dTDP-D-glucose



Compound IDCDAMM02514
Common namedTDP-D-glucose
IUPAC name[hydroxy-[[3-hydroxy-5-(5-methyl-2,4-dioxopyrimidin-1-yl)oxolan-2-yl]methoxy]phosphoryl] [3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl] hydrogen phosphate
Molecular formulaC16H26N2O16P2

Experimental data

Retention time13.6
Adduct[M+Na]+
Actual mz587.066
Theoretical mz587.065
Error1.67
Ionizaton modePositive
Instrument typeLC-MS/MS-QTOF, spectrum predicted by MS-DIAL v4.9 integrated with MS-FINDER 3.60
Score5.4852

Identifiers and class information

Inchi keyYSYKRGRSMLTJNL-KFQCIAAJSA-N
SmilesO=C1NC(=O)N(C=C1C)C2OC(COP(=O)(O)OP(=O)(O)OC3OC(CO)C(O)C(O)C3O)C(O)C2
SuperclassNucleosides, nucleotides, and analogues
ClassPyrimidine nucleotides

Pharmacokinetic properties

Number of descriptor values(#stars)8
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)15
Number of reactive functional groups (#rtvFG)3
Predicted central nervous system activity (CNS)-2
Molecular weight (mol_MW)564.333
Computed dipole moment(dipole)13.364
Total solvent accessible surface area (SASA)706.073
Hydrophobic component of SASA (FOSA)308.108
Hydrophilic component of SASA (FISA)385.619
Pie component of the SASA (PISA)10.164
Weakly polar component of the SASA (WPSA)2.181
Total solvent accesible volume (volume)1361
Number of hydrogen bond donors (donorHB)6
Number of hydrogen bond acceptors (accptHB)23.4
Free energy of solvation of dipole (dip^2/V)0.131233
Index of cohesive interaction in solids (ACxDN^.5/SA)0.0811787
Globularity descriptor (glob)0.841179
Predicted polarizability in cubic angstroms (QPpolrz)38.779
Predicted hexadecane/gas partition coefficient (QPlogPC16)14.979
Predicted octanol/gas partition coefficient (QPlogPoct)36.591
Predicted water/gas partition coefficient (QPlogPw)32.639
Predicted octanol/water partition coefficient (QPlogPo/w)-3.037
Predicted aqueous solubility (QPlogS)-0.618
Conformation-independent predicted aqueous solubility (CIQPlogS)-1.896
Predicted IC50 value for blockage of HERG K+ channels (QPlogHERG)-0.535
Predicted apparent Caco-2 cell permeability in nm/sec (QPPCaco)0.14
Predicted brain/blood partition coefficient (QPlogBB)-3.968
Predicted apparent MDCK cell permeability in nm/sec (QPPMDCK)0.056
Predicted skin permeability, log Kp (QPlogKp)-7.151
PM3 calculated ionization potential (IP(ev))9.1
PM3 calculated electron affinity (EA(eV))0.813
Number of likely metabolic reactions (#metab)7
Prediction of binding to human serum albumin (QPlogKhsa)-2.237
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)286.412
Number of nitrogen and oxygen atoms (#NandO)18
Number of violations of Lipinski’s rule of five (RuleOfFive)3
Number of violations of Jorgensen’s rule of three (RuleOfThree)2

Compound-target network

Cytoscape Graph

Protein targets associated with phytocompound

Uniprot ID Gene name Target name TTD_ID Prediction source
P04818TYMSThymidylate synthase (by homology)T98397SwissTargetPrediction and SEA
P04183TK1Thymidine kinase, cytosolicT30081SwissTargetPrediction and SEA
P06746POLBDNA polymerase beta (by homology)T06958SwissTargetPrediction and SEA
P06276BCHEButyrylcholinesteraseT99799SEA
P15692VEGFAVascular endothelial growth factor AT20761SEA
P05230FGF1Acidic fibroblast growth factorT18639SEA
P09038FGF2Basic fibroblast growth factorT31621SEA
P19971TYMPThymidine phosphorylaseT59929SEA
P47900P2RY1Purinergic receptor P2Y1T67818SEA
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
P23919DTYMKThymidylate kinaseT94400SEA
P11172UMPSUridine 5'-monophosphate synthaseT15851SEA
O94759TRPM2Transient receptor potential cation channel subfamily M member 2T78205SEA
O00142TK2Thymidine kinase, mitochondrialT22976SEA
Q15391P2RY14Purinergic receptor P2Y14T16555SwissTargetPrediction and SEA
Q05823RNASELRNase LT25200SEA
P51575P2RX1P2X purinoceptor 1T69091SEA
P28340POLD1DNA polymerase delta subunit 1T02258SwissTargetPrediction
P28340POLD1DNA polymerase delta subunit 1T02258SwissTargetPrediction and SEA
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
T98397DI0391Solid tumour/cancer[ICD-11: 2A00-2F9Z]P04818TYMS
T98397DI0395Stomach cancer[ICD-11: 2B72]P04818TYMS
T30081DI0012Acute myeloid leukaemia[ICD-11: 2A60]P04183TK1
T30081DI0184Human immunodeficiency virus disease[ICD-11: 1C60-1C62]P04183TK1
T06958DI0391Solid tumour/cancer[ICD-11: 2A00-2F9Z]P06746POLB
T99799DI0324Pain[ICD-11: MG30-MG3Z]P06276BCHE
T99799DI0411Tonus and reflex abnormality[ICD-11: MB47]P06276BCHE
T20761DI0095Colorectal cancer[ICD-11: 2B91]P15692VEGFA
T20761DI0365Retinopathy[ICD-11: 9B71]P15692VEGFA
T20761DI0430Vascular system developmental anomaly[ICD-11: LA90]P15692VEGFA
T18639DI0081Chronic arterial occlusive disease[ICD-11: BD4Z]P05230FGF1
T18639DI0102Coronary atherosclerosis[ICD-11: BA52]P05230FGF1
T31621DI0005Acne vulgaris[ICD-11: ED80]P09038FGF2
T59929DI0117Depression[ICD-11: 6A70-6A7Z]P19971TYMP
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
T02258DI0391Solid tumour/cancer[ICD-11: 2A00-2F9Z]P28340POLD1
T02258DI0391Solid tumour/cancer[ICD-11: 2A00-2F9Z]P28340POLD1
T59550DI0146Fibrosis[ICD-11: GA14-GC01]P11717IGF2R
T59550DI0368Sarcoidosis[ICD-11: 4B20]P11717IGF2R

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