-3-acetamido-4,5-dihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy({hydroxy[(6E,10E,14E,18E,22Z,26E,30E,34E,38E,42E,46E,50E,54E,58Z,62E,66E,70E,74E)-3,7,11,15,19,23,27,31,35,39,43,47,51,55,59,63,67,71,75,79-icosamethyloctaconta-6,10,14,18,22,26,30,34,38,42,46,50,54,58,62,66,70,74,78-nonadecaen-1-yl]oxyphosphoryl}oxy)phosphinic acid
Chemical FormulaC108H179NO12P2
SMILESOC[C@H]1O[C@H](OP(O)(=O)OP(O)(=O)OCCC(C)CC\C=C(/C)CC\C=C(/C)CC\C=C(/C)CC\C=C(/C)CC\C=C(\C)CC\C=C(/C)CC\C=C(/C)CC\C=C(/C)CC\C=C(/C)CC\C=C(/C)CC\C=C(/C)CC\C=C(/C)CC\C=C(/C)CC\C=C(\C)CC\C=C(/C)CC\C=C(/C)CC\C=C(/C)CC\C=C(/C)CCC=C(C)C)[C@H](NC(=O)C)[C@@H](O)[C@@H]1O
Chemical Taxonomy
Description belongs to the class of organic compounds known as polyprenyl phospho carbohydrates. These are polyprenyl phosphates with a carbohydrate moiety attached to it.
KingdomOrganic compounds
Super ClassLipids and lipid-like molecules
ClassPrenol lipids
Sub ClassPolyprenols
Direct ParentPolyprenyl phospho carbohydrates
Alternative Parents
Substituents
  • Polyterpenoid
  • Polyprenyl phospho carbohydrate
  • Dolichyl diphosphate
  • Polyprenyl monophosphate
  • Polyprenyl phosphate skeleton
  • N-acyl-alpha-hexosamine
  • Hexose monosaccharide
  • Organic pyrophosphate
  • Monosaccharide phosphate
  • Monoalkyl phosphate
  • Alkyl phosphate
  • Phosphoric acid ester
  • Oxane
  • Organic phosphoric acid derivative
  • Monosaccharide
  • Acetamide
  • Secondary carboxylic acid amide
  • Secondary alcohol
  • Carboxamide group
  • Oxacycle
  • Organoheterocyclic compound
  • Carboxylic acid derivative
  • 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
StateSolid
Charge0
Melting pointNot Available
Experimental Properties
PropertyValueReference
Water SolubilityNot AvailablePhysProp
LogPNot AvailablePhysProp
Predicted Properties
PropertyValueSource
Water Solubility0.00066 g/LALOGPS
logP9ALOGPS
logP29.76ChemAxon
logS-6.4ALOGPS
pKa (Strongest Acidic)1.75ChemAxon
pKa (Strongest Basic)-0.78ChemAxon
Physiological Charge-2ChemAxon
Hydrogen Acceptor Count9ChemAxon
Hydrogen Donor Count6ChemAxon
Polar Surface Area201.31 ŲChemAxon
Rotatable Bond Count67ChemAxon
Refractivity543.92 m³·mol⁻¹ChemAxon
Polarizability217.68 ųChemAxon
Number of Rings1ChemAxon
Bioavailability0ChemAxon
Rule of FiveYesChemAxon
Ghose FilterYesChemAxon
Veber's RuleYesChemAxon
MDDR-like RuleYesChemAxon
Biological Properties
Cellular LocationsNot Available
Organoleptic PropertiesNot Available
SMPDB PathwaysNot Available
KEGG PathwaysNot Available
SMPDB ReactionsNot Available
KEGG ReactionsNot Available
Concentrations
Intracellular ConcentrationsNot Available
Extracellular ConcentrationsNot Available
Spectra
Spectra
Spectrum TypeDescriptionSplash KeyView
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Negativesplash10-0076-9310062300-28dc19222675aae28629JSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Negativesplash10-08i0-9516020100-bc4bb4f9518437fc8fc6JSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Negativesplash10-0a4l-5900000000-90c2b85ed308702732b7JSpectraViewer
MSMass Spectrum (Electron Ionization)Not AvailableJSpectraViewer
References
References:
  • UniProt Consortium (2011). "Ongoing and future developments at the Universal Protein Resource." Nucleic Acids Res 39:D214-D219.21051339
  • Scheer, M., Grote, A., Chang, A., Schomburg, I., Munaretto, C., Rother, M., Sohngen, C., Stelzer, M., Thiele, J., Schomburg, D. (2011). "BRENDA, the enzyme information system in 2011." Nucleic Acids Res 39:D670-D676.21062828
  • Sharma, C. B., Lehle, L., Tanner, W. (1982). "Solubilization and characterization of the initial enzymes of the dolichol pathway from yeast." Eur J Biochem 126:319-325.6215245
  • Kukuruzinska, M. A., Lennon, K. (1995). "Diminished activity of the first N-glycosylation enzyme, dolichol-P-dependent N-acetylglucosamine-1-P transferase (GPT), gives rise to mutant phenotypes in yeast." Biochim Biophys Acta 1247:51-59.7873591
Synthesis Reference:Not Available
External Links:
ResourceLink
CHEBI ID18278
HMDB IDHMDB01445
Pubchem Compound ID440363
Kegg IDC04500
ChemSpider IDNot Available
FOODB IDNot Available
Wikipedia IDNot Available
BioCyc IDNot Available

Enzymes

Protein Details
1. UDP-N-acetylglucosamine--dolichyl-phosphate N-acetylglucosaminephosphotransferase
General function:
Involved in phospho-N-acetylmuramoyl-pentapeptide-transferase activity
Specific function:
Catalyzes the initial step in the synthesis of dolichol- P-P-oligosaccharides
Gene Name:
ALG7
Uniprot ID:
P07286
Molecular weight:
50367.39844
Reactions
UDP-N-acetyl-D-glucosamine + dolichyl phosphate → UMP + N-acetyl-D-glucosaminyl-diphosphodolichol.
Protein Details
2. UDP-N-acetylglucosamine transferase subunit ALG13
General function:
Involved in transferase activity, transferring hexosyl groups
Specific function:
Involved in protein N-glycosylation. Essential for the second step of the dolichol-linked oligosaccharide pathway
Gene Name:
ALG13
Uniprot ID:
P53178
Molecular weight:
22660.90039
Reactions
UDP-N-acetyl-D-glucosamine + N-acetyl-D-glucosaminyl-diphosphodolichol → UDP + N,N'-diacetylchitobiosyl-diphosphodolichol.