CDP-DG(18:1(9Z)/22:3(10Z,13Z,16Z))



Compound IDCDAMM02798
Common nameCDP-DG(18:1(9Z)/22:3(10Z,13Z,16Z))
IUPAC name[1-[[[5-(4-amino-2-oxopyrimidin-1-yl)-3,4-dihydroxyoxolan-2-yl]methoxy-hydroxyphosphoryl]oxy-hydroxyphosphoryl]oxy-3-octadec-9-enoyloxypropan-2-yl] docosa-10,13,16-trienoate
Molecular formulaC52H89N3O15P2

Experimental data

Retention time4.49
Adduct[M+Na]2+
Actual mz540.284
Theoretical mz540.285
Error0.2
Ionizaton modePositive
Instrument typeLC-MS/MS-QTOF, spectrum predicted by MS-DIAL v4.9 integrated with MS-FINDER 3.60
Score6.5634

Identifiers and class information

Inchi keyKTDSFHYGTNRDNM-CHNQJESLSA-N
SmilesO=C1N=C(N)C=CN1C2OC(COP(=O)(O)OP(=O)(O)OCC(OC(=O)CCCCCCCCC=CCC=CCC=CCCCCC)COC(=O)CCCCCCCC=CCCCCCCCC)C(O)C2O
SuperclassLipids and lipid-like molecules
ClassGlycerophospholipids

Pharmacokinetic properties

Number of descriptor values(#stars)17
Number of non-conjugated amine groups (#amine)0
Number of amidine and guanidine groups (#amidine)0
Number of carboxylic acid groups (#acid)2
Number of non-conjugated amide groups (#amide)0
Number of rotatable bonds (#rotor)48
Number of reactive functional groups (#rtvFG)5
Predicted central nervous system activity (CNS)-2
Molecular weight (mol_MW)1058.23
Computed dipole moment(dipole)18.867
Total solvent accessible surface area (SASA)1668.32
Hydrophobic component of SASA (FOSA)1138.42
Hydrophilic component of SASA (FISA)422.987
Pie component of the SASA (PISA)103.011
Weakly polar component of the SASA (WPSA)3.909
Total solvent accesible volume (volume)3328.55
Number of hydrogen bond donors (donorHB)4
Number of hydrogen bond acceptors (accptHB)21.1
Free energy of solvation of dipole (dip^2/V)0.10694
Index of cohesive interaction in solids (ACxDN^.5/SA)0.0252948
Globularity descriptor (glob)0.646231
Predicted polarizability in cubic angstroms (QPpolrz)97.218
Predicted hexadecane/gas partition coefficient (QPlogPC16)35.986
Predicted octanol/gas partition coefficient (QPlogPoct)51.277
Predicted water/gas partition coefficient (QPlogPw)23.367
Predicted octanol/water partition coefficient (QPlogPo/w)8.897
Predicted aqueous solubility (QPlogS)-9.909
Conformation-independent predicted aqueous solubility (CIQPlogS)-12.314
Predicted IC50 value for blockage of HERG K+ channels (QPlogHERG)-4.133
Predicted apparent Caco-2 cell permeability in nm/sec (QPPCaco)0.062
Predicted brain/blood partition coefficient (QPlogBB)-9.072
Predicted apparent MDCK cell permeability in nm/sec (QPPMDCK)0.024
Predicted skin permeability, log Kp (QPlogKp)-4.344
PM3 calculated ionization potential (IP(ev))9.038
PM3 calculated electron affinity (EA(eV))0.507
Number of likely metabolic reactions (#metab)11
Prediction of binding to human serum albumin (QPlogKhsa)0.634
Predicted qualitative human oral absorption (HumanOralAbsorption)1
Predicted human oral absorption on 0 to 100% scale (PercentHumanOralAbsorption)5.581
Solvent-accessible surface area of fluorine atoms (SAFluorine)0
Solvent-accessible surface area of amide oxygen atoms (SAamideO)0
Van der Waals surface area (PSA)281.033
Number of nitrogen and oxygen atoms (#NandO)18
Number of violations of Lipinski’s rule of five (RuleOfFive)4
Number of violations of Jorgensen’s rule of three (RuleOfThree)3

Compound-target network

Cytoscape Graph

Protein targets associated with phytocompound

Uniprot ID Gene name Target name TTD_ID Prediction source
P07327ADH1AAlcohol dehydrogenase alpha chainT65570SEA
P17612PRKACAcAMP-dependent protein kinase alpha-catalytic subunitT12808SEA
P06746POLBDNA polymerase beta (by homology)T06958SEA
O00206TLR4Toll-like receptor 4 (by homology)T81443SEA
P15692VEGFAVascular endothelial growth factor AT20761SEA
P55263ADKAdenosine kinaseT91661SEA
P16109SELPP-selectinT10965SEA
Q9Y4D2DAGLASn1-specific diacylglycerol lipase alphaT03150SEA
P20839IMPDH1Inosine-5'-monophosphate dehydrogenase 1T40111SEA
P12268IMPDH2Inosine-5'-monophosphate dehydrogenase 2T89360SEA
P47900P2RY1Purinergic receptor P2Y1T67818SEA
P41231P2RY2Purinergic receptor P2Y2T93515SEA
Q15077P2RY6Pyrimidinergic receptor P2Y6T90782SEA
P63000RAC1Ras-related C3 botulinum toxin substrate 1T88752SEA
P16885PLCG2Phospholipase C-gamma-2T93922SEA
Q9HBW0LPAR2Lysophosphatidic acid receptor Edg-4T39380SEA
P23919DTYMKThymidylate kinaseT94400SEA
P43657LPAR6Lysophosphatidic acid receptor 6T13484SEA
Q9H1C0LPAR5Lysophosphatidic acid receptor 5T18616SEA
P11172UMPSUridine 5'-monophosphate synthaseT15851SEA
O94759TRPM2Transient receptor potential cation channel subfamily M member 2T78205SEA
O00142TK2Thymidine kinase, mitochondrialT22976SEA
Q9UPC5GPR34Probable G-protein coupled receptor 34T73859SEA
O00398P2RY10Putative P2Y purinoceptor 10T00488SEA
Q9BXC1GPR174Probable G-protein coupled receptor 174T87661SEA
Q9UBY5LPAR3Lysophosphatidic acid receptor Edg-7T95923SEA
Q92633LPAR1Lysophosphatidic acid receptor Edg-2T92640SEA
P16885PLCG2Phospholipase C-gamma-2T93922SEA
Q99677LPAR4Lysophosphatidic acid receptor 4T58130SEA
Q15391P2RY14Purinergic receptor P2Y14T16555SEA
Q05823RNASELRNase LT25200SEA
P51575P2RX1P2X purinoceptor 1T69091SEA
Q99571P2RX4P2X purinoceptor 4T60330SEA
Q13304GPR17Uracil nucleotide/cysteinyl leukotriene receptorT33902SEA
O60603TLR2Toll-like receptor 2T82078SEA
Q9Y4W7PARGPoly(ADP-ribose) glycohydrolaseT66935SEA

Target associated diseases

TTD_ID Disease_ID Disease name ICD_11 Uniprot ID Gene names
T65570DI0139Exposure to noxious substances harmful effect[ICD-11: NE61]P07327ADH1A
T12808DI0279Muscular atrophy[ICD-11: 8B61]P17612PRKACA
T06958DI0391Solid tumour/cancer[ICD-11: 2A00-2F9Z]P06746POLB
T81443DI0022Allergic/hypersensitivity disorder[ICD-11: 4A80-4A8Z]O00206TLR4
T81443DI0346Prostate cancer[ICD-11: 2C82]O00206TLR4
T81443DI0375Sepsis[ICD-11: 1G40-1G41]O00206TLR4
T20761DI0095Colorectal cancer[ICD-11: 2B91]P15692VEGFA
T20761DI0365Retinopathy[ICD-11: 9B71]P15692VEGFA
T20761DI0430Vascular system developmental anomaly[ICD-11: LA90]P15692VEGFA
T91661DI0134Epilepsy/seizure[ICD-11: 8A61-8A6Z]P55263ADK
T10965DI0088Circulatory system disease[ICD-11: BE2Z]P16109SELP
T10965DI0381Sickle-cell disorder[ICD-11: 3A51]P16109SELP
T40111DI0062Breast cancer[ICD-11: 2C60-2C6Y]P20839IMPDH1
T40111DI0179Hepatitis virus infection[ICD-11: 1E50-1E51]P20839IMPDH1
T40111DI0250Mature B-cell lymphoma[ICD-11: 2A85]P20839IMPDH1
T40111DI0391Solid tumour/cancer[ICD-11: 2A00-2F9Z]P20839IMPDH1
T40111DI0413Transplant rejection[ICD-11: NE84]P20839IMPDH1
T89360DI0413Transplant rejection[ICD-11: NE84]P12268IMPDH2
T93515DI0436Visual system disease[ICD-11: 9E1Z]P41231P2RY2
T90782DI0025Alzheimer disease[ICD-11: 8A20]Q15077P2RY6
T88752DI0025Alzheimer disease[ICD-11: 8A20]P63000RAC1
T22976DI0206Inborn purine/pyrimidine/nucleotide metabolism error[ICD-11: 5C55]O00142TK2
T95923DI0146Fibrosis[ICD-11: GA14-GC01]Q9UBY5LPAR3
T95923DI0399Systemic sclerosis[ICD-11: 4A42]Q9UBY5LPAR3
T92640DI0146Fibrosis[ICD-11: GA14-GC01]Q92633LPAR1
T92640DI0199Idiopathic interstitial pneumonitis[ICD-11: CB03]Q92633LPAR1
T92640DI0351Psoriasis[ICD-11: EA90]Q92633LPAR1
T92640DI0399Systemic sclerosis[ICD-11: 4A42]Q92633LPAR1
T82078DI0346Prostate cancer[ICD-11: 2C82]O60603TLR2

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