Structure database (LMSD)

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LM IDLMGP13010025
Common NameCDP-DG(18:1(11Z)/20:4(5Z,8Z,11Z,14Z))
Systematic Name[({[(2R,3R,5R)-5-(4-amino-2-oxo-1,2-dihydropyrimidin-1-yl)-3,4-dihydroxyoxolan-
2-yl]methoxy}(hydroxy)phosphoryl)oxy][(2R)-2-[(5Z,8Z,11Z,14Z)-icosa-5,8,11,14-
tetraenoyloxy]-3-[(11Z)-octadec-11-enoyloxy]propoxy]phosphinic acid
SynonymsCDP-DG(38:5); CDP-DG(18:1_20:4)
Exact Mass
1027.5299 (neutral)    Calculate m/z:
FormulaC50H83N3O15P2
CategoryGlycerophospholipids [GP]
Main ClassCDP-Glycerols [GP13]
Sub ClassCDP-diacylglycerols [GP1301]
AbbrevCDP-DG 38:5
Abbrev ChainsCDP-DG 18:1_20:4
PubChem CID53477934
HMDB IDHMDB0006991
SWISSLIPIDS IDSLM:000742107
InChIKeyVKSATYKCIFBIGQ-DPJFXASKSA-N  Show lipids differing only in stereochemistry/bond geometry
InChI
InChI=1S/C50H83N3O15P2/c1-3-5-7-9-11-13-15-17-19-20-22-24-26-28-30-32-34-36-46(55)66-42(39-63-45(54)35-33-31-29-27-25-23-21-18-16-14-12-10-8-6-4-2)40-64-69(59,60)68-70(61,62)65-41-43-47(56)48(57)49(67-43)53-38-37-44(51)52-50(53)58/h11,13-14,16-17,19,22,24,28,30,37-38,42-43,47-49,56-57H,3-10,12,15,18,20-21,23,25-27,29,31-36,39-41H2,1-2H3,(H,59,60)(H,61,62)(H2,51,52,58)/b13-11-,16-14-,19-17-,24-22-,30-28-/t42-,43-,47+,48?,49-/m1/s1
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SMILES
C(OP(=O)(OP(=O)(OC[C@H]1O[C@@H](N2C=CC(N)=NC2=O)C(O)[C@H]1O)O)O)[C@]([H])(OC(=O)CCC/C=C\C/C=C\C/C=C\C/C=C\CCCCC)COC(=O)CCCCCCCCC/C=C\CCCCCC
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StatusActive
Calculated physicochemical properties (?):
 Heavy Atoms70Rings2Aromatic Rings1Rotatable Bonds43
 van der Waals
Molecular Volume
1016.05Topological Polar
Surface Area
267.56Hydrogen
Bond Donors
5Hydrogen
Bond Acceptors
17
 logP13.57Molar
Refractivity
273.52    
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.