Sinaiticin



Compound IDCDAMM02808
Common nameSinaiticin
IUPAC name5,7-dihydroxy-2-[3-(hydroxymethyl)-2-(4-hydroxyphenyl)-2,3-dihydro-1,4-benzodioxin-6-yl]chromen-4-one
Molecular formulaC24H18O8

Experimental data

Retention time13.58
Adduct[M+H]+
Actual mz435.111
Theoretical mz435.107
Error7.87
Ionizaton modePositive
Instrument typeLC-MS/MS-QTOF, spectrum predicted by MS-DIAL v4.9 integrated with MS-FINDER 3.60
Score6.728

Identifiers and class information

Inchi keyQGMULYBZWIWTIF-WDDKZSKVNA-N
SmilesO=C1C=C(OC=2C=C(O)C=C(O)C12)C=3C=CC=4OC(C5=CC=C(O)C=C5)C(OC4C3)CO
SuperclassLignans, neolignans and related compounds
ClassFlavonolignans

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)0
Number of non-conjugated amide groups (#amide)0
Number of rotatable bonds (#rotor)5
Number of reactive functional groups (#rtvFG)0
Predicted central nervous system activity (CNS)-2
Molecular weight (mol_MW)434.401
Computed dipole moment(dipole)5.525
Total solvent accessible surface area (SASA)706.784
Hydrophobic component of SASA (FOSA)70.098
Hydrophilic component of SASA (FISA)246.418
Pie component of the SASA (PISA)390.268
Weakly polar component of the SASA (WPSA)0
Total solvent accesible volume (volume)1247.99
Number of hydrogen bond donors (donorHB)3
Number of hydrogen bond acceptors (accptHB)6.95
Free energy of solvation of dipole (dip^2/V)0.0244588
Index of cohesive interaction in solids (ACxDN^.5/SA)0.0170317
Globularity descriptor (glob)0.793145
Predicted polarizability in cubic angstroms (QPpolrz)44.307
Predicted hexadecane/gas partition coefficient (QPlogPC16)15.035
Predicted octanol/gas partition coefficient (QPlogPoct)23.822
Predicted water/gas partition coefficient (QPlogPw)15.888
Predicted octanol/water partition coefficient (QPlogPo/w)2.66
Predicted aqueous solubility (QPlogS)-5.655
Conformation-independent predicted aqueous solubility (CIQPlogS)-6.565
Predicted IC50 value for blockage of HERG K+ channels (QPlogHERG)-6.74
Predicted apparent Caco-2 cell permeability in nm/sec (QPPCaco)45.616
Predicted brain/blood partition coefficient (QPlogBB)-2.349
Predicted apparent MDCK cell permeability in nm/sec (QPPMDCK)17.58
Predicted skin permeability, log Kp (QPlogKp)-4.206
PM3 calculated ionization potential (IP(ev))9.038
PM3 calculated electron affinity (EA(eV))0.722
Number of likely metabolic reactions (#metab)5
Prediction of binding to human serum albumin (QPlogKhsa)0.354
Predicted qualitative human oral absorption (HumanOralAbsorption)2
Predicted human oral absorption on 0 to 100% scale (PercentHumanOralAbsorption)72.213
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)138.345
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)0

Compound-target network

Cytoscape Graph

Protein targets associated with phytocompound

Uniprot ID Gene name Target name TTD_ID Prediction source
P02766TTRTransthyretinT86462SEA
P43166CA7Carbonic anhydrase VIIT37541SEA
P22748CA4Carbonic anhydrase IVT53378SEA
P15121AKR1B1Aldose reductaseT26623SEA
P05164MPOMyeloperoxidaseT23471SEA
Q6B0I6KDM4DLysine-specific demethylase 4DT17036SEA
Q92731ESR2Estrogen receptor betaT80896SEA
P03372ESR1Estrogen receptor alphaT02506SEA
Q9HC97GPR35G-protein coupled receptor 35T56143SEA
P33527ABCC1Multidrug resistance-associated protein 1T11288SwissTargetPrediction and SEA
P08183ABCB1P-glycoprotein 1T25258SwissTargetPrediction and SEA
P11474ESRRAEstrogen-related receptor alphaT72841SEA
O95718ESRRBEstrogen-related receptor betaT42025SEA
O95271TNKSTankyrase-1T83059SEA
P20151KLK2Kallikrein 2T01908SEA
P15692VEGFAVascular endothelial growth factor AT20761SEA
P60568IL2Interleukin-2T61698SEA
P49763PGFPlacenta growth factorT70792SEA
P04049RAF1Serine/threonine-protein kinase RAFT51883SwissTargetPrediction
Q9UNQ0ABCG2ATP-binding cassette sub-family G member 2T56556SEA
Q9NPH5NOX4NADPH oxidase 4T29741SEA
P47989XDHXanthine dehydrogenaseT40954SEA
Q16678CYP1B1Cytochrome P450 1B1T92521SwissTargetPrediction and SEA
Q04760GLO1Glyoxalase IT88285SEA
Q9HC98NEK6Serine/threonine-protein kinase NEK6T78992SEA
P16152CBR1Carbonyl reductase [NADPH] 1T70518SEA
Q13564NAE1NEDD8-activating enzyme E1 regulatory subunitT01447SEA
Q13332PTPRSReceptor-type tyrosine-protein phosphatase ST10147SEA
Q99417MYCBPMYCBP messenger RNAT37298SEA
P16220CREB1Cyclic AMP-responsive element-binding proteinT92098SEA
Q15717ELAVL1ELAV-like protein 1T78349SEA
P30837ALDH1B1Acetaldehyde dehydrogenaseT99641SEA
Q96HK3CALMCalmodulinT39610SEA
Q9UK17KCND3Voltage-gated potassium channel Kv4.3T74500SEA

Target associated diseases

TTD_ID Disease_ID Disease name ICD_11 Uniprot ID Gene names
T86462DI0026Amyloidosis[ICD-11: 5D00]P02766TTR
T53378DI0046Bacterial infection[ICD-11: 1A00-1C4Z]P22748CA4
T53378DI0166Glaucoma[ICD-11: 9C61]P22748CA4
T53378DI0372Seborrhoeic dermatitis[ICD-11: EA81]P22748CA4
T26623DI0298Neuropathy[ICD-11: 8C0Z]P15121AKR1B1
T26623DI0366Rheumatoid arthritis[ICD-11: FA20]P15121AKR1B1
T23471DI0229Left ventricular failure[ICD-11: BD11]P05164MPO
T23471DI0339Postoperative inflammation[ICD-11: 1A00-CA43]P05164MPO
T80896DI0062Breast cancer[ICD-11: 2C60-2C6Y]Q92731ESR2
T80896DI0108Cushing syndrome[ICD-11: 5A70]Q92731ESR2
T80896DI0254Menopausal disorder[ICD-11: GA30]Q92731ESR2
T80896DI0432Vasomotor/allergic rhinitis[ICD-11: CA08]Q92731ESR2
T02506DI0106COVID-19[ICD-11: 1D6Y]P03372ESR1
T11288DI0167Gout[ICD-11: FA25]P33527ABCC1
T25258DI0238Lung cancer[ICD-11: 2C25]P08183ABCB1
T72841DI0366Rheumatoid arthritis[ICD-11: FA20]P11474ESRRA
T83059DI0060Brain cancer[ICD-11: 2A00]O95271TNKS
T83059DI0062Breast cancer[ICD-11: 2C60-2C6Y]O95271TNKS
T83059DI0321Ovarian cancer[ICD-11: 2C73]O95271TNKS
T83059DI0391Solid tumour/cancer[ICD-11: 2A00-2F9Z]O95271TNKS
T01908DI0213Innate/adaptive immunodeficiency[ICD-11: 4A00]P20151KLK2
T20761DI0095Colorectal cancer[ICD-11: 2B91]P15692VEGFA
T20761DI0365Retinopathy[ICD-11: 9B71]P15692VEGFA
T20761DI0430Vascular system developmental anomaly[ICD-11: LA90]P15692VEGFA
T61698DI0275Multiple sclerosis[ICD-11: 8A40]P60568IL2
T61698DI0361Renal cell carcinoma[ICD-11: 2C90]P60568IL2
T70792DI0095Colorectal cancer[ICD-11: 2B91]P49763PGF
T51883DI0252Melanoma[ICD-11: 2C30]P04049RAF1
T51883DI0303Non-small-cell lung cancer[ICD-11: 2C25]P04049RAF1
T51883DI0321Ovarian cancer[ICD-11: 2C73]P04049RAF1
T51883DI0391Solid tumour/cancer[ICD-11: 2A00-2F9Z]P04049RAF1
T56556DI0218Irritable bowel syndrome[ICD-11: DD91]Q9UNQ0ABCG2
T56556DI0366Rheumatoid arthritis[ICD-11: FA20]Q9UNQ0ABCG2
T29741DI0146Fibrosis[ICD-11: GA14-GC01]Q9NPH5NOX4
T40954DI0206Inborn purine/pyrimidine/nucleotide metabolism error[ICD-11: 5C55]P47989XDH
T40954DI0266Mineral deficiency[ICD-11: 5B5K]P47989XDH
T88285DI0210Influenza[ICD-11: 1E30-1E32]Q04760GLO1
T70518DI0037Asthma[ICD-11: CA23]P16152CBR1
T01447DI0284Myelodysplastic syndrome[ICD-11: 2A37]Q13564NAE1
T10147DI0057Bone paget disease[ICD-11: FB85]Q13332PTPRS
T37298DI0235Liver cancer[ICD-11: 2C12]Q99417MYCBP
T99641DI0396Substance abuse[ICD-11: 6C40]P30837ALDH1B1
T39610DI0068Cardiac arrhythmia[ICD-11: BC9Z]Q96HK3CALM
T39610DI0243Malaria[ICD-11: 1F40-1F45]Q96HK3CALM
T39610DI0370Schizophrenia[ICD-11: 6A20]Q96HK3CALM
T74500DI0004Acidosis[ICD-11: 5C73]Q9UK17KCND3

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