2-(cyclopentylformamido)-3-(2,4-dioxo-1,2,3,4-tetrahydropyrimidin-1-yl)propanoic acid



Compound IDCDAMM00112
Common name2-(cyclopentylformamido)-3-(2,4-dioxo-1,2,3,4-tetrahydropyrimidin-1-yl)propanoic acid
IUPAC name2-(cyclopentanecarbonylamino)-3-(2,4-dioxopyrimidin-1-yl)propanoic acid
Molecular formulaC13H17N3O5

Experimental data

Retention time29.92
Adduct[M+H]+
Actual mz296.125
Theoretical mz296.124
Error3.07
Ionizaton modePositive
Instrument typeLC-MS/MS-QTOF, spectrum predicted by MS-DIAL v4.9 integrated with MS-FINDER 3.60
Score6.1083

Identifiers and class information

Inchi keyNDUYBZNXWIUCHG-UHFFFAOYSA-N
SmilesC1CCC(C1)C(=O)NC(CN2C=CC(=O)NC2=O)C(=O)O
SuperclassOrganic acids and derivatives
ClassCarboxylic acids and derivatives

Pharmacokinetic properties

Number of descriptor values(#stars)1
Number of non-conjugated amine groups (#amine)0
Number of amidine and guanidine groups (#amidine)0
Number of carboxylic acid groups (#acid)1
Number of non-conjugated amide groups (#amide)1
Number of rotatable bonds (#rotor)5
Number of reactive functional groups (#rtvFG)0
Predicted central nervous system activity (CNS)-2
Molecular weight (mol_MW)295.294
Computed dipole moment(dipole)12.752
Total solvent accessible surface area (SASA)540.6
Hydrophobic component of SASA (FOSA)252.476
Hydrophilic component of SASA (FISA)224.856
Pie component of the SASA (PISA)63.268
Weakly polar component of the SASA (WPSA)0
Total solvent accesible volume (volume)922.817
Number of hydrogen bond donors (donorHB)2.25
Number of hydrogen bond acceptors (accptHB)7.25
Free energy of solvation of dipole (dip^2/V)0.176205
Index of cohesive interaction in solids (ACxDN^.5/SA)0.0201166
Globularity descriptor (glob)0.847943
Predicted polarizability in cubic angstroms (QPpolrz)28.171
Predicted hexadecane/gas partition coefficient (QPlogPC16)9.285
Predicted octanol/gas partition coefficient (QPlogPoct)18.811
Predicted water/gas partition coefficient (QPlogPw)13.83
Predicted octanol/water partition coefficient (QPlogPo/w)0.41
Predicted aqueous solubility (QPlogS)-2.28
Conformation-independent predicted aqueous solubility (CIQPlogS)-2.116
Predicted IC50 value for blockage of HERG K+ channels (QPlogHERG)-1.112
Predicted apparent Caco-2 cell permeability in nm/sec (QPPCaco)12.708
Predicted brain/blood partition coefficient (QPlogBB)-1.823
Predicted apparent MDCK cell permeability in nm/sec (QPPMDCK)8.43
Predicted skin permeability, log Kp (QPlogKp)-4.961
PM3 calculated ionization potential (IP(ev))9.844
PM3 calculated electron affinity (EA(eV))0.619
Number of likely metabolic reactions (#metab)2
Prediction of binding to human serum albumin (QPlogKhsa)-0.881
Predicted qualitative human oral absorption (HumanOralAbsorption)2
Predicted human oral absorption on 0 to 100% scale (PercentHumanOralAbsorption)49.109
Solvent-accessible surface area of fluorine atoms (SAFluorine)0
Solvent-accessible surface area of amide oxygen atoms (SAamideO)20.491
Van der Waals surface area (PSA)153.299
Number of nitrogen and oxygen atoms (#NandO)8
Number of violations of Lipinski’s rule of five (RuleOfFive)0
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
P08473MMENeprilysinT05409SEA
P42261GRIA1Glutamate receptor ionotropic, AMPA 1T33584SEA
Q16478GRIK5Glutamate receptor ionotropic kainate 5T87930SEA
P42262GRIA2Glutamate receptor ionotropic, AMPA 2T42392SEA
P51681CCR5C-C chemokine receptor type 5T09960SEA
Q9BYF1ACE2Angiotensin-converting enzyme 2T27889SEA
P05556ITGB1Integrin alpha2/beta1T01851SEA
O00763ACACBAcetyl-CoA carboxylase 2T08922SEA
P26010ITGB7Integrin alpha-4/beta-7T07403SEA
P41231P2RY2Purinergic receptor P2Y2T93515SEA
Q15077P2RY6Pyrimidinergic receptor P2Y6T90782SEA
P03951F11Coagulation factor XIT46040SEA
O14939PLD2Phospholipase D2T10383SEA
Q13451FKBP5Peptidyl-prolyl cis-trans isomerase FKBP5T98337SEA
P33316DUTdUTP pyrophosphataseT39054SEA
P13612ITGA4Integrin alpha-4T97587SEA
Q9UJM8HAO1Hydroxyacid oxidase 1T63170SEA
Q96SW2CRBNProtein cereblonT27861SEA

Target associated diseases

TTD_ID Disease_ID Disease name ICD_11 Uniprot ID Gene names
T05409DI0175Heart failure[ICD-11: BD10-BD1Z]P08473MME
T33584DI0298Neuropathy[ICD-11: 8C0Z]P42261GRIA1
T42392DI0298Neuropathy[ICD-11: 8C0Z]P42262GRIA2
T09960DI0184Human immunodeficiency virus disease[ICD-11: 1C60-1C62]P51681CCR5
T27889DI0009Acute diabete complication[ICD-11: 5A2Y]Q9BYF1ACE2
T27889DI0217Intrathoracic organs injury[ICD-11: NB32]Q9BYF1ACE2
T27889DI0356Pulmonary hypertension[ICD-11: BB01]Q9BYF1ACE2
T01851DI0060Brain cancer[ICD-11: 2A00]P05556ITGB1
T01851DI0238Lung cancer[ICD-11: 2C25]P05556ITGB1
T01851DI0365Retinopathy[ICD-11: 9B71]P05556ITGB1
T08922DI0417Type 2 diabetes mellitus[ICD-11: 5A11]O00763ACACB
T07403DI0107Crohn disease[ICD-11: DD70]P26010ITGB7
T93515DI0436Visual system disease[ICD-11: 9E1Z]P41231P2RY2
T90782DI0025Alzheimer disease[ICD-11: 8A20]Q15077P2RY6
T46040DI0074Cerebral ischaemic stroke[ICD-11: 8B11]P03951F11
T46040DI0089Clotting disorder[ICD-11: 3B4Z]P03951F11
T10383DI0091Coagulation defect[ICD-11: 3B10]O14939PLD2
T39054DI0238Lung cancer[ICD-11: 2C25]P33316DUT
T39054DI0391Solid tumour/cancer[ICD-11: 2A00-2F9Z]P33316DUT
T97587DI0107Crohn disease[ICD-11: DD70]P13612ITGA4
T97587DI0275Multiple sclerosis[ICD-11: 8A40]P13612ITGA4
T97587DI0419Ulcerative colitis[ICD-11: DD71]P13612ITGA4
T63170DI0201Inborn carbohydrate metabolism error[ICD-11: 5C51]Q9UJM8HAO1
T27861DI0060Brain cancer[ICD-11: 2A00]Q96SW2CRBN
T27861DI0123Diffuse large B-cell lymphoma[ICD-11: 2A81]Q96SW2CRBN
T27861DI0235Liver cancer[ICD-11: 2C12]Q96SW2CRBN
T27861DI0239Lupus erythematosus[ICD-11: 4A40]Q96SW2CRBN
T27861DI0241Lymphoma[ICD-11: 2A80-2A86]Q96SW2CRBN
T27861DI0249Mature B-cell leukaemia[ICD-11: 2A82]Q96SW2CRBN
T27861DI0274Multiple myeloma[ICD-11: 2A83]Q96SW2CRBN
T27861DI0368Sarcoidosis[ICD-11: 4B20]Q96SW2CRBN
T27861DI0391Solid tumour/cancer[ICD-11: 2A00-2F9Z]Q96SW2CRBN

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