Vitamin A



Compound IDCDAMM00974
Common nameVitamin A
IUPAC name3,7-dimethyl-9-(2,6,6-trimethylcyclohexen-1-yl)nona-2,4,6,8-tetraen-1-ol
Molecular formulaC20H30O

Experimental data

Retention time18.22
Adduct[2M+H]+
Actual mz573.461
Theoretical mz573.467
Error10.77
Ionizaton modePositive
Instrument typeLC-MS/MS-QTOF, spectrum predicted by MS-DIAL v4.9 integrated with MS-FINDER 3.60
Score5.8401

Identifiers and class information

Inchi keyFPIPGXGPPPQFEQ-OVSJKPMPSA-N
SmilesOCC=C(C=CC=C(C=CC1=C(C)CCCC1(C)C)C)C
SuperclassLipids and lipid-like molecules
ClassPrenol lipids

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)0
Number of rotatable bonds (#rotor)9
Number of reactive functional groups (#rtvFG)0
Predicted central nervous system activity (CNS)0
Molecular weight (mol_MW)286.456
Computed dipole moment(dipole)1.496
Total solvent accessible surface area (SASA)653.108
Hydrophobic component of SASA (FOSA)546.079
Hydrophilic component of SASA (FISA)56.635
Pie component of the SASA (PISA)50.394
Weakly polar component of the SASA (WPSA)0
Total solvent accesible volume (volume)1143.65
Number of hydrogen bond donors (donorHB)1
Number of hydrogen bond acceptors (accptHB)1.7
Free energy of solvation of dipole (dip^2/V)0.0019579
Index of cohesive interaction in solids (ACxDN^.5/SA)0.0026029
Globularity descriptor (glob)0.809795
Predicted polarizability in cubic angstroms (QPpolrz)34.317
Predicted hexadecane/gas partition coefficient (QPlogPC16)9.817
Predicted octanol/gas partition coefficient (QPlogPoct)12.688
Predicted water/gas partition coefficient (QPlogPw)3.173
Predicted octanol/water partition coefficient (QPlogPo/w)5.411
Predicted aqueous solubility (QPlogS)-6.097
Conformation-independent predicted aqueous solubility (CIQPlogS)-4.408
Predicted IC50 value for blockage of HERG K+ channels (QPlogHERG)-4.85
Predicted apparent Caco-2 cell permeability in nm/sec (QPPCaco)2876.29
Predicted brain/blood partition coefficient (QPlogBB)-0.555
Predicted apparent MDCK cell permeability in nm/sec (QPPMDCK)1549.87
Predicted skin permeability, log Kp (QPlogKp)-1.522
PM3 calculated ionization potential (IP(ev))8.444
PM3 calculated electron affinity (EA(eV))0.347
Number of likely metabolic reactions (#metab)5
Prediction of binding to human serum albumin (QPlogKhsa)1.029
Predicted qualitative human oral absorption (HumanOralAbsorption)3
Predicted human oral absorption on 0 to 100% scale (PercentHumanOralAbsorption)100
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)22.908
Number of nitrogen and oxygen atoms (#NandO)1
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
P10276RARARetinoic acid receptor alphaT94085SwissTargetPrediction and SEA
P18089ADRA2BAlpha-2b adrenergic receptorT41580SwissTargetPrediction
O43174CYP26A1Cytochrome P450 26A1T84634SEA
P19793RXRARetinoid X receptor alpha (by homology)T13726SwissTargetPrediction and SEA
P02753RBP4Plasma retinol-binding proteinT55703SwissTargetPrediction and SEA
P35398RORANuclear receptor ROR-alphaT43206SwissTargetPrediction and SEA
P28702RXRBRetinoid X receptor betaT60077SwissTargetPrediction and SEA
P13631RARGRetinoic acid receptor gammaT82146SwissTargetPrediction and SEA
P48443RXRGRetinoid X receptor gammaT46456SwissTargetPrediction and SEA
P10826RARBRetinoic acid receptor betaT61657SwissTargetPrediction and SEA
Q92753RORBNuclear receptor ROR-betaT48812SwissTargetPrediction and SEA
Q9UJM8HAO1Hydroxyacid oxidase 1T63170SEA

Target associated diseases

TTD_ID Disease_ID Disease name ICD_11 Uniprot ID Gene names
T94085DI0025Alzheimer disease[ICD-11: 8A20]P10276RARA
T94085DI0251Mature T-cell lymphoma[ICD-11: 2A90]P10276RARA
T41580DI0396Substance abuse[ICD-11: 6C40]P18089ADRA2B
T84634DI0314Oesophagitis[ICD-11: DA24]O43174CYP26A1
T13726DI0225Kaposi sarcoma[ICD-11: 2B57]P19793RXRA
T13726DI0283Mycosis fungoides[ICD-11: 2B01]P19793RXRA
T55703DI0212Inherited retinal dystrophy[ICD-11: 9B70]P02753RBP4
T43206DI0235Liver cancer[ICD-11: 2C12]P35398RORA
T43206DI0417Type 2 diabetes mellitus[ICD-11: 5A11]P35398RORA
T60077DI0225Kaposi sarcoma[ICD-11: 2B57]P28702RXRB
T82146DI0005Acne vulgaris[ICD-11: ED80]P13631RARG
T82146DI0012Acute myeloid leukaemia[ICD-11: 2A60]P13631RARG
T82146DI0225Kaposi sarcoma[ICD-11: 2B57]P13631RARG
T82146DI0277Muscle calcification/ossification[ICD-11: FB31]P13631RARG
T82146DI0351Psoriasis[ICD-11: EA90]P13631RARG
T46456DI0225Kaposi sarcoma[ICD-11: 2B57]P48443RXRG
T46456DI0232Light sensitivity impairment[ICD-11: 9D45]P48443RXRG
T61657DI0225Kaposi sarcoma[ICD-11: 2B57]P10826RARB
T63170DI0201Inborn carbohydrate metabolism error[ICD-11: 5C51]Q9UJM8HAO1

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