P1-uridyl-P2-methyl diphosphate



Compound IDCDAMM01547
Common nameP1-uridyl-P2-methyl diphosphate
IUPAC name[[(2R,3S,4R,5R)-5-(2,4-dioxopyrimidin-1-yl)-3,4-dihydroxyoxolan-2-yl]methoxy-oxidophosphoryl] methyl phosphate
Molecular formulaC10H14N2O12P2

Experimental data

Retention time17.56
Adduct[M+H]+
Actual mz417.014
Theoretical mz417.009
Error11.09
Ionizaton modePositive
Instrument typeLC-MS/MS-QTOF, spectrum predicted by MS-DIAL v4.9 integrated with MS-FINDER 3.60
Score7.0584

Identifiers and class information

Inchi keyQEXWQSCECHIMQL-UNDLAESJNA-L
SmilesO=C1N=C([O-])C=CN1C2OC(COP(=O)(O)OP(=O)([O-])OC)C(O)C2O
SuperclassNucleosides, nucleotides, and analogues
ClassPyrimidine nucleotides

Pharmacokinetic properties

Number of descriptor values(#stars)5
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)10
Number of reactive functional groups (#rtvFG)3
Predicted central nervous system activity (CNS)-2
Molecular weight (mol_MW)418.19
Computed dipole moment(dipole)13.835
Total solvent accessible surface area (SASA)523.324
Hydrophobic component of SASA (FOSA)109.861
Hydrophilic component of SASA (FISA)369.174
Pie component of the SASA (PISA)31.56
Weakly polar component of the SASA (WPSA)12.729
Total solvent accesible volume (volume)986.463
Number of hydrogen bond donors (donorHB)3
Number of hydrogen bond acceptors (accptHB)16.6
Free energy of solvation of dipole (dip^2/V)0.194023
Index of cohesive interaction in solids (ACxDN^.5/SA)0.0549412
Globularity descriptor (glob)0.91576
Predicted polarizability in cubic angstroms (QPpolrz)27.205
Predicted hexadecane/gas partition coefficient (QPlogPC16)11.261
Predicted octanol/gas partition coefficient (QPlogPoct)25.638
Predicted water/gas partition coefficient (QPlogPw)22.247
Predicted octanol/water partition coefficient (QPlogPo/w)-2.254
Predicted aqueous solubility (QPlogS)-0.157
Conformation-independent predicted aqueous solubility (CIQPlogS)-1.724
Predicted IC50 value for blockage of HERG K+ channels (QPlogHERG)0.569
Predicted apparent Caco-2 cell permeability in nm/sec (QPPCaco)0.201
Predicted brain/blood partition coefficient (QPlogBB)-2.943
Predicted apparent MDCK cell permeability in nm/sec (QPPMDCK)0.095
Predicted skin permeability, log Kp (QPlogKp)-7.252
PM3 calculated ionization potential (IP(ev))9.342
PM3 calculated electron affinity (EA(eV))0.428
Number of likely metabolic reactions (#metab)3
Prediction of binding to human serum albumin (QPlogKhsa)-1.876
Predicted qualitative human oral absorption (HumanOralAbsorption)1
Predicted human oral absorption on 0 to 100% scale (PercentHumanOralAbsorption)0
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)230.032
Number of nitrogen and oxygen atoms (#NandO)14
Number of violations of Lipinski’s rule of five (RuleOfFive)1
Number of violations of Jorgensen’s rule of three (RuleOfThree)1

Compound-target network

Cytoscape Graph

Protein targets associated with phytocompound

Uniprot ID Gene name Target name TTD_ID Prediction source
P07327ADH1AAlcohol dehydrogenase alpha chainT65570SEA
P04818TYMSThymidylate synthase (by homology)T98397SwissTargetPrediction
P0DMS8ADORA3Adenosine A3 receptorT36059SEA
P49137MAPKAPK2MAP kinase-activated protein kinase 2T21307SwissTargetPrediction
P06746POLBDNA polymerase beta (by homology)T06958SwissTargetPrediction and SEA
P0DMV8HSPA1AHeat shock 70 kDa protein 1T49639SwissTargetPrediction
P12931SRCTyrosine-protein kinase SRCT85943SwissTargetPrediction
P32320CDACytidine deaminase (by homology)T79027SEA
P55263ADKAdenosine kinaseT91661SEA
P11142HSPA8Heat shock cognate 71 kDa proteinT12817SwissTargetPrediction
P04406GAPDHGlyceraldehyde-3-phosphate dehydrogenase liverT39321SEA
P11021HSPA578 kDa glucose-regulated proteinT77594SwissTargetPrediction
P20839IMPDH1Inosine-5'-monophosphate dehydrogenase 1T40111SEA
P12268IMPDH2Inosine-5'-monophosphate dehydrogenase 2T89360SwissTargetPrediction and SEA
P47900P2RY1Purinergic receptor P2Y1T67818SwissTargetPrediction and SEA
P41231P2RY2Purinergic receptor P2Y2T93515SwissTargetPrediction and SEA
Q15077P2RY6Pyrimidinergic receptor P2Y6T90782SwissTargetPrediction and SEA
P63000RAC1Ras-related C3 botulinum toxin substrate 1T88752SwissTargetPrediction and SEA
P06730EIF4EEukaryotic translation initation factor (by homology)T31186SwissTargetPrediction
P16885PLCG2Phospholipase C-gamma-2T93922SEA
P23919DTYMKThymidylate kinaseT94400SEA
P11172UMPSUridine 5'-monophosphate synthaseT15851SwissTargetPrediction and SEA
O94759TRPM2Transient receptor potential cation channel subfamily M member 2T78205SEA
Q15391P2RY14Purinergic receptor P2Y14T16555SwissTargetPrediction and SEA
Q05823RNASELRNase LT25200SEA
P51575P2RX1P2X purinoceptor 1T69091SEA
P28340POLD1DNA polymerase delta subunit 1T02258SEA
Q99571P2RX4P2X purinoceptor 4T60330SEA
P11717IGF2RInsulin-like growth factor II receptorT59550SEA
Q13304GPR17Uracil nucleotide/cysteinyl leukotriene receptorT33902SEA
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
T98397DI0391Solid tumour/cancer[ICD-11: 2A00-2F9Z]P04818TYMS
T98397DI0395Stomach cancer[ICD-11: 2B72]P04818TYMS
T36059DI0351Psoriasis[ICD-11: EA90]P0DMS8ADORA3
T36059DI0391Solid tumour/cancer[ICD-11: 2A00-2F9Z]P0DMS8ADORA3
T21307DI0011Acute laryngitis/tracheitis[ICD-11: CA05]P49137MAPKAPK2
T21307DI0181Hidradenitis suppurativa[ICD-11: ED92]P49137MAPKAPK2
T21307DI0269Monogenic autoinflammatory syndrome[ICD-11: 4A60]P49137MAPKAPK2
T21307DI0334Peritoneal cancer[ICD-11: 2C51]P49137MAPKAPK2
T21307DI0352Psoriatic arthritis[ICD-11: FA21]P49137MAPKAPK2
T21307DI0366Rheumatoid arthritis[ICD-11: FA20]P49137MAPKAPK2
T21307DI0391Solid tumour/cancer[ICD-11: 2A00-2F9Z]P49137MAPKAPK2
T06958DI0391Solid tumour/cancer[ICD-11: 2A00-2F9Z]P06746POLB
T49639DI0121Diabetic foot ulcer[ICD-11: BD54]P0DMV8HSPA1A
T49639DI0180Herpes simplex infection[ICD-11: 1F00]P0DMV8HSPA1A
T49639DI0231Leukaemia[ICD-11: 2A60-2B33]P0DMV8HSPA1A
T49639DI0244Malignant digestive organ neoplasm[ICD-11: 2C11]P0DMV8HSPA1A
T49639DI0260Metastatic malignant neoplasm[ICD-11: 2D50-2E09]P0DMV8HSPA1A
T49639DI0298Neuropathy[ICD-11: 8C0Z]P0DMV8HSPA1A
T49639DI0391Solid tumour/cancer[ICD-11: 2A00-2F9Z]P0DMV8HSPA1A
T49639DI0395Stomach cancer[ICD-11: 2B72]P0DMV8HSPA1A
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
T79027DI0391Solid tumour/cancer[ICD-11: 2A00-2F9Z]P32320CDA
T91661DI0134Epilepsy/seizure[ICD-11: 8A61-8A6Z]P55263ADK
T39321DI0279Muscular atrophy[ICD-11: 8B61]P04406GAPDH
T39321DI0280Muscular dystrophy[ICD-11: 8C70]P04406GAPDH
T77594DI0252Melanoma[ICD-11: 2C30]P11021HSPA5
T77594DI0391Solid tumour/cancer[ICD-11: 2A00-2F9Z]P11021HSPA5
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
T02258DI0391Solid tumour/cancer[ICD-11: 2A00-2F9Z]P28340POLD1
T59550DI0146Fibrosis[ICD-11: GA14-GC01]P11717IGF2R
T59550DI0368Sarcoidosis[ICD-11: 4B20]P11717IGF2R

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