Compound ID	CDAMM02515
Common name	4,6-Dideoxy-4-oxo-dTDP-D-glucose
IUPAC name	(3,4-dihydroxy-6-methyl-5-oxooxan-2-yl) [hydroxy-[[3-hydroxy-5-(5-methyl-2,4-dioxopyrimidin-1-yl)oxolan-2-yl]methoxy]phosphoryl] hydrogen phosphate
Molecular formula	C₁₆H₂₄N₂O₁₅P₂

Experimental data

Retention time	24
Adduct	[M+H]+
Actual mz	547.066
Theoretical mz	547.072
Error	11.47
Ionizaton mode	Positive
Instrument type	LC-MS/MS-QTOF, spectrum predicted by MS-DIAL v4.9 integrated with MS-FINDER 3.60
Score	6.0374

Identifiers and class information

Inchi key	PSXWNITXWWECNY-SRPWTXKTSA-N
Smiles	O=C1NC(=O)N(C=C1C)C2OC(COP(=O)(O)OP(=O)(O)OC3OC(C(=O)C(O)C3O)C)C(O)C2
Superclass	Nucleosides, nucleotides, and analogues
Class	Pyrimidine nucleotides

Plant source

Convolvulus prostratus Forssk.

External sources

HMDB ID	HMDB0001399
KNApSAcK ID
FooDB ID	FDB022601
DrugBank ID
ChEBI ID	CHEBI:15744
Pubchem Compound ID	685
PlantCyc ID	DTDP-DEOH-DEOXY-GLUC
UNPD ID
Coconut ID	CNP0343624
LipidMAPS ID
NANPDB ID

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)	2
Number of non-conjugated amide groups (#amide)	0
Number of rotatable bonds (#rotor)	12
Number of reactive functional groups (#rtvFG)	4
Predicted central nervous system activity (CNS)	-2
Molecular weight (mol_MW)	546.318
Computed dipole moment(dipole)	6.44
Total solvent accessible surface area (SASA)	671.026
Hydrophobic component of SASA (FOSA)	311.257
Hydrophilic component of SASA (FISA)	344.63
Pie component of the SASA (PISA)	14.572
Weakly polar component of the SASA (WPSA)	0.567
Total solvent accesible volume (volume)	1315.23
Number of hydrogen bond donors (donorHB)	4
Number of hydrogen bond acceptors (accptHB)	22
Free energy of solvation of dipole (dip^2/V)	0.0315316
Index of cohesive interaction in solids (ACxDN^.5/SA)	0.0655712
Globularity descriptor (glob)	0.865153
Predicted polarizability in cubic angstroms (QPpolrz)	38.915
Predicted hexadecane/gas partition coefficient (QPlogPC16)	13.846
Predicted octanol/gas partition coefficient (QPlogPoct)	31.579
Predicted water/gas partition coefficient (QPlogPw)	28.658
Predicted octanol/water partition coefficient (QPlogPo/w)	-2.464
Predicted aqueous solubility (QPlogS)	-0.411
Conformation-independent predicted aqueous solubility (CIQPlogS)	-2.124
Predicted IC50 value for blockage of HERG K+ channels (QPlogHERG)	-0.168
Predicted apparent Caco-2 cell permeability in nm/sec (QPPCaco)	0.343
Predicted brain/blood partition coefficient (QPlogBB)	-3.228
Predicted apparent MDCK cell permeability in nm/sec (QPPMDCK)	0.145
Predicted skin permeability, log Kp (QPlogKp)	-6.668
PM3 calculated ionization potential (IP(ev))	9.263
PM3 calculated electron affinity (EA(eV))	0.443
Number of likely metabolic reactions (#metab)	6
Prediction of binding to human serum albumin (QPlogKhsa)	-2.175
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)	275.733
Number of nitrogen and oxygen atoms (#NandO)	17
Number of violations of Lipinski’s rule of five (RuleOfFive)	3
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
P04818	TYMS	Thymidylate synthase (by homology)	T98397	SwissTargetPrediction and SEA
P04183	TK1	Thymidine kinase, cytosolic	T30081	SwissTargetPrediction and SEA
P06746	POLB	DNA polymerase beta (by homology)	T06958	SwissTargetPrediction and SEA
P19971	TYMP	Thymidine phosphorylase	T59929	SEA
P47900	P2RY1	Purinergic receptor P2Y1	T67818	SEA
P41231	P2RY2	Purinergic receptor P2Y2	T93515	SwissTargetPrediction and SEA
Q15077	P2RY6	Pyrimidinergic receptor P2Y6	T90782	SwissTargetPrediction and SEA
P63000	RAC1	Ras-related C3 botulinum toxin substrate 1	T88752	SEA
P23919	DTYMK	Thymidylate kinase	T94400	SEA
P11172	UMPS	Uridine 5'-monophosphate synthase	T15851	SEA
O94759	TRPM2	Transient receptor potential cation channel subfamily M member 2	T78205	SEA
O00142	TK2	Thymidine kinase, mitochondrial	T22976	SEA
Q15391	P2RY14	Purinergic receptor P2Y14	T16555	SwissTargetPrediction and SEA
Q05823	RNASEL	RNase L	T25200	SEA
P51575	P2RX1	P2X purinoceptor 1	T69091	SEA
P28340	POLD1	DNA polymerase delta subunit 1	T02258	SwissTargetPrediction
P28340	POLD1	DNA polymerase delta subunit 1	T02258	SwissTargetPrediction and SEA
Q99571	P2RX4	P2X purinoceptor 4	T60330	SEA
Q13304	GPR17	Uracil nucleotide/cysteinyl leukotriene receptor	T33902	SEA
Q9Y4W7	PARG	Poly(ADP-ribose) glycohydrolase	T66935	SEA

Target associated diseases

TTD_ID	Disease_ID	Disease name	ICD_11	Uniprot ID	Gene names
T98397	DI0391	Solid tumour/cancer	[ICD-11: 2A00-2F9Z]	P04818	TYMS
T98397	DI0395	Stomach cancer	[ICD-11: 2B72]	P04818	TYMS
T30081	DI0012	Acute myeloid leukaemia	[ICD-11: 2A60]	P04183	TK1
T30081	DI0184	Human immunodeficiency virus disease	[ICD-11: 1C60-1C62]	P04183	TK1
T06958	DI0391	Solid tumour/cancer	[ICD-11: 2A00-2F9Z]	P06746	POLB
T59929	DI0117	Depression	[ICD-11: 6A70-6A7Z]	P19971	TYMP
T93515	DI0436	Visual system disease	[ICD-11: 9E1Z]	P41231	P2RY2
T90782	DI0025	Alzheimer disease	[ICD-11: 8A20]	Q15077	P2RY6
T88752	DI0025	Alzheimer disease	[ICD-11: 8A20]	P63000	RAC1
T22976	DI0206	Inborn purine/pyrimidine/nucleotide metabolism error	[ICD-11: 5C55]	O00142	TK2
T02258	DI0391	Solid tumour/cancer	[ICD-11: 2A00-2F9Z]	P28340	POLD1
T02258	DI0391	Solid tumour/cancer	[ICD-11: 2A00-2F9Z]	P28340	POLD1