Geranylfarnesyl diphosphate



Compound IDCDAMM02560
Common nameGeranylfarnesyl diphosphate
IUPAC name3,7,11,15,19-pentamethylicosa-2,6,10,14,18-pentaenyl phosphono hydrogen phosphate
Molecular formulaC25H44O7P2

Experimental data

Retention time13.17
Adduct[M+H]+
Actual mz519.266
Theoretical mz519.263
Error4.48
Ionizaton modePositive
Instrument typeLC-MS/MS-QTOF, spectrum predicted by MS-DIAL v4.9 integrated with MS-FINDER 3.60
Score5.9898

Identifiers and class information

Inchi keyJMVSBFJBMXQNJW-GIXZANJINA-N
SmilesO=P(O)(O)OP(=O)(O)OCC=C(C)CCC=C(C)CCC=C(C)CCC=C(C)CCC=C(C)C
SuperclassLipids and lipid-like molecules
ClassPrenol lipids

Pharmacokinetic properties

Number of descriptor values(#stars)6
Number of non-conjugated amine groups (#amine)0
Number of amidine and guanidine groups (#amidine)0
Number of carboxylic acid groups (#acid)3
Number of non-conjugated amide groups (#amide)0
Number of rotatable bonds (#rotor)20
Number of reactive functional groups (#rtvFG)2
Predicted central nervous system activity (CNS)-2
Molecular weight (mol_MW)518.566
Computed dipole moment(dipole)7.321
Total solvent accessible surface area (SASA)963.45
Hydrophobic component of SASA (FOSA)676.122
Hydrophilic component of SASA (FISA)230.808
Pie component of the SASA (PISA)45.35
Weakly polar component of the SASA (WPSA)11.17
Total solvent accesible volume (volume)1759.28
Number of hydrogen bond donors (donorHB)0
Number of hydrogen bond acceptors (accptHB)7
Free energy of solvation of dipole (dip^2/V)0.0304687
Index of cohesive interaction in solids (ACxDN^.5/SA)0
Globularity descriptor (glob)0.731519
Predicted polarizability in cubic angstroms (QPpolrz)51.843
Predicted hexadecane/gas partition coefficient (QPlogPC16)17.173
Predicted octanol/gas partition coefficient (QPlogPoct)20.954
Predicted water/gas partition coefficient (QPlogPw)6.403
Predicted octanol/water partition coefficient (QPlogPo/w)7.409
Predicted aqueous solubility (QPlogS)-7.602
Conformation-independent predicted aqueous solubility (CIQPlogS)-6.839
Predicted IC50 value for blockage of HERG K+ channels (QPlogHERG)-0.67
Predicted apparent Caco-2 cell permeability in nm/sec (QPPCaco)1.042
Predicted brain/blood partition coefficient (QPlogBB)-3.49
Predicted apparent MDCK cell permeability in nm/sec (QPPMDCK)0.701
Predicted skin permeability, log Kp (QPlogKp)-3.693
PM3 calculated ionization potential (IP(ev))9.038
PM3 calculated electron affinity (EA(eV))0.158
Number of likely metabolic reactions (#metab)15
Prediction of binding to human serum albumin (QPlogKhsa)0.52
Predicted qualitative human oral absorption (HumanOralAbsorption)1
Predicted human oral absorption on 0 to 100% scale (PercentHumanOralAbsorption)44.731
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)121.04
Number of nitrogen and oxygen atoms (#NandO)7
Number of violations of Lipinski’s rule of five (RuleOfFive)2
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
P12821ACEAngiotensin-converting enzymeT98311SwissTargetPrediction
P42336PIK3CAPI3-kinase p110-alpha subunitT80276SwissTargetPrediction
P48449LSSLanosterol synthaseT56175SEA
P08473MMENeprilysinT05409SwissTargetPrediction
P15121AKR1B1Aldose reductaseT26623SwissTargetPrediction
P15090FABP4Fatty acid binding protein adipocyteT07217SwissTargetPrediction
Q07869PPARAPeroxisome proliferator-activated receptor alphaT86591SwissTargetPrediction
Q03181PPARDPeroxisome proliferator-activated receptor deltaT36557SwissTargetPrediction
O14842FFAR1Free fatty acid receptor 1T25608SwissTargetPrediction
P08253MMP2Matrix metalloproteinase 2T68251SwissTargetPrediction
P22894MMP8Matrix metalloproteinase 8T08856SwissTargetPrediction
P08254MMP3Matrix metalloproteinase 3T86702SwissTargetPrediction
P14780MMP9Matrix metalloproteinase 9T54156SwissTargetPrediction
O15054KDM6BLysine-specific demethylase 6BT56057SwissTargetPrediction
Q14534SQLESqualene monooxygenase (by homology)T93344SEA
P21731TBXA2RThromboxane A2 receptorT76198SwissTargetPrediction
P55072VCPTransitional endoplasmic reticulum ATPaseT12646SwissTargetPrediction
P45452MMP13Matrix metalloproteinase 13T34296SwissTargetPrediction
P00742F10Thrombin and coagulation factor XT84631SwissTargetPrediction
P37231PPARGPeroxisome proliferator-activated receptor gammaT58921SwissTargetPrediction
Q9Y5Y4PTGDR2G protein-coupled receptor 44T61722SwissTargetPrediction
P49356FNTBFarnesyl protein transferaseT13127SwissTargetPrediction and SEA
Q15722LTB4RLeukotriene B4 receptor 1T59626SwissTargetPrediction
P47871GCGRGlucagon receptorT60182SwissTargetPrediction
P29466CASP1Caspase-1T98269SwissTargetPrediction
P12931SRCTyrosine-protein kinase SRCT85943SwissTargetPrediction
Q96EB6SIRT1NAD-dependent deacetylase sirtuin 1T14731SwissTargetPrediction
P39900MMP12Matrix metalloproteinase 12T03500SwissTargetPrediction
P42574CASP3Caspase-3T57943SwissTargetPrediction
P10619CTSALysosomal protective proteinT37154SwissTargetPrediction
P50281MMP14Matrix metalloproteinase 14T65019SwissTargetPrediction
P55212CASP6Caspase-6T20600SwissTargetPrediction
Q9UQ81MCH5Caspase-8T15700SwissTargetPrediction
P43119PTGIRProstanoid IP receptorT99954SwissTargetPrediction
Q99683MAP3K5Mitogen-activated protein kinase kinase kinase 5T97589SwissTargetPrediction
P21453S1PR1Sphingosine 1-phosphate receptor Edg-1T13852SwissTargetPrediction
P46663BDKRB1Bradykinin B1 receptorT58589SwissTargetPrediction
Q9UHD2TBK1Serine/threonine-protein kinase TBK1T63024SwissTargetPrediction
P53609PGGT1BGeranylgeranyl transferase type IT76396SwissTargetPrediction and SEA
P09238MMP10Matrix metalloproteinase 10T40488SwissTargetPrediction
P42226STAT6Signal transducer and activator of transcription 6T20585SwissTargetPrediction
Q92523CPT1BCarnitine O-palmitoyltransferase 1, muscle isoform (by homology)T75888SwissTargetPrediction
Q13822ENPP2AutotaxinT63512SwissTargetPrediction
P49356FNTBFarnesyl protein transferaseT13127SEA
O95749GGPS1GeranyltranstransferaseT86528SEA
P53602MVDDiphosphomevalonate decarboxylaseT96862SEA
P55211CASP9Caspase-9T93903SwissTargetPrediction

Target associated diseases

TTD_ID Disease_ID Disease name ICD_11 Uniprot ID Gene names
T98311DI0175Heart failure[ICD-11: BD10-BD1Z]P12821ACE
T98311DI0190Hypertension[ICD-11: BA00-BA04]P12821ACE
T80276DI0062Breast cancer[ICD-11: 2C60-2C6Y]P42336PIK3CA
T80276DI0151Follicular lymphoma[ICD-11: 2A80]P42336PIK3CA
T80276DI0245Malignant haematopoietic neoplasm[ICD-11: 2B33]P42336PIK3CA
T56175DI0035Arterial occlusive disease[ICD-11: BD40]P48449LSS
T05409DI0175Heart failure[ICD-11: BD10-BD1Z]P08473MME
T26623DI0298Neuropathy[ICD-11: 8C0Z]P15121AKR1B1
T26623DI0366Rheumatoid arthritis[ICD-11: FA20]P15121AKR1B1
T86591DI0187Hyperlipidemia[ICD-11: 5C80]Q07869PPARA
T86591DI0188Hyper-lipoproteinaemia[ICD-11: 5C80]Q07869PPARA
T86591DI0417Type 2 diabetes mellitus[ICD-11: 5A11]Q07869PPARA
T36557DI0302Non-alcoholic fatty liver disease[ICD-11: DB92]Q03181PPARD
T36557DI0308Obesity[ICD-11: 5B80-5B81]Q03181PPARD
T25608DI0417Type 2 diabetes mellitus[ICD-11: 5A11]O14842FFAR1
T68251DI0238Lung cancer[ICD-11: 2C25]P08253MMP2
T08856DI0366Rheumatoid arthritis[ICD-11: FA20]P22894MMP8
T86702DI0101Corneal disease[ICD-11: 9A76-9A78]P08254MMP3
T86702DI0179Hepatitis virus infection[ICD-11: 1E50-1E51]P08254MMP3
T86702DI0199Idiopathic interstitial pneumonitis[ICD-11: CB03]P08254MMP3
T86702DI0275Multiple sclerosis[ICD-11: 8A40]P08254MMP3
T86702DI0287Myocardial infarction[ICD-11: BA41-BA43]P08254MMP3
T86702DI0320Osteoarthritis[ICD-11: FA00-FA05]P08254MMP3
T86702DI0366Rheumatoid arthritis[ICD-11: FA20]P08254MMP3
T54156DI0219Ischaemic/haemorrhagic stroke[ICD-11: 8B20]P14780MMP9
T54156DI0391Solid tumour/cancer[ICD-11: 2A00-2F9Z]P14780MMP9
T54156DI0395Stomach cancer[ICD-11: 2B72]P14780MMP9
T54156DI0419Ulcerative colitis[ICD-11: DD71]P14780MMP9
T93344DI0118Dermatophytosis[ICD-11: 1F28]Q14534SQLE
T93344DI0385Skin fungal infection disorder[ICD-11: EA60]Q14534SQLE
T76198DI0102Coronary atherosclerosis[ICD-11: BA52]P21731TBXA2R
T76198DI0121Diabetic foot ulcer[ICD-11: BD54]P21731TBXA2R
T76198DI0287Myocardial infarction[ICD-11: BA41-BA43]P21731TBXA2R
T76198DI0378Sexual dysfunction[ICD-11: HA00-HA01]P21731TBXA2R
T12646DI0012Acute myeloid leukaemia[ICD-11: 2A60]P55072VCP
T12646DI0274Multiple myeloma[ICD-11: 2A83]P55072VCP
T12646DI0284Myelodysplastic syndrome[ICD-11: 2A37]P55072VCP
T12646DI0391Solid tumour/cancer[ICD-11: 2A00-2F9Z]P55072VCP
T34296DI0391Solid tumour/cancer[ICD-11: 2A00-2F9Z]P45452MMP13
T84631DI0053Blood-forming organ disease[ICD-11: 3C0Z]P00742F10
T84631DI0080Christmas disease[ICD-11: 3B11]P00742F10
T84631DI0091Coagulation defect[ICD-11: 3B10]P00742F10
T84631DI0103Coronary thrombosis[ICD-11: BA43]P00742F10
T84631DI0114Deep vein thrombosis[ICD-11: BD71]P00742F10
T84631DI0397Supraventricular tachyarrhythmia[ICD-11: BC81]P00742F10
T84631DI0405Thrombosis[ICD-11: DB61-GB90]P00742F10
T84631DI0433Venous thromboembolism[ICD-11: BD72]P00742F10
T58921DI0009Acute diabete complication[ICD-11: 5A2Y]P37231PPARG
T58921DI0025Alzheimer disease[ICD-11: 8A20]P37231PPARG
T58921DI0417Type 2 diabetes mellitus[ICD-11: 5A11]P37231PPARG
T61722DI0102Coronary atherosclerosis[ICD-11: BA52]Q9Y5Y4PTGDR2
T13127DI0342Premature ageing appearance[ICD-11: LD2B]P49356FNTB
T59626DI0184Human immunodeficiency virus disease[ICD-11: 1C60-1C62]Q15722LTB4R
T59626DI0355Pulmonary disease[ICD-11: 1B10-1F85]Q15722LTB4R
T59626DI0361Renal cell carcinoma[ICD-11: 2C90]Q15722LTB4R
T60182DI0193Hypo-glycaemia[ICD-11: 5A41]P47871GCGR
T98269DI0134Epilepsy/seizure[ICD-11: 8A61-8A6Z]P29466CASP1
T98269DI0146Fibrosis[ICD-11: GA14-GC01]P29466CASP1
T98269DI0366Rheumatoid arthritis[ICD-11: FA20]P29466CASP1
T98269DI0417Type 2 diabetes mellitus[ICD-11: 5A11]P29466CASP1
T85943DI0062Breast cancer[ICD-11: 2C60-2C6Y]P12931SRC
T85943DI0220Ischemia[ICD-11: 8B10-8B11]P12931SRC
T85943DI0286Myeloproliferative neoplasm[ICD-11: 2A20]P12931SRC
T85943DI0391Solid tumour/cancer[ICD-11: 2A00-2F9Z]P12931SRC
T14731DI0366Rheumatoid arthritis[ICD-11: FA20]Q96EB6SIRT1
T14731DI0399Systemic sclerosis[ICD-11: 4A42]Q96EB6SIRT1
T14731DI0431Vasculitis[ICD-11: 4A44]Q96EB6SIRT1
T03500DI0037Asthma[ICD-11: CA23]P39900MMP12
T03500DI0238Lung cancer[ICD-11: 2C25]P39900MMP12
T03500DI0361Renal cell carcinoma[ICD-11: 2C90]P39900MMP12
T57943DI0060Brain cancer[ICD-11: 2A00]P42574CASP3
T37154DI0009Acute diabete complication[ICD-11: 5A2Y]P10619CTSA
T65019DI0178Hepatic fibrosis/cirrhosis[ICD-11: DB93]P50281MMP14
T15700DI0120Diabetes mellitus[ICD-11: 5A10]Q9UQ81MCH5
T15700DI0391Solid tumour/cancer[ICD-11: 2A00-2F9Z]Q9UQ81MCH5
T99954DI0003Abortion[ICD-11: JA00]P43119PTGIR
T99954DI0102Coronary atherosclerosis[ICD-11: BA52]P43119PTGIR
T99954DI0356Pulmonary hypertension[ICD-11: BB01]P43119PTGIR
T97589DI0083Chronic kidney disease[ICD-11: GB61]Q99683MAP3K5
T97589DI0356Pulmonary hypertension[ICD-11: BB01]Q99683MAP3K5
T13852DI0275Multiple sclerosis[ICD-11: 8A40]P21453S1PR1
T13852DI0419Ulcerative colitis[ICD-11: DD71]P21453S1PR1
T58589DI0320Osteoarthritis[ICD-11: FA00-FA05]P46663BDKRB1
T58589DI0365Retinopathy[ICD-11: 9B71]P46663BDKRB1
T58589DI0366Rheumatoid arthritis[ICD-11: FA20]P46663BDKRB1
T76396DI0241Lymphoma[ICD-11: 2A80-2A86]P53609PGGT1B
T75888DI0030Angina pectoris[ICD-11: BA40]Q92523CPT1B
T75888DI0265Mild neurocognitive disorder[ICD-11: 6D71]Q92523CPT1B
T75888DI0306Nutritional deficiency[ICD-11: 5B50-5B71]Q92523CPT1B
T63512DI0199Idiopathic interstitial pneumonitis[ICD-11: CB03]Q13822ENPP2
T13127DI0342Premature ageing appearance[ICD-11: LD2B]P49356FNTB
T86528DI0057Bone paget disease[ICD-11: FB85]O95749GGPS1
T86528DI0237Low bone mass disorder[ICD-11: FB83]O95749GGPS1
T86528DI0267Mineral excesses[ICD-11: 5B91]O95749GGPS1
T86528DI0281Musculoskeletal disorder[ICD-11: FA00-FC0Z]O95749GGPS1
T93903DI0110Cystic fibrosis[ICD-11: CA25]P55211CASP9

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