Vignatic acid A



Compound IDCDAMM02814
Common nameVignatic acid A
IUPAC name7-benzyl-4-[(2-hydroxy-4-methylpentanoyl)amino]-5,8-dioxo-3-propan-2-yl-2-oxa-6,9-diazabicyclo[10.2.2]hexadeca-1(14),12,15-triene-10-carboxylic acid
Molecular formulaC30H39N3O7

Experimental data

Retention time23.96
Adduct[M+H]+
Actual mz554.288
Theoretical mz554.286
Error2.57
Ionizaton modePositive
Instrument typeLC-MS/MS-QTOF, spectrum predicted by MS-DIAL v4.9 integrated with MS-FINDER 3.60
Score6.3909

Identifiers and class information

Inchi keyOEJLUFSEWIDXDN-UHFFFAOYNA-N
SmilesO=C(O)C1NC(=O)C(NC(=O)C(NC(=O)C(O)CC(C)C)C(OC2=CC=C(C=C2)C1)C(C)C)CC=3C=CC=CC3
SuperclassOrganic acids and derivatives
ClassCarboxylic acids and derivatives

Pharmacokinetic properties

Number of descriptor values(#stars)0
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)3
Number of rotatable bonds (#rotor)9
Number of reactive functional groups (#rtvFG)0
Predicted central nervous system activity (CNS)-2
Molecular weight (mol_MW)553.654
Computed dipole moment(dipole)6.676
Total solvent accessible surface area (SASA)852.733
Hydrophobic component of SASA (FOSA)405.509
Hydrophilic component of SASA (FISA)183.767
Pie component of the SASA (PISA)263.457
Weakly polar component of the SASA (WPSA)0
Total solvent accesible volume (volume)1675.26
Number of hydrogen bond donors (donorHB)2.75
Number of hydrogen bond acceptors (accptHB)9.7
Free energy of solvation of dipole (dip^2/V)0.0266065
Index of cohesive interaction in solids (ACxDN^.5/SA)0.0188636
Globularity descriptor (glob)0.799968
Predicted polarizability in cubic angstroms (QPpolrz)57.627
Predicted hexadecane/gas partition coefficient (QPlogPC16)17.487
Predicted octanol/gas partition coefficient (QPlogPoct)29.183
Predicted water/gas partition coefficient (QPlogPw)20.205
Predicted octanol/water partition coefficient (QPlogPo/w)3.188
Predicted aqueous solubility (QPlogS)-4.916
Conformation-independent predicted aqueous solubility (CIQPlogS)-4.951
Predicted IC50 value for blockage of HERG K+ channels (QPlogHERG)-0.094
Predicted apparent Caco-2 cell permeability in nm/sec (QPPCaco)17.728
Predicted brain/blood partition coefficient (QPlogBB)-1.893
Predicted apparent MDCK cell permeability in nm/sec (QPPMDCK)22.233
Predicted skin permeability, log Kp (QPlogKp)-3.114
PM3 calculated ionization potential (IP(ev))9.287
PM3 calculated electron affinity (EA(eV))0.21
Number of likely metabolic reactions (#metab)6
Prediction of binding to human serum albumin (QPlogKhsa)-0.312
Predicted qualitative human oral absorption (HumanOralAbsorption)2
Predicted human oral absorption on 0 to 100% scale (PercentHumanOralAbsorption)55.003
Solvent-accessible surface area of fluorine atoms (SAFluorine)0
Solvent-accessible surface area of amide oxygen atoms (SAamideO)51.278
Van der Waals surface area (PSA)163.359
Number of nitrogen and oxygen atoms (#NandO)10
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
P00797RENReninT61622SEA
P15144ANPEPAminopeptidase NT67272SEA
P08514ITGA2BIntegrin alpha-IIb/beta-3T50688SEA
P08473MMENeprilysinT05409SEA
P43235CTSKCathepsin KT11388SEA
Q9BZP6CHIAAcidic mammalian chitinase (by homology)T51597SEA
P08253MMP2Matrix metalloproteinase 2T68251SEA
P08254MMP3Matrix metalloproteinase 3T86702SEA
P03956MMP1Matrix metalloproteinase 1T52450SEA
P17655CAPN2Calpain 2T86837SEA
P35372OPRM1Mu opioid receptorT47768SwissTargetPrediction
P78536ADAM17ADAM17T82393SEA
P09237MMP7Matrix metalloproteinase 7T73475SEA
P30559OXTROxytocin receptor (by homology)T84486SEA
Q9UBU3GHRLAppetite-regulating hormoneT06850SEA
P07711CTSLCathepsin LT98691SEA
P32245MC4RMelanocortin receptor 4T72458SEA
P07858CTSBCathepsin (B and K)T61746SEA
P41143OPRD1Delta opioid receptorT58992SEA
Q01726MC1RMelanocortin receptor 1T35842SEA
Q13489BIRC3Baculoviral IAP repeat-containing protein 3T35173SEA
Q13490BIRC2Baculoviral IAP repeat-containing protein 2T84780SEA
O43193MLNRMotilin receptorT62306SEA
P49810PSEN2Gamma-secretaseT99204SEA
P29466CASP1Caspase-1T98269SEA
P25774CTSSCathepsin ST68290SEA
Q9ULA0DNPEPAspartyl aminopeptidaseT45287SEA
P06756ITGAVVitronectin receptor alphaT67103SEA
P17301ITGA2Integrin alpha-2T55293SEA
P05556ITGB1Integrin alpha2/beta1T01851SEA
P42574CASP3Caspase-3T57943SEA
P21730C5AR1C5a anaphylatoxin chemotactic receptorT15439SEA
P30874SSTR2Somatostatin receptor 2T53024SEA
P31391SSTR4Somatostatin receptor 4T62974SEA
O75908SOAT2Acyl coenzyme A:cholesterol acyltransferase 2T14463SEA
P21452TACR2Neurokinin 2 receptorT52790SEA
Q9UKP6UTS2RUrotensin II receptorT49072SEA
Q9UIQ6LNPEPCystinyl aminopeptidaseT97537SEA
O43497CACNA1GVoltage-gated T-type calcium channel alpha-1G subunitT64795SEA
P51511MMP15Matrix metalloproteinase 15T81658SEA
Q96DB2HDAC11Histone deacetylase 11T97903SEA
P49768PSEN1Presenilin 1T93105SEA
Q969S8HDAC10Histone deacetylase 10T94324SEA
Q96BI3APH1AGamma-secretaseT99840SEA
P21462FPR1Formyl peptide receptor 1T87831SEA
P15169CPN1Carboxypeptidase N, catalytic subunitT34471SEA
P04632CAPNS1HUMAN calpain-1 or calpain small subunit 1 heterodimerT00099SEA
P78325ADAM8Cell surface antigen MS2T95761SEA
P05106ITGB3Integrin beta-3T26457SEA
Q9UQ81MCH5Caspase-8T15700SEA
P08648ITGA5Integrin alpha-5T29879SEA
Q96BI3APH1AGamma-secretaseT99840SEA

Target associated diseases

TTD_ID Disease_ID Disease name ICD_11 Uniprot ID Gene names
T61622DI0190Hypertension[ICD-11: BA00-BA04]P00797REN
T67272DI0351Psoriasis[ICD-11: EA90]P15144ANPEP
T50688DI0007Acquired hypermelanosis[ICD-11: ED60]P08514ITGA2B
T50688DI0030Angina pectoris[ICD-11: BA40]P08514ITGA2B
T50688DI0287Myocardial infarction[ICD-11: BA41-BA43]P08514ITGA2B
T05409DI0175Heart failure[ICD-11: BD10-BD1Z]P08473MME
T11388DI0237Low bone mass disorder[ICD-11: FB83]P43235CTSK
T68251DI0238Lung cancer[ICD-11: 2C25]P08253MMP2
T86702DI0101Corneal disease[ICD-11: 9A76-9A78]P08254MMP3
T86702DI0179Hepatitis virus infection[ICD-11: 1E50-1E51]P08254MMP3
T86702DI0199Idiopathic interstitial pneumonitis[ICD-11: CB03]P08254MMP3
T86702DI0275Multiple sclerosis[ICD-11: 8A40]P08254MMP3
T86702DI0287Myocardial infarction[ICD-11: BA41-BA43]P08254MMP3
T86702DI0320Osteoarthritis[ICD-11: FA00-FA05]P08254MMP3
T86702DI0366Rheumatoid arthritis[ICD-11: FA20]P08254MMP3
T52450DI0238Lung cancer[ICD-11: 2C25]P03956MMP1
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
T82393DI0062Breast cancer[ICD-11: 2C60-2C6Y]P78536ADAM17
T82393DI0366Rheumatoid arthritis[ICD-11: FA20]P78536ADAM17
T73475DI0238Lung cancer[ICD-11: 2C25]P09237MMP7
T84486DI0009Acute diabete complication[ICD-11: 5A2Y]P30559OXTR
T84486DI0041Autism spectrum disorder[ICD-11: 6A02]P30559OXTR
T84486DI0340Postpartum haemorrhage[ICD-11: JA43]P30559OXTR
T06850DI0120Diabetes mellitus[ICD-11: 5A10]Q9UBU3GHRL
T98691DI0263Middle East Respiratory Syndrome[ICD-11: 1D64]P07711CTSL
T98691DI0376Severe acute respiratory syndrome[ICD-11: 1D65]P07711CTSL
T72458DI0192Hypoactive sexual desire dysfunction[ICD-11: HA00]P32245MC4R
T72458DI0228Large intestine motility disorder[ICD-11: DB32]P32245MC4R
T72458DI0308Obesity[ICD-11: 5B80-5B81]P32245MC4R
T61746DI0023Alopecia[ICD-11: ED70]P07858CTSB
T61746DI0025Alzheimer disease[ICD-11: 8A20]P07858CTSB
T61746DI0037Asthma[ICD-11: CA23]P07858CTSB
T61746DI0055Bone cancer[ICD-11: 2B5Z]P07858CTSB
T61746DI0060Brain cancer[ICD-11: 2A00]P07858CTSB
T61746DI0067Cardiac arrest[ICD-11: MC82]P07858CTSB
T61746DI0074Cerebral ischaemic stroke[ICD-11: 8B11]P07858CTSB
T61746DI0086Chronic obstructive pulmonary disease[ICD-11: CA22]P07858CTSB
T61746DI0087Chronic pain[ICD-11: MG30]P07858CTSB
T61746DI0110Cystic fibrosis[ICD-11: CA25]P07858CTSB
T61746DI0124Digestive system disease[ICD-11: DE2Z]P07858CTSB
T61746DI0178Hepatic fibrosis/cirrhosis[ICD-11: DB93]P07858CTSB
T61746DI0199Idiopathic interstitial pneumonitis[ICD-11: CB03]P07858CTSB
T61746DI0253Meningioma[ICD-11: 2A01]P07858CTSB
T61746DI0262Metastatic tumour[ICD-11: 2D50-2E2Z]P07858CTSB
T61746DI0275Multiple sclerosis[ICD-11: 8A40]P07858CTSB
T61746DI0296Neurodegenerative disorder[ICD-11: 8A20-8A23]P07858CTSB
T61746DI0320Osteoarthritis[ICD-11: FA00-FA05]P07858CTSB
T61746DI0351Psoriasis[ICD-11: EA90]P07858CTSB
T61746DI0366Rheumatoid arthritis[ICD-11: FA20]P07858CTSB
T58992DI0059Bowel habit change[ICD-11: ME05]P41143OPRD1
T58992DI0218Irritable bowel syndrome[ICD-11: DD91]P41143OPRD1
T58992DI0324Pain[ICD-11: MG30-MG3Z]P41143OPRD1
T35842DI0192Hypoactive sexual desire dysfunction[ICD-11: HA00]Q01726MC1R
T35842DI0205Inborn porphyrin/heme metabolism error[ICD-11: 5C58]Q01726MC1R
T35173DI0259Metastatic lymph node neoplasm[ICD-11: 2D60]Q13489BIRC3
T84780DI0259Metastatic lymph node neoplasm[ICD-11: 2D60]Q13490BIRC2
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
T99204DI0320Osteoarthritis[ICD-11: FA00-FA05]P49810PSEN2
T99204DI0380Shoulder lesion[ICD-11: FB53]P49810PSEN2
T99204DI0390Soft tissue disorder[ICD-11: FB56]P49810PSEN2
T98269DI0134Epilepsy/seizure[ICD-11: 8A61-8A6Z]P29466CASP1
T98269DI0146Fibrosis[ICD-11: GA14-GC01]P29466CASP1
T98269DI0366Rheumatoid arthritis[ICD-11: FA20]P29466CASP1
T98269DI0417Type 2 diabetes mellitus[ICD-11: 5A11]P29466CASP1
T68290DI0042Autoimmune disease[ICD-11: 4A40-4A45]P25774CTSS
T68290DI0092Coeliac disease[ICD-11: DA95]P25774CTSS
T68290DI0107Crohn disease[ICD-11: DD70]P25774CTSS
T68290DI0120Diabetes mellitus[ICD-11: 5A10]P25774CTSS
T68290DI0163General pain disorder[ICD-11: 8E43]P25774CTSS
T68290DI0324Pain[ICD-11: MG30-MG3Z]P25774CTSS
T68290DI0382Sjogren syndrome[ICD-11: 4A43]P25774CTSS
T45287DI0190Hypertension[ICD-11: BA00-BA04]Q9ULA0DNPEP
T67103DI0095Colorectal cancer[ICD-11: 2B91]P06756ITGAV
T67103DI0391Solid tumour/cancer[ICD-11: 2A00-2F9Z]P06756ITGAV
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
T57943DI0060Brain cancer[ICD-11: 2A00]P42574CASP3
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
T14463DI0017Adrenal cancer[ICD-11: 2D11]O75908SOAT2
T52790DI0218Irritable bowel syndrome[ICD-11: DD91]P21452TACR2
T49072DI0037Asthma[ICD-11: CA23]Q9UKP6UTS2R
T64795DI0134Epilepsy/seizure[ICD-11: 8A61-8A6Z]O43497CACNA1G
T64795DI0190Hypertension[ICD-11: BA00-BA04]O43497CACNA1G
T64795DI0276Multiple structural anomalies syndrome[ICD-11: LD2F]O43497CACNA1G
T64795DI0326Pancreatic cancer[ICD-11: 2C10]O43497CACNA1G
T64795DI0370Schizophrenia[ICD-11: 6A20]O43497CACNA1G
T93105DI0320Osteoarthritis[ICD-11: FA00-FA05]P49768PSEN1
T93105DI0380Shoulder lesion[ICD-11: FB53]P49768PSEN1
T93105DI0390Soft tissue disorder[ICD-11: FB56]P49768PSEN1
T94324DI0391Solid tumour/cancer[ICD-11: 2A00-2F9Z]Q969S8HDAC10
T99840DI0119Desmoid tumour[ICD-11: 2F7C]Q96BI3APH1A
T87831DI0333Peptic ulcer[ICD-11: DA61]P21462FPR1
T00099DI0106COVID-19[ICD-11: 1D6Y]P04632CAPNS1
T15700DI0120Diabetes mellitus[ICD-11: 5A10]Q9UQ81MCH5
T15700DI0391Solid tumour/cancer[ICD-11: 2A00-2F9Z]Q9UQ81MCH5
T29879DI0365Retinopathy[ICD-11: 9B71]P08648ITGA5
T99840DI0119Desmoid tumour[ICD-11: 2F7C]Q96BI3APH1A

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