Bovine Metabolome Database: Showing metabocard for Dolichyl diphosphate (BMDB0001513)

Identification Taxonomy Physical properties Pathways Spectra Concentrations Links References enzymes (4) Show 4 proteins XML

Record Information

Version

1.0

Creation Date

2016-09-30 22:47:02 UTC

Update Date

2020-04-22 15:08:31 UTC

BMDB ID

BMDB0001513

Secondary Accession Numbers

BMDB01513

Metabolite Identification

Common Name

Dolichyl diphosphate

Description

Dolichyl diphosphate belongs to the class of organic compounds known as organic pyrophosphates. These are organic compounds containing the pyrophosphate oxoanion, with the structure OP([O-])(=O)OP(O)([O-])=O. Dolichyl diphosphate is a moderately acidic compound (based on its pKa).

Structure

MOL SDF PDB SMILES InChI

Synonyms

Value	Source
Dolichyl diphosphoric acid	Generator
[({[(7E)-3,8-dimethyldec-7-en-1-yl]oxy}(hydroxy)phosphoryl)oxy]phosphonate	HMDB

Chemical Formula

C₁₂H₂₆O₇P₂

Average Molecular Weight

344.2782

Monoisotopic Molecular Weight

344.11537621

IUPAC Name

[({[(7E)-3,8-dimethyldec-7-en-1-yl]oxy}(hydroxy)phosphoryl)oxy]phosphonic acid

Traditional Name

{[(7E)-3,8-dimethyldec-7-en-1-yl]oxy(hydroxy)phosphoryl}oxyphosphonic acid

CAS Registry Number

37247-98-6

SMILES

CC\C(C)=C\CCCC(C)CCOP(O)(=O)OP(O)(O)=O

InChI Identifier

InChI=1S/C12H26O7P2/c1-4-11(2)7-5-6-8-12(3)9-10-18-21(16,17)19-20(13,14)15/h7,12H,4-6,8-10H2,1-3H3,(H,16,17)(H2,13,14,15)/b11-7+

InChI Key

FFBTVOMODCZDNV-YRNVUSSQSA-N

Chemical Taxonomy

Description

belongs to the class of organic compounds known as organic pyrophosphates. These are organic compounds containing the pyrophosphate oxoanion, with the structure OP([O-])(=O)OP(O)([O-])=O.

Kingdom

Organic compounds

Super Class

Organic oxygen compounds

Class

Organic oxoanionic compounds

Sub Class

Organic pyrophosphates

Direct Parent

Organic pyrophosphates

Alternative Parents

Substituents

Organic pyrophosphate
Monoalkyl phosphate
Alkyl phosphate
Phosphoric acid ester
Organic phosphoric acid derivative
Organic oxide
Hydrocarbon derivative
Organooxygen compound
Aliphatic acyclic compound

Molecular Framework

Aliphatic acyclic compounds

External Descriptors

Not Available

Ontology

Status

Expected but not Quantified

Origin

Endogenous

Biofunction

Not Available

Application

Not Available

Cellular locations

Cell membrane
Membrane

Physical Properties

State

Solid

Experimental Properties

Property	Value	Reference
Melting Point	Not Available	Not Available
Boiling Point	Not Available	Not Available
Water Solubility	Not Available	Not Available
LogP	Not Available	Not Available

Predicted Properties

Property	Value	Source
logP	1.95	ALOGPS
logP	3.1	ChemAxon
logS	-2.7	ALOGPS
pKa (Strongest Acidic)	1.78	ChemAxon
Physiological Charge	-2	ChemAxon
Hydrogen Acceptor Count	5	ChemAxon
Hydrogen Donor Count	3	ChemAxon
Polar Surface Area	113.29 Å²	ChemAxon
Rotatable Bond Count	11	ChemAxon
Refractivity	81.43 m³·mol⁻¹	ChemAxon
Polarizability	33.28 Å³	ChemAxon
Number of Rings	0	ChemAxon
Bioavailability	Yes	ChemAxon
Rule of Five	Yes	ChemAxon
Ghose Filter	Yes	ChemAxon
Veber's Rule	Yes	ChemAxon
MDDR-like Rule	Yes	ChemAxon

Spectra

Spectrum Type	Description	Splash Key
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (Non-derivatized) - 70eV, Positive	splash10-004j-7941000000-2ec278b43517dee66858	View in MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Positive	splash10-014j-2935000000-cdbfdcfd713383271f9c	View in MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Positive	splash10-014j-7910000000-961764090194a7d65f56	View in MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Positive	splash10-066s-9300000000-d06c65f0400bf425eeda	View in MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Negative	splash10-0006-0409000000-766a46992b3cea1592a9	View in MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Negative	splash10-004i-9300000000-1133b11c65ac65f06c66	View in MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Negative	splash10-004i-9000000000-9fcecdd44b53bc65fe73	View in MoNA

Biological Properties

Cellular Locations

Cell membrane
Membrane

Biospecimen Locations

Not Available

Pathways

Not Available

Name	SMPDB/Pathwhiz	KEGG

Normal Concentrations

Not Available

Abnormal Concentrations

Not Available

External Links

HMDB ID

HMDB0001513

DrugBank ID

Not Available

Phenol Explorer Compound ID

Not Available

FooDB ID

FDB022667

KNApSAcK ID

Not Available

Chemspider ID

13748633

KEGG Compound ID

C00621

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

6290

PubChem Compound

5462166

PDB ID

Not Available

ChEBI ID

15750

References

Synthesis Reference

Not Available

Material Safety Data Sheet (MSDS)

Not Available

General References

Not Available

Enzymes

Enzyme Details

1. Dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit DAD1

General function:: Involved in dolichyl-diphosphooligosaccharide-protein g
Specific function:: Subunit of the oligosaccharyl transferase (OST) complex that catalyzes the initial transfer of a defined glycan (Glc(3)Man(9)GlcNAc(2) in eukaryotes) from the lipid carrier dolichol-pyrophosphate to an asparagine residue within an Asn-X-Ser/Thr consensus motif in nascent polypeptide chains, the first step in protein N-glycosylation. N-glycosylation occurs cotranslationally and the complex associates with the Sec61 complex at the channel-forming translocon complex that mediates protein translocation across the endoplasmic reticulum (ER). All subunits are required for a maximal enzyme activity.
Gene Name:: DAD1
Uniprot ID:: Q5E9C2
Molecular weight:: 12495.0

Enzyme Details

2. Dolichyl-diphosphooligosaccharide--protein glycosyltransferase 48 kDa subunit

General function:: Involved in dolichyl-diphosphooligosaccharide-protein g
Specific function:: Subunit of the oligosaccharyl transferase (OST) complex that catalyzes the initial transfer of a defined glycan (Glc(3)Man(9)GlcNAc(2) in eukaryotes) from the lipid carrier dolichol-pyrophosphate to an asparagine residue within an Asn-X-Ser/Thr consensus motif in nascent polypeptide chains, the first step in protein N-glycosylation. N-glycosylation occurs cotranslationally and the complex associates with the Sec61 complex at the channel-forming translocon complex that mediates protein translocation across the endoplasmic reticulum (ER). All subunits are required for a maximal enzyme activity (By similarity). Required for the assembly of both SST3A- and SS3B-containing OST complexes (By similarity).
Gene Name:: DDOST
Uniprot ID:: A6QPY0
Molecular weight:: 48791.0

Enzyme Details

3. Dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit 2

General function:: Involved in dolichyl-diphosphooligosaccharide-protein g
Specific function:: Subunit of the oligosaccharyl transferase (OST) complex that catalyzes the initial transfer of a defined glycan (Glc(3)Man(9)GlcNAc(2) in eukaryotes) from the lipid carrier dolichol-pyrophosphate to an asparagine residue within an Asn-X-Ser/Thr consensus motif in nascent polypeptide chains, the first step in protein N-glycosylation. N-glycosylation occurs cotranslationally and the complex associates with the Sec61 complex at the channel-forming translocon complex that mediates protein translocation across the endoplasmic reticulum (ER). All subunits are required for a maximal enzyme activity.
Gene Name:: RPN2
Uniprot ID:: Q3SZI6
Molecular weight:: 69214.0

Enzyme Details

4. Dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit STT3A

General function:: Involved in dolichyl-diphosphooligosaccharide-protein g
Specific function:: Catalytic subunit of the oligosaccharyl transferase (OST) complex that catalyzes the initial transfer of a defined glycan (Glc(3)Man(9)GlcNAc(2) in eukaryotes) from the lipid carrier dolichol-pyrophosphate to an asparagine residue within an Asn-X-Ser/Thr consensus motif in nascent polypeptide chains, the first step in protein N-glycosylation. N-glycosylation occurs cotranslationally and the complex associates with the Sec61 complex at the channel-forming translocon complex that mediates protein translocation across the endoplasmic reticulum (ER). All subunits are required for a maximal enzyme activity. This subunit contains the active site and the acceptor peptide and donor lipid-linked oligosaccharide (LLO) binding pockets (By similarity). STT3A is present in the majority of OST complexes and mediates cotranslational N-glycosylation of most sites on target proteins, while STT3B-containing complexes are required for efficient post-translational glycosylation and mediate glycosylation of sites that have been skipped by STT3A (By similarity).
Gene Name:: STT3A
Uniprot ID:: Q2KJI2
Molecular weight:: 80656.0

Showing metabocard for Dolichyl diphosphate (BMDB0001513)

Structure for BMDB0001513 (Dolichyl diphosphate)

Enzymes