Nodulapeptin A



Compound IDCDAMM02312
Common nameNodulapeptin A
IUPAC name2-[[6-[2-(4-hydroxyphenyl)ethyl]-7-methyl-12-(2-methylsulfonylethyl)-2,5,8,11,14-pentaoxo-3-(3-oxobutyl)-9-(2-phenylethyl)-1,4,7,10,13-pentazacyclononadec-15-yl]carbamoylamino]-3-methylpentanoic acid
Molecular formulaC45H65N7O12S

Experimental data

Retention time5.11
Adduct[M+H]+
Actual mz928.449
Theoretical mz928.448
Error0.46
Ionizaton modePositive
Instrument typeLC-MS/MS-QTOF, spectrum predicted by MS-DIAL v4.9 integrated with MS-FINDER 3.60
Score5.2466

Identifiers and class information

Inchi keyYTPAHVTZZQJJCC-DFISRZJPNA-N
SmilesO=C(NC1C(=O)NC(C(=O)NC(C(=O)N(C)C(C(=O)NC(C(=O)NCCCC1)CCC(=O)C)CCC2=CC=C(O)C=C2)CCC=3C=CC=CC3)CCS(=O)(=O)C)NC(C(=O)O)C(C)CC
SuperclassOrganic acids and derivatives
ClassCarboxylic acids and derivatives

Pharmacokinetic properties

Number of descriptor values(#stars)11
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)6
Number of rotatable bonds (#rotor)32
Number of reactive functional groups (#rtvFG)1
Predicted central nervous system activity (CNS)-2
Molecular weight (mol_MW)928.108
Computed dipole moment(dipole)12.046
Total solvent accessible surface area (SASA)1202.51
Hydrophobic component of SASA (FOSA)577.674
Hydrophilic component of SASA (FISA)315.604
Pie component of the SASA (PISA)308.855
Weakly polar component of the SASA (WPSA)0.373
Total solvent accesible volume (volume)2608.57
Number of hydrogen bond donors (donorHB)4.25
Number of hydrogen bond acceptors (accptHB)20
Free energy of solvation of dipole (dip^2/V)0.0556309
Index of cohesive interaction in solids (ACxDN^.5/SA)0.0342876
Globularity descriptor (glob)0.762102
Predicted polarizability in cubic angstroms (QPpolrz)80.643
Predicted hexadecane/gas partition coefficient (QPlogPC16)27.205
Predicted octanol/gas partition coefficient (QPlogPoct)45.618
Predicted water/gas partition coefficient (QPlogPw)32.364
Predicted octanol/water partition coefficient (QPlogPo/w)1.761
Predicted aqueous solubility (QPlogS)-2.076
Conformation-independent predicted aqueous solubility (CIQPlogS)-6.595
Predicted IC50 value for blockage of HERG K+ channels (QPlogHERG)3.2
Predicted apparent Caco-2 cell permeability in nm/sec (QPPCaco)0.493
Predicted brain/blood partition coefficient (QPlogBB)-4.987
Predicted apparent MDCK cell permeability in nm/sec (QPPMDCK)0.995
Predicted skin permeability, log Kp (QPlogKp)-3.176
PM3 calculated ionization potential (IP(ev))9.364
PM3 calculated electron affinity (EA(eV))0.194
Number of likely metabolic reactions (#metab)10
Prediction of binding to human serum albumin (QPlogKhsa)-1.907
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)89.706
Van der Waals surface area (PSA)318.465
Number of nitrogen and oxygen atoms (#NandO)19
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
Q9BZP6CHIAAcidic mammalian chitinase (by homology)T51597SEA
P17655CAPN2Calpain 2T86837SEA
P35372OPRM1Mu opioid receptorT47768SEA
Q9UBU3GHRLAppetite-regulating hormoneT06850SEA
Q92847GHSRGhrelin receptorT59604SEA
P41143OPRD1Delta opioid receptorT58992SEA
Q13489BIRC3Baculoviral IAP repeat-containing protein 3T35173SEA
O43193MLNRMotilin receptorT62306SEA
P06756ITGAVVitronectin receptor alphaT67103SEA
P21730C5AR1C5a anaphylatoxin chemotactic receptorT15439SEA
P30874SSTR2Somatostatin receptor 2T53024SEA
P31391SSTR4Somatostatin receptor 4T62974SEA
P14735IDEInsulin-degrading enzymeT81900SEA
P28074PSMB5Proteasome Macropain subunit MB1T49031SEA
P25106ACKR3C-X-C chemokine receptor type 7T10491SEA
P61073CXCR4C-X-C chemokine receptor type 4T96079SEA
P15169CPN1Carboxypeptidase N, catalytic subunitT34471SEA
P08648ITGA5Integrin alpha-5T29879SEA

Target associated diseases

TTD_ID Disease_ID Disease name ICD_11 Uniprot ID Gene names
T86837DI0106COVID-19[ICD-11: 1D6Y]P17655CAPN2
T47768DI0013Acute pain[ICD-11: MG31]P35372OPRM1
T47768DI0059Bowel habit change[ICD-11: ME05]P35372OPRM1
T47768DI0087Chronic pain[ICD-11: MG30]P35372OPRM1
T47768DI0101Corneal disease[ICD-11: 9A76-9A78]P35372OPRM1
T47768DI0105Cough[ICD-11: MD12]P35372OPRM1
T47768DI0117Depression[ICD-11: 6A70-6A7Z]P35372OPRM1
T47768DI0124Digestive system disease[ICD-11: DE2Z]P35372OPRM1
T47768DI0218Irritable bowel syndrome[ICD-11: DD91]P35372OPRM1
T47768DI0228Large intestine motility disorder[ICD-11: DB32]P35372OPRM1
T47768DI0317Opioid use disorder[ICD-11: 6C43]P35372OPRM1
T47768DI0324Pain[ICD-11: MG30-MG3Z]P35372OPRM1
T47768DI0349Pruritus[ICD-11: EC90]P35372OPRM1
T47768DI0374Sensation disturbance[ICD-11: MB40]P35372OPRM1
T06850DI0120Diabetes mellitus[ICD-11: 5A10]Q9UBU3GHRL
T59604DI0087Chronic pain[ICD-11: MG30]Q92847GHSR
T59604DI0337Pituitary gland disorder[ICD-11: 5A60-5A61]Q92847GHSR
T58992DI0059Bowel habit change[ICD-11: ME05]P41143OPRD1
T58992DI0218Irritable bowel syndrome[ICD-11: DD91]P41143OPRD1
T58992DI0324Pain[ICD-11: MG30-MG3Z]P41143OPRD1
T35173DI0259Metastatic lymph node neoplasm[ICD-11: 2D60]Q13489BIRC3
T62306DI0124Digestive system disease[ICD-11: DE2Z]O43193MLNR
T62306DI0159Gastroduodenal motor/secretory disorder[ICD-11: DA41]O43193MLNR
T62306DI0161Gastro-oesophageal reflux disease[ICD-11: DA22]O43193MLNR
T62306DI0218Irritable bowel syndrome[ICD-11: DD91]O43193MLNR
T62306DI0324Pain[ICD-11: MG30-MG3Z]O43193MLNR
T67103DI0095Colorectal cancer[ICD-11: 2B91]P06756ITGAV
T67103DI0391Solid tumour/cancer[ICD-11: 2A00-2F9Z]P06756ITGAV
T15439DI0431Vasculitis[ICD-11: 4A44]P21730C5AR1
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
T81900DI0383Skin and skin-structure infection[ICD-11: 1F28-1G0Z]P14735IDE
T10491DI0037Asthma[ICD-11: CA23]P25106ACKR3
T10491DI0391Solid tumour/cancer[ICD-11: 2A00-2F9Z]P25106ACKR3
T96079DI0245Malignant haematopoietic neoplasm[ICD-11: 2B33]P61073CXCR4
T96079DI0274Multiple myeloma[ICD-11: 2A83]P61073CXCR4
T29879DI0365Retinopathy[ICD-11: 9B71]P08648ITGA5

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