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Record Information
Version5.0
StatusExpected but not Quantified
Creation Date2009-04-06 16:19:39 UTC
Update Date2022-03-07 02:51:21 UTC
HMDB IDHMDB0012126
Secondary Accession Numbers
  • HMDB12126
Metabolite Identification
Common Name(N-Acetylglucosaminyl)2-diphosphodolichol
Description(N-Acetylglucosaminyl)2-diphosphodolichol is a lipid-linked disaccharide that is an intermediate in dolichyl-diphosphooligosaccharide biosynthesis. The dolichyl-diphosphooligosaccharide biosynthesis pathway is of particular interest in humans, because defects in the glycosyltransferases involved lead to congenital disorders of glycosylation. The genetic analysis of this pathway in a model organism, the budding yeast Saccharomyces cerevisiae, has helped to elucidate the molecular basis of these disorders. Humanization of the N-glycosylation pathway in yeast may allow production of therapeutically useful glycoproteins. Humanization is necessary because N-glycosylation in yeast is of the high-mannose type, which would create a shorter glycoprotein half-life in humans. In this biosynthetic pathway, N-Acetylglucosaminyl)2-diphosphodolichol is a substrate for Chitobiosyldiphosphodolichol α-mannosyltransferase and formed from the enzymatic glycosylation of N-Acetylglucosaminyl-diphosphodolichol.
Structure
Data?1582753017
Synonyms
ValueSource
ChitobiosyldiphosphodolicholHMDB
N,N'-diacetylchitobiosyldiphosphodolicholHMDB
[N-Acetyl-b-D-glucosaminyl-(1->4)- N-acetyl-D-glucosaminyl]diphosphodolicholHMDB
[N-Acetyl-beta-D-glucosaminyl-(1->4)- N-acetyl-D-glucosaminyl]diphosphodolicholHMDB
[N-Acetyl-beta-delta-glucosaminyl-(1->4)- N-acetyl-delta-glucosaminyl]diphosphodolicholHMDB
Chemical FormulaC96H160N2O17P2
Average Molecular Weight1676.2483
Monoisotopic Molecular Weight1675.119224728
IUPAC Name{[(2S,3R,4R,5S,6R)-3-acetamido-5-{[(2S,3R,4R,5S,6R)-3-acetamido-4,5-dihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}-4-hydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}[({[(6E,10E,14E,18E,22E,26E,30E,34E,38E,42E,46E,50E,54E,58E)-3,7,11,15,19,23,27,31,35,39,43,47,51,55,59,63-hexadecamethyltetrahexaconta-6,10,14,18,22,26,30,34,38,42,46,50,54,58,62-pentadecaen-1-yl]oxy}(hydroxy)phosphoryl)oxy]phosphinic acid
Traditional Name[(2S,3R,4R,5S,6R)-3-acetamido-5-{[(2S,3R,4R,5S,6R)-3-acetamido-4,5-dihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}-4-hydroxy-6-(hydroxymethyl)oxan-2-yl]oxy({[(6E,10E,14E,18E,22E,26E,30E,34E,38E,42E,46E,50E,54E,58E)-3,7,11,15,19,23,27,31,35,39,43,47,51,55,59,63-hexadecamethyltetrahexaconta-6,10,14,18,22,26,30,34,38,42,46,50,54,58,62-pentadecaen-1-yl]oxy(hydroxy)phosphoryl}oxy)phosphinic acid
CAS Registry NumberNot Available
SMILES
OC[C@H]1O[C@@H](O[C@H]2[C@H](O)[C@@H](NC(C)=O)[C@@H](O[C@@H]2CO)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)CCC=C(C)C)[C@H](NC(C)=O)[C@@H](O)[C@@H]1O
InChI Identifier
InChI=1S/C96H160N2O17P2/c1-69(2)35-20-36-70(3)37-21-38-71(4)39-22-40-72(5)41-23-42-73(6)43-24-44-74(7)45-25-46-75(8)47-26-48-76(9)49-27-50-77(10)51-28-52-78(11)53-29-54-79(12)55-30-56-80(13)57-31-58-81(14)59-32-60-82(15)61-33-62-83(16)63-34-64-84(17)65-66-110-116(106,107)115-117(108,109)114-96-90(98-86(19)102)93(105)94(88(68-100)112-96)113-95-89(97-85(18)101)92(104)91(103)87(67-99)111-95/h35,37,39,41,43,45,47,49,51,53,55,57,59,61,63,84,87-96,99-100,103-105H,20-34,36,38,40,42,44,46,48,50,52,54,56,58,60,62,64-68H2,1-19H3,(H,97,101)(H,98,102)(H,106,107)(H,108,109)/b70-37+,71-39+,72-41+,73-43+,74-45+,75-47+,76-49+,77-51+,78-53+,79-55+,80-57+,81-59+,82-61+,83-63+/t84?,87-,88-,89-,90-,91-,92-,93-,94-,95+,96+/m1/s1
InChI KeyAGKFOAYTTMSUFA-AYIKJQCISA-N
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
  • Polyprenyl phospho oligosaccharide
  • Polyterpenoid
  • Polyprenyl phospho carbohydrate
  • Dolichyl diphosphate
  • Polyprenyl monophosphate
  • Polyprenyl phosphate skeleton
  • Disaccharide phosphate
  • N-acyl-alpha-hexosamine
  • O-glycosyl compound
  • Glycosyl compound
  • Disaccharide
  • Organic pyrophosphate
  • Monoalkyl phosphate
  • Organic phosphoric acid derivative
  • Alkyl phosphate
  • Oxane
  • Phosphoric acid ester
  • Acetamide
  • Secondary carboxylic acid amide
  • Secondary alcohol
  • Carboxamide group
  • Oxacycle
  • Organoheterocyclic compound
  • Carboxylic acid derivative
  • Acetal
  • Hydrocarbon derivative
  • Organonitrogen compound
  • Alcohol
  • Organooxygen compound
  • Organic nitrogen compound
  • Organic oxygen compound
  • Organopnictogen compound
  • Organic oxide
  • Carbonyl group
  • Primary alcohol
  • Aliphatic heteromonocyclic compound
Molecular FrameworkAliphatic heteromonocyclic compounds
External DescriptorsNot Available
Ontology
Physiological effectNot Available
Disposition
Process
Role
Physical Properties
StateSolid
Experimental Molecular Properties
PropertyValueReference
Melting PointNot AvailableNot Available
Boiling PointNot AvailableNot Available
Water SolubilityNot AvailableNot Available
LogPNot AvailableNot Available
Experimental Chromatographic PropertiesNot Available
Predicted Molecular Properties
PropertyValueSource
Water Solubility0.0005 g/LALOGPS
logP8.4ALOGPS
logP21.06ChemAxon
logS-6.5ALOGPS
pKa (Strongest Acidic)1.74ChemAxon
pKa (Strongest Basic)-3ChemAxon
Physiological Charge-2ChemAxon
Hydrogen Acceptor Count14ChemAxon
Hydrogen Donor Count9ChemAxon
Polar Surface Area289.33 ŲChemAxon
Rotatable Bond Count59ChemAxon
Refractivity492.23 m³·mol⁻¹ChemAxon
Polarizability203.07 ųChemAxon
Number of Rings2ChemAxon
BioavailabilityNoChemAxon
Rule of FiveNoChemAxon
Ghose FilterNoChemAxon
Veber's RuleNoChemAxon
MDDR-like RuleNoChemAxon
Predicted Chromatographic Properties

Predicted Retention Times

Underivatized

Chromatographic MethodRetention TimeReference
Measured using a Waters Acquity ultraperformance liquid chromatography (UPLC) ethylene-bridged hybrid (BEH) C18 column (100 mm × 2.1 mm; 1.7 μmparticle diameter). Predicted by Afia on May 17, 2022. Predicted by Afia on May 17, 2022.-1.61 minutes32390414
Predicted by Siyang on May 30, 202242.4987 minutes33406817
Predicted by Siyang using ReTip algorithm on June 8, 20223.26 minutes32390414
AjsUoB = Accucore 150 Amide HILIC with 10mM Ammonium Formate, 0.1% Formic Acid189.8 seconds40023050
Fem_Long = Waters ACQUITY UPLC HSS T3 C18 with Water:MeOH and 0.1% Formic Acid10638.4 seconds40023050
Fem_Lipids = Ascentis Express C18 with (60:40 water:ACN):(90:10 IPA:ACN) and 10mM NH4COOH + 0.1% Formic Acid157.4 seconds40023050
Life_Old = Waters ACQUITY UPLC BEH C18 with Water:(20:80 acetone:ACN) and 0.1% Formic Acid548.3 seconds40023050
Life_New = RP Waters ACQUITY UPLC HSS T3 C18 with Water:(30:70 MeOH:ACN) and 0.1% Formic Acid211.3 seconds40023050
RIKEN = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid372.8 seconds40023050
Eawag_XBridgeC18 = XBridge C18 3.5u 2.1x50 mm with Water:MeOH and 0.1% Formic Acid2082.8 seconds40023050
BfG_NTS_RP1 =Agilent Zorbax Eclipse Plus C18 (2.1 mm x 150 mm, 3.5 um) with Water:ACN and 0.1% Formic Acid2043.9 seconds40023050
HILIC_BDD_2 = Merck SeQuant ZIC-HILIC with ACN(0.1% formic acid):water(16 mM ammonium formate)233.8 seconds40023050
UniToyama_Atlantis = RP Waters Atlantis T3 (2.1 x 150 mm, 5 um) with ACN:Water and 0.1% Formic Acid4387.6 seconds40023050
BDD_C18 = Hypersil Gold 1.9µm C18 with Water:ACN and 0.1% Formic Acid2082.6 seconds40023050
UFZ_Phenomenex = Kinetex Core-Shell C18 2.6 um, 3.0 x 100 mm, Phenomenex with Water:MeOH and 0.1% Formic Acid2275.6 seconds40023050
SNU_RIKEN_POS = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid1563.1 seconds40023050
RPMMFDA = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid968.8 seconds40023050
MTBLS87 = Merck SeQuant ZIC-pHILIC column with ACN:Water and :ammonium carbonate280.6 seconds40023050
KI_GIAR_zic_HILIC_pH2_7 = Merck SeQuant ZIC-HILIC with ACN:Water and 0.1% FA542.4 seconds40023050
Meister zic-pHILIC pH9.3 = Merck SeQuant ZIC-pHILIC column with ACN:Water 5mM NH4Ac pH9.3 and 5mM ammonium acetate in water15.7 seconds40023050

Predicted Kovats Retention Indices

Not Available
Spectra

GC-MS Spectra

Spectrum TypeDescriptionSplash KeyDeposition DateSourceView
MSMass Spectrum (Electron Ionization)Not Available2022-08-06Not AvailableView Spectrum

MS/MS Spectra

Spectrum TypeDescriptionSplash KeyDeposition DateSourceView
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - (N-Acetylglucosaminyl)2-diphosphodolichol 10V, Positive-QTOFsplash10-052f-6010319000-bba7db1d675717edd6f72017-09-01Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - (N-Acetylglucosaminyl)2-diphosphodolichol 20V, Positive-QTOFsplash10-0006-9221212000-99015c6ad993213c09742017-09-01Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - (N-Acetylglucosaminyl)2-diphosphodolichol 40V, Positive-QTOFsplash10-0006-9111002000-0f6ee3c46488576617a32017-09-01Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - (N-Acetylglucosaminyl)2-diphosphodolichol 10V, Negative-QTOFsplash10-00r6-2191000000-38d90409c07f91c975152017-09-01Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - (N-Acetylglucosaminyl)2-diphosphodolichol 20V, Negative-QTOFsplash10-08i1-9472452000-1d689f2ac72a31c86e322017-09-01Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - (N-Acetylglucosaminyl)2-diphosphodolichol 40V, Negative-QTOFsplash10-0a6v-4940200000-5b29fd9d452ed8b13ef22017-09-01Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - (N-Acetylglucosaminyl)2-diphosphodolichol 10V, Negative-QTOFsplash10-05fr-0000109000-fe8e77c1b992c933b0672021-09-22Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - (N-Acetylglucosaminyl)2-diphosphodolichol 20V, Negative-QTOFsplash10-0pi0-3130937000-c154a59ced911edb5c992021-09-22Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - (N-Acetylglucosaminyl)2-diphosphodolichol 40V, Negative-QTOFsplash10-0a6r-3921111000-50e3e07dd6baa06862772021-09-22Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - (N-Acetylglucosaminyl)2-diphosphodolichol 10V, Positive-QTOFsplash10-069r-2020029000-b60e082e0d239128cc892021-09-23Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - (N-Acetylglucosaminyl)2-diphosphodolichol 20V, Positive-QTOFsplash10-00pj-2000239136-10f29554ab93013b491e2021-09-23Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - (N-Acetylglucosaminyl)2-diphosphodolichol 40V, Positive-QTOFsplash10-0mlb-8101947354-e178345eb9b568944acf2021-09-23Wishart LabView Spectrum
Biological Properties
Cellular Locations
  • Extracellular
  • Membrane
Biospecimen LocationsNot Available
Tissue LocationsNot Available
Pathways
Normal Concentrations
Not Available
Abnormal Concentrations
Not Available
Associated Disorders and Diseases
Disease ReferencesNone
Associated OMIM IDsNone
DrugBank IDNot Available
Phenol Explorer Compound IDNot Available
FooDB IDFDB028790
KNApSAcK IDNot Available
Chemspider ID35032410
KEGG Compound IDC04537
BioCyc IDNN-DIACETYLCHITOBIOSYLDIPHOSPHODOLICHO
BiGG IDNot Available
Wikipedia LinkNot Available
METLIN IDNot Available
PubChem Compound53481378
PDB IDNot Available
ChEBI IDNot Available
Food Biomarker OntologyNot Available
VMH IDNot Available
MarkerDB IDNot Available
Good Scents IDNot Available
References
Synthesis ReferenceNot Available
Material Safety Data Sheet (MSDS)Not Available
General References
  1. Simons K, Toomre D: Lipid rafts and signal transduction. Nat Rev Mol Cell Biol. 2000 Oct;1(1):31-9. [PubMed:11413487 ]
  2. Watson AD: Thematic review series: systems biology approaches to metabolic and cardiovascular disorders. Lipidomics: a global approach to lipid analysis in biological systems. J Lipid Res. 2006 Oct;47(10):2101-11. Epub 2006 Aug 10. [PubMed:16902246 ]
  3. Sethi JK, Vidal-Puig AJ: Thematic review series: adipocyte biology. Adipose tissue function and plasticity orchestrate nutritional adaptation. J Lipid Res. 2007 Jun;48(6):1253-62. Epub 2007 Mar 20. [PubMed:17374880 ]
  4. Lingwood D, Simons K: Lipid rafts as a membrane-organizing principle. Science. 2010 Jan 1;327(5961):46-50. doi: 10.1126/science.1174621. [PubMed:20044567 ]
  5. Gunstone, Frank D., John L. Harwood, and Albert J. Dijkstra (2007). The lipid handbook with CD-ROM. CRC Press.

Enzymes

General function:
Involved in biosynthetic process
Specific function:
Participates in the formation of the lipid-linked precursor oligosaccharide for N-glycosylation. Involved in assembling the dolichol-pyrophosphate-GlcNAc(2)-Man(5) intermediate on the cytoplasmic surface of the ER.
Gene Name:
ALG1
Uniprot ID:
Q9BT22
Molecular weight:
52517.685
Reactions
Guanosine diphosphate mannose + (N-Acetylglucosaminyl)2-diphosphodolichol → Guanosine diphosphate + beta-1,4-D-mannosylchitobiosyldiphosphodolicholdetails