N-benzyl-4-(methylsulfanyl)-2-({9-oxo-10,20-diazapentacyclo[11.7.0.0?,??.0?,?.0??,??]icosa-1(13),3,5,7,14,16,18-heptaen-11-yl}formamido)butanamide



Compound IDCDAMM00216
Common nameN-benzyl-4-(methylsulfanyl)-2-({9-oxo-10,20-diazapentacyclo[11.7.0.0?,??.0?,?.0??,??]icosa-1(13),3,5,7,14,16,18-heptaen-11-yl}formamido)butanamide
IUPAC nameN-[1-(benzylamino)-4-methylsulfanyl-1-oxobutan-2-yl]-9-oxo-10,20-diazapentacyclo[11.7.0.02,10.03,8.014,19]icosa-1(13),3,5,7,14,16,18-heptaene-11-carboxamide
Molecular formulaC31H30N4O3S

Experimental data

Retention time29.41
Adduct[M+NH4]+
Actual mz556.237
Theoretical mz556.238
Error0.32
Ionizaton modePositive
Instrument typeLC-MS/MS-QTOF, spectrum predicted by MS-DIAL v4.9 integrated with MS-FINDER 3.60
Score4.7713

Identifiers and class information

Inchi keyQSHBITULIXIKGP-UHFFFAOYSA-N
SmilesCSCCC(C(=O)NCC1=CC=CC=C1)NC(=O)C2CC3=C(C4N2C(=O)C5=CC=CC=C45)NC6=CC=CC=C36
SuperclassOrganoheterocyclic compounds
ClassIndoles and derivatives

Pharmacokinetic properties

Number of descriptor values(#stars)2
Number of non-conjugated amine groups (#amine)0
Number of amidine and guanidine groups (#amidine)0
Number of carboxylic acid groups (#acid)0
Number of non-conjugated amide groups (#amide)2
Number of rotatable bonds (#rotor)8
Number of reactive functional groups (#rtvFG)0
Predicted central nervous system activity (CNS)-1
Molecular weight (mol_MW)538.663
Computed dipole moment(dipole)7.127
Total solvent accessible surface area (SASA)865.981
Hydrophobic component of SASA (FOSA)225.378
Hydrophilic component of SASA (FISA)92.327
Pie component of the SASA (PISA)522.113
Weakly polar component of the SASA (WPSA)26.162
Total solvent accesible volume (volume)1619.19
Number of hydrogen bond donors (donorHB)2.25
Number of hydrogen bond acceptors (accptHB)7.75
Free energy of solvation of dipole (dip^2/V)0.0313663
Index of cohesive interaction in solids (ACxDN^.5/SA)0.0134241
Globularity descriptor (glob)0.770056
Predicted polarizability in cubic angstroms (QPpolrz)58.495
Predicted hexadecane/gas partition coefficient (QPlogPC16)18.472
Predicted octanol/gas partition coefficient (QPlogPoct)27.715
Predicted water/gas partition coefficient (QPlogPw)18.956
Predicted octanol/water partition coefficient (QPlogPo/w)4.826
Predicted aqueous solubility (QPlogS)-6.12
Conformation-independent predicted aqueous solubility (CIQPlogS)-7.066
Predicted IC50 value for blockage of HERG K+ channels (QPlogHERG)-4.994
Predicted apparent Caco-2 cell permeability in nm/sec (QPPCaco)514.784
Predicted brain/blood partition coefficient (QPlogBB)-0.892
Predicted apparent MDCK cell permeability in nm/sec (QPPMDCK)928.459
Predicted skin permeability, log Kp (QPlogKp)-0.614
PM3 calculated ionization potential (IP(ev))8.291
PM3 calculated electron affinity (EA(eV))0.538
Number of likely metabolic reactions (#metab)5
Prediction of binding to human serum albumin (QPlogKhsa)0.429
Predicted qualitative human oral absorption (HumanOralAbsorption)3
Predicted human oral absorption on 0 to 100% scale (PercentHumanOralAbsorption)90.778
Solvent-accessible surface area of fluorine atoms (SAFluorine)0
Solvent-accessible surface area of amide oxygen atoms (SAamideO)51.349
Van der Waals surface area (PSA)107.56
Number of nitrogen and oxygen atoms (#NandO)7
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
P98170XIAPInhibitor of apoptosis protein 3T16769SEA
P00747PLGPlasminogenT89034SEA
P08575PTPRCLeukocyte common antigenT43115SEA
P52732KIF11Kinesin-like protein 1T28484SEA
P00750PLATTissue-type plasminogen activatorT45299SEA
P49356FNTBFarnesyl protein transferaseT13127SEA
P17301ITGA2Integrin alpha-2T55293SEA
P05556ITGB1Integrin alpha2/beta1T01851SEA
P35346SSTR5Somatostatin receptor 5T64830SEA
P30874SSTR2Somatostatin receptor 2T53024SEA
P31391SSTR4Somatostatin receptor 4T62974SEA
P30872SSTR1Somatostatin receptor 1T16633SEA
P32745SSTR3Somatostatin receptor 3T13644SEA
O76074PDE5APhosphodiesterase 5AT07663SEA
P03952KLKB1Plasma kallikreinT82739SEA
P08709F7Coagulation factor VIIT43332SEA
P28074PSMB5Proteasome Macropain subunit MB1T49031SEA
P29371TACR3Neurokinin 3 receptorT29683SEA
Q08752PPIDPeptidyl-prolyl cis-trans isomerase DT52447SEA
P03951F11Coagulation factor XIT46040SEA
P28336NMBRNeuromedin B receptorT68887SEA
Q96DB2HDAC11Histone deacetylase 11T97903SEA
P06734FCER2Immunoglobulin epsilon Fc receptorT67207SEA
Q969S8HDAC10Histone deacetylase 10T94324SEA
P13612ITGA4Integrin alpha-4T97587SEA
Q9HCR9PDE11APhosphodiesterase 11AT99802SEA
Q00975CACNA1BVoltage-gated N-type calcium channel alpha-1B subunitT38338SEA
P21462FPR1Formyl peptide receptor 1T87831SEA
P04070PROCVitamin K-dependent protein CT24836SEA
P00748F12Coagulation factor XIIT38509SEA
P09958FURHUMAN dibasic-processing enzymeT98945SEA
P49356FNTBFarnesyl protein transferaseT13127SEA
Q9HCN6GP6Platelet glycoprotein VIT60514SEA
Q9UCV4C1SComplement C1s componentT76024SEA

Target associated diseases

TTD_ID Disease_ID Disease name ICD_11 Uniprot ID Gene names
T16769DI0259Metastatic lymph node neoplasm[ICD-11: 2D60]P98170XIAP
T89034DI0030Angina pectoris[ICD-11: BA40]P00747PLG
T89034DI0052Bleeding disorder[ICD-11: GA20-GA21]P00747PLG
T89034DI0254Menopausal disorder[ICD-11: GA30]P00747PLG
T89034DI0287Myocardial infarction[ICD-11: BA41-BA43]P00747PLG
T89034DI0345Procedure injury[ICD-11: NE81]P00747PLG
T89034DI0357Pulmonary thromboembolism[ICD-11: BB00]P00747PLG
T43115DI0012Acute myeloid leukaemia[ICD-11: 2A60]P08575PTPRC
T43115DI0414Transplanted organ/tissue[ICD-11: QB63]P08575PTPRC
T28484DI0012Acute myeloid leukaemia[ICD-11: 2A60]P52732KIF11
T28484DI0172Head and neck cancer[ICD-11: 2D42]P52732KIF11
T28484DI0241Lymphoma[ICD-11: 2A80-2A86]P52732KIF11
T28484DI0245Malignant haematopoietic neoplasm[ICD-11: 2B33]P52732KIF11
T28484DI0274Multiple myeloma[ICD-11: 2A83]P52732KIF11
T28484DI0321Ovarian cancer[ICD-11: 2C73]P52732KIF11
T28484DI0361Renal cell carcinoma[ICD-11: 2C90]P52732KIF11
T28484DI0391Solid tumour/cancer[ICD-11: 2A00-2F9Z]P52732KIF11
T45299DI0052Bleeding disorder[ICD-11: GA20-GA21]P00750PLAT
T45299DI0345Procedure injury[ICD-11: NE81]P00750PLAT
T13127DI0342Premature ageing appearance[ICD-11: LD2B]P49356FNTB
T55293DI0095Colorectal cancer[ICD-11: 2B91]P17301ITGA2
T55293DI0391Solid tumour/cancer[ICD-11: 2A00-2F9Z]P17301ITGA2
T01851DI0060Brain cancer[ICD-11: 2A00]P05556ITGB1
T01851DI0238Lung cancer[ICD-11: 2C25]P05556ITGB1
T01851DI0365Retinopathy[ICD-11: 9B71]P05556ITGB1
T64830DI0108Cushing syndrome[ICD-11: 5A70]P35346SSTR5
T53024DI0108Cushing syndrome[ICD-11: 5A70]P30874SSTR2
T53024DI0122Diagnostic imaging[ICD-11: N.A.]P30874SSTR2
T53024DI0337Pituitary gland disorder[ICD-11: 5A60-5A61]P30874SSTR2
T62974DI0087Chronic pain[ICD-11: MG30]P31391SSTR4
T62974DI0179Hepatitis virus infection[ICD-11: 1E50-1E51]P31391SSTR4
T16633DI0108Cushing syndrome[ICD-11: 5A70]P30872SSTR1
T16633DI0395Stomach cancer[ICD-11: 2B72]P30872SSTR1
T13644DI0108Cushing syndrome[ICD-11: 5A70]P32745SSTR3
T07663DI0190Hypertension[ICD-11: BA00-BA04]O76074PDE5A
T07663DI0213Innate/adaptive immunodeficiency[ICD-11: 4A00]O76074PDE5A
T07663DI0378Sexual dysfunction[ICD-11: HA00-HA01]O76074PDE5A
T07663DI0411Tonus and reflex abnormality[ICD-11: MB47]O76074PDE5A
T82739DI0213Innate/adaptive immunodeficiency[ICD-11: 4A00]P03952KLKB1
T82739DI0364Retinal vascular occlusion[ICD-11: 9B74]P03952KLKB1
T43332DI0091Coagulation defect[ICD-11: 3B10]P08709F7
T29683DI0254Menopausal disorder[ICD-11: GA30]P29371TACR3
T46040DI0074Cerebral ischaemic stroke[ICD-11: 8B11]P03951F11
T46040DI0089Clotting disorder[ICD-11: 3B4Z]P03951F11
T68887DI0062Breast cancer[ICD-11: 2C60-2C6Y]P28336NMBR
T68887DI0391Solid tumour/cancer[ICD-11: 2A00-2F9Z]P28336NMBR
T67207DI0231Leukaemia[ICD-11: 2A60-2B33]P06734FCER2
T94324DI0391Solid tumour/cancer[ICD-11: 2A00-2F9Z]Q969S8HDAC10
T97587DI0107Crohn disease[ICD-11: DD70]P13612ITGA4
T97587DI0275Multiple sclerosis[ICD-11: 8A40]P13612ITGA4
T97587DI0419Ulcerative colitis[ICD-11: DD71]P13612ITGA4
T38338DI0264Migraine[ICD-11: 8A80]Q00975CACNA1B
T38338DI0305Non-thrombocytopenic purpura[ICD-11: 3B60]Q00975CACNA1B
T38338DI0324Pain[ICD-11: MG30-MG3Z]Q00975CACNA1B
T87831DI0333Peptic ulcer[ICD-11: DA61]P21462FPR1
T24836DI0084Chronic lower extremities peripheral venous insufficiency[ICD-11: BD74]P04070PROC
T24836DI0177Hemangioma[ICD-11: 2E81-2F2Y]P04070PROC
T38509DI0213Innate/adaptive immunodeficiency[ICD-11: 4A00]P00748F12
T98945DI0263Middle East Respiratory Syndrome[ICD-11: 1D64]P09958FUR
T13127DI0342Premature ageing appearance[ICD-11: LD2B]P49356FNTB
T60514DI0035Arterial occlusive disease[ICD-11: BD40]Q9HCN6GP6
T60514DI0074Cerebral ischaemic stroke[ICD-11: 8B11]Q9HCN6GP6
T76024DI0170Haemolytic anemia[ICD-11: 3A20-3A2Z]Q9UCV4C1S
T76024DI0213Innate/adaptive immunodeficiency[ICD-11: 4A00]Q9UCV4C1S

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