Structure Database (LMSD)
Common Name
CDP-2,3-bis-O-(geranylgeranyl)-sn-glycerol
Systematic Name
2,3-digeranylgeranyl-sn-glycero-1-cytidine-5'-diphosphate
Synonyms
LM ID
LMGP13040001
Formula
Exact Mass
Calculate m/z
1021.555768
Sum Composition
Status
Active
3D model of CDP-2,3-bis-O-(geranylgeranyl)-sn-glycerol
Please note: Where there are chiral atoms but the stereochemistry is undefined, the 3D model takes an arbitrary conformation
Main
Classification
Category
Main Class
Sub Class
String Representations
InChiKey (Click to copy)
DCAZOLWWPLSROK-DXHGDTBASA-N
InChi (Click to copy)
InChI=1S/C52H85N3O13P2/c1-38(2)17-11-19-40(5)21-13-23-42(7)25-15-27-44(9)30-33-63-35-46(64-34-31-45(10)28-16-26-43(8)24-14-22-41(6)20-12-18-39(3)4)36-65-69(59,60)68-70(61,62)66-37-47-49(56)50(57)51(67-47)55-32-29-48(53)54-52(55)58/h17-18,21-22,25-26,29-32,46-47,49-51,56-57H,11-16,19-20,23-24,27-28,33-37H2,1-10H3,(H,59,60)(H,61,62)(H2,53,54,58)/b40-21+,41-22+,42-25+,43-26+,44-30+,45-31+/t46-,47+,49+,50+,51+/m0/s1
SMILES (Click to copy)
C(O[C@@](COP(=O)(O)OP(OC[C@H]1O[C@H]([C@@H]([C@@H]1O)O)N1C=CC(=NC1=O)N)(O)=O)([H])COC/C=C(\C)/CC/C=C(\C)/CC/C=C(\C)/CC/C=C(\C)/C)/C=C(\C)/CC/C=C(\C)/CC/C=C(\C)/CC/C=C(\C)/C
References
Taxonomy Information
Curated from
NCBI taxonomy class
Reference
Methanothermobacter thermautotrophicus
(#145262)
Methanobacteria
(#183925)
CDP-2,3-Di-O-geranylgeranyl-sn-glycerol:L-serine O-archaetidyltransferase (archaetidylserine synthase) in the methanogenic archaeon Methanothermobacter thermautotrophicus.,
J Bacteriol, 2003
J Bacteriol, 2003
Pubmed ID:
12562787
Other Databases
Calculated Physicochemical Properties
Heavy Atoms
70
Rings
2
Aromatic Rings
1
Rotatable Bonds
34
Van der Waals Molecular Volume
1030.43
Topological Polar Surface Area
233.42
Hydrogen Bond Donors
5
Hydrogen Bond Acceptors
16
logP
15.20
Molar Refractivity
283.17
Reactions
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Reactions are shown if the E.C. number of the enzyme catalysing it is annotated in the UniProt database for a species belonging to the selected taxonomic class.
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Admin
Created at
24th Nov 2023
Updated at
24th Nov 2023
LIPID MAPS® abbreviations for glycerophospholipids (GP)
The LIPID MAPS® glycerophospholipid abbreviations (PC, PE, etc.) are used here to refer to species with one or two radyl side-chains where the structures of the side chains are indicated within parentheses in the 'Headgroup(sn1/sn2)' format (e.g. PC(16:0/18:1(9Z)). By default, R stereochemistry at the C-2 carbon of glycerol and attachment of the headgroup at the sn3 position is assumed. Also, acyl chains are assumed by default. The 'O-' prefix is used to indicate the presence of an alkyl ether substituent e.g. PC(O-16:0/18:1(9Z)), whereas the 'P-' prefix is used for the 1Z-alkenyl ether (Plasmalogen) substituent e.g. PC(P-16:0/18:1(9Z)).
For molecules with opposite (S) stereochemistry at C2 of the glycerol group and attachment of the headgroup at the sn1 position, the stereochemistry specification of [S] is appended to the abbreviation. The 'Headgroup(sn3/sn2)' abbreviation format is used.
For molecules with unknown stereochemistry at the C-2 carbon of the glycerol group, the stereochemistry specification of [U] is appended to the abbreviation and the structure is drawn with C-2 stereochemistry unspecified.
The LIPID MAPS® glycerophospholipid abbreviations (PC, PE, etc.) are used here to refer to species with one or two radyl side-chains where the structures of the side chains are indicated within parentheses in the 'Headgroup(sn1/sn2)' format (e.g. PC(16:0/18:1(9Z)). By default, R stereochemistry at the C-2 carbon of glycerol and attachment of the headgroup at the sn3 position is assumed. Also, acyl chains are assumed by default. The 'O-' prefix is used to indicate the presence of an alkyl ether substituent e.g. PC(O-16:0/18:1(9Z)), whereas the 'P-' prefix is used for the 1Z-alkenyl ether (Plasmalogen) substituent e.g. PC(P-16:0/18:1(9Z)).
For molecules with opposite (S) stereochemistry at C2 of the glycerol group and attachment of the headgroup at the sn1 position, the stereochemistry specification of [S] is appended to the abbreviation. The 'Headgroup(sn3/sn2)' abbreviation format is used.
For molecules with unknown stereochemistry at the C-2 carbon of the glycerol group, the stereochemistry specification of [U] is appended to the abbreviation and the structure is drawn with C-2 stereochemistry unspecified.