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Record Information
Version5.0
StatusExpected but not Quantified
Creation Date2009-04-06 16:19:33 UTC
Update Date2022-03-07 02:51:21 UTC
HMDB IDHMDB0012121
Secondary Accession Numbers
  • HMDB12121
Metabolite Identification
Common Name(Mannosyl)5-(N-acetylglucosaminyl)2-diphosphodolichol
Description(Mannosyl)5-(N-acetylglucosaminyl)2-diphosphodolichol (Man5GlcNAc2-Dol) is an isoprene-based lipid where an oligosaccharide moiety Man5GlcNAc2 is linked to dolichol lipid via a pyrophosphate linkage. Man5GlcNAc2-Dol is an intermediate in dolichyl-diphosphooligosaccaride biosynthesis pathway and synthesis of N-glycans. The biosynthetic pathway for this lipid-linked precursor begins with the phosphorylation of dolichol, followed by stepwise addition of sugar residues to form the product dolichyl-diphosphooligosaccharide. This pathway is of particular interest in humans, because defects in the glycosyltransferases involved lead to congenital disorders of N-glycosylation of proteins. In this pathway, (Mannosyl)5-(N-acetylglucosaminyl)2-diphosphodolichol is formed from (Mannosyl)4-(N-acetylglucosaminyl)2-diphosphodolichol via reaction with Dolichyl β-D-mannosyl phosphate. In the next step, one more mannose residue is added to Man5GlcNAc2-Dol via reaction with Dolichyl β-D-mannosyl phosphate. (Adapted from Human Cyc).
Structure
Data?1582753015
SynonymsNot Available
Chemical FormulaC126H210N2O42P2
Average Molecular Weight2486.9513
Monoisotopic Molecular Weight2485.383341878
IUPAC Name{[(2S,3R,4R,5S,6R)-5-{[(2S,3R,4R,5S,6R)-5-{[(2S,3S,4S,5R,6R)-4-{[(2R,3S,4S,5S,6R)-3-{[(2R,3S,4S,5S,6R)-4,5-dihydroxy-6-(hydroxymethyl)-3-{[(2R,3S,4S,5S,6R)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}oxan-2-yl]oxy}-4,5-dihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}-3,5-dihydroxy-6-({[(2S,3S,4S,5S,6R)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}methyl)oxan-2-yl]oxy}-3-acetamido-4-hydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}-3-acetamido-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)-5-{[(2S,3R,4R,5S,6R)-5-{[(2S,3S,4S,5R,6R)-4-{[(2R,3S,4S,5S,6R)-3-{[(2R,3S,4S,5S,6R)-4,5-dihydroxy-6-(hydroxymethyl)-3-{[(2R,3S,4S,5S,6R)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}oxan-2-yl]oxy}-4,5-dihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}-3,5-dihydroxy-6-({[(2S,3S,4S,5S,6R)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}methyl)oxan-2-yl]oxy}-3-acetamido-4-hydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}-3-acetamido-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](OC[C@H]2O[C@@H](O[C@H]3[C@H](O)[C@@H](NC(C)=O)[C@@H](O[C@@H]3CO)O[C@H]3[C@H](O)[C@@H](NC(C)=O)[C@@H](O[C@@H]3CO)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](O)[C@@H](O[C@H]3O[C@H](CO)[C@@H](O)[C@H](O)[C@@H]3O[C@H]3O[C@H](CO)[C@@H](O)[C@H](O)[C@@H]3O[C@H]3O[C@H](CO)[C@@H](O)[C@H](O)[C@@H]3O)[C@@H]2O)[C@@H](O)[C@@H](O)[C@@H]1O
InChI Identifier
InChI=1S/C126H210N2O42P2/c1-74(2)35-20-36-75(3)37-21-38-76(4)39-22-40-77(5)41-23-42-78(6)43-24-44-79(7)45-25-46-80(8)47-26-48-81(9)49-27-50-82(10)51-28-52-83(11)53-29-54-84(12)55-30-56-85(13)57-31-58-86(14)59-32-60-87(15)61-33-62-88(16)63-34-64-89(17)65-66-156-171(151,152)170-172(153,154)169-121-100(128-91(19)136)107(143)115(97(72-134)162-121)164-120-99(127-90(18)135)106(142)116(96(71-133)161-120)165-124-114(150)117(105(141)98(163-124)73-155-122-112(148)108(144)101(137)92(67-129)157-122)166-125-119(111(147)104(140)94(69-131)159-125)168-126-118(110(146)103(139)95(70-132)160-126)167-123-113(149)109(145)102(138)93(68-130)158-123/h35,37,39,41,43,45,47,49,51,53,55,57,59,61,63,89,92-126,129-134,137-150H,20-34,36,38,40,42,44,46,48,50,52,54,56,58,60,62,64-73H2,1-19H3,(H,127,135)(H,128,136)(H,151,152)(H,153,154)/b75-37+,76-39+,77-41+,78-43+,79-45+,80-47+,81-49+,82-51+,83-53+,84-55+,85-57+,86-59+,87-61+,88-63+/t89?,92-,93-,94-,95-,96-,97-,98-,99-,100-,101-,102-,103-,104-,105-,106-,107-,108+,109+,110+,111+,112+,113+,114+,115-,116-,117+,118+,119+,120+,121+,122+,123-,124+,125-,126-/m1/s1
InChI KeyWMSWZXXUBKPOOZ-CPZBINJNSA-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
  • Oligosaccharide phosphate
  • Polyprenyl monophosphate
  • Oligosaccharide
  • Polyprenyl phosphate skeleton
  • N-acyl-alpha-hexosamine
  • Glycosyl compound
  • O-glycosyl compound
  • Organic pyrophosphate
  • Monoalkyl phosphate
  • Organic phosphoric acid derivative
  • Alkyl phosphate
  • Oxane
  • Phosphoric acid ester
  • Acetamide
  • Secondary alcohol
  • Secondary carboxylic acid amide
  • Carboxamide group
  • Polyol
  • Carboxylic acid derivative
  • Oxacycle
  • Organoheterocyclic compound
  • Acetal
  • Organic nitrogen compound
  • Organic oxide
  • Hydrocarbon derivative
  • Alcohol
  • Organonitrogen compound
  • Organooxygen compound
  • Carbonyl group
  • Organic oxygen compound
  • Organopnictogen compound
  • 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 Solubility0.0097 g/LALOGPS
logP5.43ALOGPS
logP12.21ChemAxon
logS-5.4ALOGPS
pKa (Strongest Acidic)1.74ChemAxon
pKa (Strongest Basic)-3.7ChemAxon
Physiological Charge-2ChemAxon
Hydrogen Acceptor Count39ChemAxon
Hydrogen Donor Count24ChemAxon
Polar Surface Area685.08 ŲChemAxon
Rotatable Bond Count74ChemAxon
Refractivity654.3 m³·mol⁻¹ChemAxon
Polarizability278.66 ųChemAxon
Number of Rings7ChemAxon
BioavailabilityNoChemAxon
Rule of FiveNoChemAxon
Ghose FilterNoChemAxon
Veber's RuleNoChemAxon
MDDR-like RuleYesChemAxon
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.-7.58 minutes32390414
Predicted by Siyang on May 30, 202232.5603 minutes33406817
Predicted by Siyang using ReTip algorithm on June 8, 20223.42 minutes32390414
AjsUoB = Accucore 150 Amide HILIC with 10mM Ammonium Formate, 0.1% Formic Acid334.5 seconds40023050
Fem_Long = Waters ACQUITY UPLC HSS T3 C18 with Water:MeOH and 0.1% Formic Acid10880.7 seconds40023050
Fem_Lipids = Ascentis Express C18 with (60:40 water:ACN):(90:10 IPA:ACN) and 10mM NH4COOH + 0.1% Formic Acid101.9 seconds40023050
Life_Old = Waters ACQUITY UPLC BEH C18 with Water:(20:80 acetone:ACN) and 0.1% Formic Acid508.5 seconds40023050
Life_New = RP Waters ACQUITY UPLC HSS T3 C18 with Water:(30:70 MeOH:ACN) and 0.1% Formic Acid267.9 seconds40023050
RIKEN = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid337.1 seconds40023050
Eawag_XBridgeC18 = XBridge C18 3.5u 2.1x50 mm with Water:MeOH and 0.1% Formic Acid1251.8 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 Acid1529.0 seconds40023050
HILIC_BDD_2 = Merck SeQuant ZIC-HILIC with ACN(0.1% formic acid):water(16 mM ammonium formate)645.3 seconds40023050
UniToyama_Atlantis = RP Waters Atlantis T3 (2.1 x 150 mm, 5 um) with ACN:Water and 0.1% Formic Acid2992.7 seconds40023050
BDD_C18 = Hypersil Gold 1.9µm C18 with Water:ACN and 0.1% Formic Acid1974.4 seconds40023050
UFZ_Phenomenex = Kinetex Core-Shell C18 2.6 um, 3.0 x 100 mm, Phenomenex with Water:MeOH and 0.1% Formic Acid2123.4 seconds40023050
SNU_RIKEN_POS = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid1199.5 seconds40023050
RPMMFDA = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid990.5 seconds40023050
MTBLS87 = Merck SeQuant ZIC-pHILIC column with ACN:Water and :ammonium carbonate580.3 seconds40023050
KI_GIAR_zic_HILIC_pH2_7 = Merck SeQuant ZIC-HILIC with ACN:Water and 0.1% FA169.3 seconds40023050
Meister zic-pHILIC pH9.3 = Merck SeQuant ZIC-pHILIC column with ACN:Water 5mM NH4Ac pH9.3 and 5mM ammonium acetate in water15.4 seconds40023050

Predicted Kovats Retention Indices

Not Available
Spectra

MS/MS Spectra

Spectrum TypeDescriptionSplash KeyDeposition DateSourceView
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - (Mannosyl)5-(N-acetylglucosaminyl)2-diphosphodolichol 10V, Positive-QTOFsplash10-05mo-4313903001-46d6cd6b427b79f378b52017-09-01Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - (Mannosyl)5-(N-acetylglucosaminyl)2-diphosphodolichol 20V, Positive-QTOFsplash10-052f-9413604002-9c076935f9641fdc412a2017-09-01Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - (Mannosyl)5-(N-acetylglucosaminyl)2-diphosphodolichol 40V, Positive-QTOFsplash10-05ox-9502507002-ae55291059894158d0b22017-09-01Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - (Mannosyl)5-(N-acetylglucosaminyl)2-diphosphodolichol 10V, Negative-QTOFsplash10-014i-2952401235-2ef83d9b82d21d328df32017-09-01Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - (Mannosyl)5-(N-acetylglucosaminyl)2-diphosphodolichol 20V, Negative-QTOFsplash10-00mk-4654912002-8da9f9bae1959e3e59882017-09-01Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - (Mannosyl)5-(N-acetylglucosaminyl)2-diphosphodolichol 40V, Negative-QTOFsplash10-054n-2952200000-0e1254fa242817daa5bc2017-09-01Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - (Mannosyl)5-(N-acetylglucosaminyl)2-diphosphodolichol 10V, Positive-QTOFsplash10-00or-1001900000-a2e6af397121b9535e232021-09-22Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - (Mannosyl)5-(N-acetylglucosaminyl)2-diphosphodolichol 20V, Positive-QTOFsplash10-00n0-1001913114-5f29b43366d13c3397a12021-09-22Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - (Mannosyl)5-(N-acetylglucosaminyl)2-diphosphodolichol 40V, Positive-QTOFsplash10-000i-3202924232-7b75be78f5e6bee1dee92021-09-22Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - (Mannosyl)5-(N-acetylglucosaminyl)2-diphosphodolichol 10V, Negative-QTOFsplash10-001i-0101900000-75a9481c2b5b2cd2b4372021-09-23Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - (Mannosyl)5-(N-acetylglucosaminyl)2-diphosphodolichol 20V, Negative-QTOFsplash10-001i-1004900001-f216bc9bb1d5bebffb102021-09-23Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - (Mannosyl)5-(N-acetylglucosaminyl)2-diphosphodolichol 40V, Negative-QTOFsplash10-0pc0-6782965000-35a2aa70e9fd9495dd442021-09-23Wishart 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 IDFDB028785
KNApSAcK IDNot Available
Chemspider ID35032405
KEGG Compound IDNot Available
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkNot Available
METLIN IDNot Available
PubChem Compound53481373
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.