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Dolichyl diphosphate (YMDB00927)

Identification
YMDB IDYMDB00927
NameDolichyl diphosphate
SpeciesSaccharomyces cerevisiae
StrainBaker's yeast
DescriptionDolichyl diphosphate is involved in dolichyl-diphosphooligosaccharide biosynthesis (N-linked glycosylation) pathway. N-linked glycosylation is an important process found in eukaryotes and archaea, and very rarely in bacteria. During this process certain oligosaccharides are attached to an asparagine residue in the polypeptide chain of the target protein. [Biocyc MANNOSYL-CHITO-DOLICHOL-BIOSYNTHESIS]
Structure
Thumb
MOLSDFPDBSMILESInChI
Synonyms
  • Dolichyl diphosphate
  • Dolichyl diphosphic acid
  • Dolichyl diphosphoric acid
CAS number37247-98-6
WeightAverage: 1542.3314
Monoisotopic: 1541.21088069
InChI KeyQQXIZBNULDQRRT-OYHKHEHLSA-N
InChIInChI=1S/C100H166O7P2/c1-81(2)41-22-42-82(3)43-23-44-83(4)45-24-46-84(5)47-25-48-85(6)49-26-50-86(7)51-27-52-87(8)53-28-54-88(9)55-29-56-89(10)57-30-58-90(11)59-31-60-91(12)61-32-62-92(13)63-33-64-93(14)65-34-66-94(15)67-35-68-95(16)69-36-70-96(17)71-37-72-97(18)73-38-74-98(19)75-39-76-99(20)77-40-78-100(21)79-80-106-109(104,105)107-108(101,102)103/h41,43,45,47,49,51,53,55,57,59,61,63,65,67,69,71,73,75,77,100H,22-40,42,44,46,48,50,52,54,56,58,60,62,64,66,68,70,72,74,76,78-80H2,1-21H3,(H,104,105)(H2,101,102,103)/b82-43+,83-45+,84-47+,85-49+,86-51-,87-53+,88-55+,89-57+,90-59+,91-61+,92-63+,93-65+,94-67+,95-69-,96-71+,97-73+,98-75+,99-77+
IUPAC Name{[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}phosphonic acid
Traditional IUPAC Name{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}oxyphosphonic acid
Chemical FormulaC100H166O7P2
SMILESCC(CCOP(O)(=O)OP(O)(O)=O)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
Chemical Taxonomy
Description belongs to the class of organic compounds known as dolichyl diphosphates. These are polyprenyl compounds consisting of a diphosphate group substituted by a dolichyl moiety.
KingdomOrganic compounds
Super ClassLipids and lipid-like molecules
ClassPrenol lipids
Sub ClassPolyprenols
Direct ParentDolichyl diphosphates
Alternative Parents
Substituents
  • Polyterpenoid
  • Polyprenyl diphosphate
  • Dolichyl diphosphate
  • Polyprenyl monophosphate
  • Organic pyrophosphate
  • Monoalkyl phosphate
  • Alkyl phosphate
  • Phosphoric acid ester
  • Organic phosphoric acid derivative
  • Organic oxygen compound
  • Organic oxide
  • Hydrocarbon derivative
  • Organooxygen compound
  • Aliphatic acyclic compound
Molecular FrameworkAliphatic acyclic compounds
External DescriptorsNot Available
Physical Properties
StateSolid
Charge0
Melting pointNot Available
Experimental Properties
PropertyValueReference
Water SolubilityNot AvailablePhysProp
LogPNot AvailablePhysProp
Predicted Properties
PropertyValueSource
Water Solubility0.00042 g/LALOGPS
logP9.68ALOGPS
logP32.08ChemAxon
logS-6.6ALOGPS
pKa (Strongest Acidic)1.78ChemAxon
Physiological Charge-2ChemAxon
Hydrogen Acceptor Count5ChemAxon
Hydrogen Donor Count3ChemAxon
Polar Surface Area113.29 ŲChemAxon
Rotatable Bond Count63ChemAxon
Refractivity500.68 m³·mol⁻¹ChemAxon
Polarizability198.08 ųChemAxon
Number of Rings0ChemAxon
Bioavailability0ChemAxon
Rule of FiveYesChemAxon
Ghose FilterYesChemAxon
Veber's RuleYesChemAxon
MDDR-like RuleYesChemAxon
Biological Properties
Cellular LocationsNot Available
Organoleptic PropertiesNot Available
SMPDB Pathways
N-Glycan biosynthesisPW002501 ThumbThumb?image type=greyscaleThumb?image type=simple
Terpenoid backbone biosynthesisPW002485 ThumbThumb?image type=greyscaleThumb?image type=simple
KEGG Pathways
N-Glycan biosynthesisec00510 Map00510
Terpenoid backbone biosynthesisec00900 Map00900
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, Negativesplash10-0006-0400090000-2f5c5cbe04da26ccdfe3JSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Negativesplash10-056r-7900010000-3bfcba852a7c2d1f0f4bJSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Negativesplash10-004i-9000000000-9425ea96424395ce5634JSpectraViewer
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
  • Fernandez, F., Rush, J. S., Toke, D. A., Han, G. S., Quinn, J. E., Carman, G. M., Choi, J. Y., Voelker, D. R., Aebi, M., Waechter, C. J. (2001). "The CWH8 gene encodes a dolichyl pyrophosphate phosphatase with a luminally oriented active site in the endoplasmic reticulum of Saccharomyces cerevisiae." J Biol Chem 276:41455-41464.11504728
Synthesis Reference:Not Available
External Links:
ResourceLink
CHEBI ID15750
HMDB IDHMDB01513
Pubchem Compound ID391
Kegg IDC00621
ChemSpider IDNot Available
FOODB IDNot Available
Wikipedia IDNot Available
BioCyc IDCPD-224

Enzymes

Protein Details
1. Dolichyldiphosphatase
General function:
Involved in catalytic activity
Specific function:
Non-essential protein which is required for efficient N- glycosylation. Necessary for maintaining optimal levels of dolichol-linked oligosaccharides. Hydrolyzes dolichyl pyrophosphate at a very high rate and dolichyl monophosphate at a much lower rate. Does not act on phosphatidate
Gene Name:
CAX4
Uniprot ID:
P53223
Molecular weight:
27648.80078
Reactions
Dolichyl diphosphate + H(2)O → dolichyl phosphate + phosphate.