ivanovaml/G9a_onlyInhibitors_targetEfficacy_withAqueousSolubility

Dataset Purpose

The dataset G9a_onlyInhibitors_targetEfficacy_basic had been used in the study "Targeting neurodegeneration: three machine learning methods for G9a inhibitors discovery using PubChem and scikit-learn" https://doi.org/10.1007/s10822-025-00642-z as the Dataset_3.

Info

This dataset is from samples used in the PubChem AID 504332 bioassay "qHTS Assay for Inhibitors of Histone Lysine Methyltransferase G9a", https://pubchem.ncbi.nlm.nih.gov/bioassay/504332

Some of the features in this datasets had been engineered during the study "Application of machine learning for predicting G9a inhibitors" https://doi.org/10.1039/d4dd00101j

Source code

Datasets: https://github.com/articlesmli/G9a_Inhibitors_efficacy/tree/main/1.G9a_inhibitor_efficacy_magnitude_ML_model

Feature engineering: https://github.com/articlesmli/G9a_clsf/blob/main/with%20solubility/data_sets_generation_with_SMOTE.ipynb

Dataset Details

Rows: 3,890

Columns: 22

A note: Remove the column "Unnamed: 0".

• Column 1: Efficacy of the G9a inhibition (target)
• Column 2: MW - Molecular weight is calculated as the sum of the mass of each constituent atom multiplied by the number of atoms of that element in the molecular formula.
• Column 3: TPSA -The topological polar surface area is an estimate of the polar surface area of a molecule, computed as the surface sum over polar atoms in the molecule
• Column 4: XLogP3 is a predicted octanol-water partition coefficient measuring the hydrophilicity or hydrophobicity of a molecule
• Column 5: HAC - Heavy Atom Count is the number of heavy atoms (i.e., non-hydrogen atoms) in the given compound.
• Column 6: HBDC - Hydrogen Bond Donor Count in the compound
• Column 7: HBAC - Hydrogen Bond Acceptor Count in the compound
• Column 8: RBC - Rotatable Bond Count is defined as any single-order non-ring bond, where atoms on either side of the bond are in turn bound to nonterminal heavy (i.e., non-hydrogen) atoms. That is, where rotation around the bond axis changes the overall shape of the molecule and generates conformers
• Column 9: CBUC - Covalently Bonded Unit Count is the number of groups of atoms connected by covalent bonds
• Column 10: MMX6 - Difference between Min and Max of the atoms' coordinates of the compounds. Based on the PubChem database, in other to distinguish the isomers from each other, the minima of the 2D coordinates of the substances were subtracted from the maxima along the x axis performed for carbon atoms only (given that carbon atoms create the "skeleton" of the organic compound)
• Column 11: MMX - Difference between Min and Max of the atoms' coordinates of the compounds. Based on the PubChem database, in other to distinguish the isomers from each other, the minima of the 2D coordinates of the substances were subtracted from the maxima along the x axis performed for all atoms
• Column 12: SX6 - Skewness of the atom coordinate distribution. The feature derived from 2D coordinates related to the distribution of the atoms along the x axis. The values of skewness were calculated for the carbon atoms only
• Column 13: SX - Skewness of the atom coordinate distribution. The feature derived from 2D coordinates related to the distribution of the atoms along the x axis. The values of skewness were calculated for all atoms
• Column 14: MMY6 - Difference between Min and Max of the atoms' coordinates of the compounds. Based on the PubChem database, in other to distinguish the isomers from each other, the minima of the 2D coordinates of the substances were subtracted from the maxima along the y axis performed for carbon atoms only (given that carbon atoms create the "skeleton" of the organic compound)
• Column 15: MMY - Difference between Min and Max of the atoms' coordinates of the compounds. Based on the PubChem database, in other to distinguish the isomers from each other, the minima of the 2D coordinates of the substances were subtracted from the maxima along the y axis performed for all atoms
• Column 16: SY6 - Skewness of the atom coordinate distribution. The feature derived from 2D coordinates related to the distribution of the atoms along the y axis. The values of skewness were calculated for the carbon atoms only
• Column 17: SY - Skewness of the atom coordinate distribution. The feature derived from 2D coordinates related to the distribution of the atoms along the y axis. The values of skewness were calculated for all atoms
• Column 18: Volume_1 - Hypothetical volumes of the molecules Type 1 calculated based on the 2D coordinates that carry information about the isomers. Since atoms, respectively molecules are not flat, the 2D data of the atomic coordinates of the substances were used to obtain a hypothetical 3D volume of the compounds. These computations were based on the previously obtained min-max values of the atoms' coordinates.
• Column 19: Volume_2 - Hypothetical volumes of the molecules Type 2 calculated using the already computed skewness of the atoms coordinates. Since atoms, respectively molecules are not flat, the 2D data of the atomic coordinates of the substances were used to obtain a hypothetical 3D volume of the compounds. These computations were based on the previously computed skewness of the atoms coordinates
• Column 20: MMX6_3D - Difference between Min and Max of the atoms' coordinates of the compounds where the minima of the 3D coordinates of the compound was subtracted from the maxima along the x axis performed for carbon atoms only (given that carbon atoms create the "skeleton" of the organic compound)
• Column 21: MMX_3D - Difference between Min and Max of the atoms' coordinates of the compounds where the minima of the 3D coordinates of the compound was subtracted from the maxima along the x axis performed for all atoms.
• Column 22: SX6_3D - Skewness derived from the 3D coordinates related to the distribution of C atoms along the z axis.
• Column 23: SX_3D - Skewness derived from the 3D coordinates related to the distribution of all atoms along the x axis.
• Column 24: MMY6_3D - Difference between Min and Max of the atoms' coordinates of the compounds where the minima of the 3D coordinates of the compound was subtracted from the maxima along the Y axis performed for carbon atoms only (given that carbon atoms create the "skeleton" of the organic compound)
• Column 25: MMY_3D - Difference between Min and Max of the atoms' coordinates of the compounds where the minima of the 3D coordinates of the compound was subtracted from the maxima along the y axis performed for all atoms.
• Column 26: SY6_3D - Skewness derived from the 3D coordinates related to the distribution of C atoms along the y axis.
• Column 27: SY_3D - Skewness derived from the 3D coordinates related to the distribution of all atoms along the y axis.
• Column 28: MMZ6_3D - Difference between Min and Max of the atoms' coordinates of the compounds where the minima of the 3D coordinates of the compound was subtracted from the maxima along the z axis performed for carbon atoms only (given that carbon atoms create the "skeleton" of the organic compound)
• Column 29: MMZ_3D - Difference between Min and Max of the atoms' coordinates of the compounds where the minima of the 3D coordinates of the compound was subtracted from the maxima along the z axis performed for all atoms.
• Column 30: SZ6_3D - Skewness derived from the 3D coordinates related to the distribution of C atoms along the z axis.
• Column 31: SZ_3D - Skewness derived from 3D coordinates related to the distribution of all atoms along the z axis.
• Column 32: Volume_1_3D - Hypothetical volume based on 3D coordinates of the atoms` coordinates.
• Column 33: XY_3D_volume - Hypothetical volume based on the skewness and the difference of min and max derived from the 3D coordinates: an XY variant
• Column 34: XZ_3D_volume - Hypothetical volume based on the skewness and the difference of min and max derived from the 3D coordinates: an XZ variant
• Column 35: YZ_3D_volume - Hypothetical volume based on the skewness and the difference of min and max derived from the 3D coordinates: an YZ variant
• Column 36: C_relative - The relative proportion of the C atom in the molecules of the considered compounds is a feature that carry information about the proportion of the number of C atoms to the total number of atoms in the given compound.
• Column 37: H_relative - The relative proportion of the H atom in the molecules of the considered compounds is a feature that carry information about the proportion of the number of H atoms to the total number of atoms in the given compound.
• Column 38: O_relative - The relative proportion of the O atom in the molecules of the considered compounds is a feature that carry information about the proportion of the number of O atoms to the total number of atoms in the given compound.
• Column 39: S_relative - The relative proportion of the S atom in the molecules of the considered compounds is a feature that carry information about the proportion of the number of S atoms to the total number of atoms in the given compound.
• Column 40: N_relative - The relative proportion of the N atom in the molecules of the considered compounds is a feature that carry information about the proportion of the number of N atoms to the total number of atoms in the given compound.
• Column 41: Br_relative - The relative proportion of the Br atom in the molecules of the considered compounds is a feature that carry information about the proportion of the number of Br atoms to the total number of atoms in the given compound.
• Column 42: Cl_relative - The relative proportion of the Cl atom in the molecules of the considered compounds is a feature that carry information about the proportion of the number of Cl atoms to the total number of atoms in the given compound.
• Column 43: F_relative - The relative proportion of the F atom in the molecules of the considered compounds is a feature that carry information about the proportion of the number of F atoms to the total number of atoms in the given compound.
• Column 44: C - The mass proportion of the C atom in the molecules of the considered compound calculated as the proportion of the mass of all identical atoms in the molecule to the mass of all atoms in the molecule of the given compound
• Column 45: H - The mass proportion of the H atom in the molecules of the considered compound calculated as the proportion of the mass of all identical atoms in the molecule to the mass of all atoms in the molecule of the given compound
• Column 46: O - The mass proportion of the O atom in the molecules of the considered compound calculated as the proportion of the mass of all identical atoms in the molecule to the mass of all atoms in the molecule of the given compound
• Column 47: S - The mass proportion of the S atom in the molecules of the considered compound calculated as the proportion of the mass of all identical atoms in the molecule to the mass of all atoms in the molecule of the given compound
• Column 48: N - The mass proportion of the N atom in the molecules of the considered compound calculated as the proportion of the mass of all identical atoms in the molecule to the mass of all atoms in the molecule of the given compound
• Column 49: Br - The mass proportion of the Br atom in the molecules of the considered compound calculated as the proportion of the mass of all identical atoms in the molecule to the mass of all atoms in the molecule of the given compound
• Column 50: Cl - The mass proportion of the Cl atom in the molecules of the considered compound calculated as the proportion of the mass of all identical atoms in the molecule to the mass of all atoms in the molecule of the given compound
• Column 51: F - The mass proportion of the F atom in the molecules of the considered compound calculated as the proportion of the mass of all identical atoms in the molecule to the mass of all atoms in the molecule of the given compound
• Column 52: C_rel_2D - The size ratio of the molecules based on 2D C atoms` coordinates
• Column 53: allAtoms_rel_2D - The size ratio of the molecules based on 2D atoms` coordinates
• Column 54: C_rel_XY_3D - The size ratio of the molecules based on 2D C atoms` coordinates along the X and Y axes
• Column 55: allAtoms_rel_XY_3D - The size ratio of the molecules based on 3D atoms` coordinates along the X and Y axes
• Column 56: C_rel_XZ_3D - The size ratio of the molecules based on 2D C atoms` coordinates along the X and Z axes
• Column 57: allAtoms_rel_XZ_3D - The size ratio of the molecules based on 3D atoms` coordinates along the X and Z axes
• Column 58: C_rel_YZ_3D - The size ratio of the molecules based on 2D C atoms` coordinates along the Y and Z axes
• Column 59: allAtoms_rel_YZ_3D - The size ratio of the molecules based on 3D atoms` coordinates along the Y and Z axes
• Column 60: Similarity - The feature is based on the comparison between SMILES of the compounds and Lysine. Lysine was chosen because the methylation has been performed in the Lysine residue. The “Similarity” feature was generated using the toolkit for cheminformatics RDKit‘s packages.
• Column 61: Solubility_at_pH_7_4
• Column 62: Similarity_1 - The feature is based on the comparison between SMILES of the compounds and 6-methoxy-N-methyl-2-(5-methylfuran-2-yl)-N-(1-methylpiperidin-4-yl)-7-(3-pyrrolidin-1-ylpropoxy) quinolin-4-amine (https://pubchem.ncbi.nlm.nih.gov/bioassay/1938431#section=Data-Table)
• Column 63: Similarity_2 - The feature is based on the comparison between SMILES of the compounds and Bix-01294 (https://pubchem.ncbi.nlm.nih.gov/compound/25150857#section=InChIKey)
• Column 64: Similarity_3 - The feature is based on the comparison between SMILES of the compounds and N-[2-[[4-[(1-benzylpiperidin-4-yl) amino]-7-methoxyquinazolin-2-yl] amino]ethyl]-N'-hydroxyhexanediamide;hydrochloride (https://pubchem.ncbi.nlm.nih.gov/compound/171347753#section=InChIKey)
• Column 65: C_rel**MMY6_3D - the relative ratio of Carbon atoms raised to a power equal to the length of the carbon chain of the compound along the 3D Y axis.
• Column 66: C_rel**MMZ6_3D - the relative ratio of Carbon atoms raised to a power equal to the length of the carbon chain of the compound along the 3D Z axis.
• Column 67: mean_C_rel**MM6_3D - Mean value of the relative ratio of Carbon atoms raised to a power equal to the length of the carbon chain of the compound along the 3D axis.
• Column 68: mean_C_rel**C_rel_3D - Mean value of the relative ratio of Carbon atoms raised to a power equal to the relative ratio of the Carbon chain sizes along the 3D axes.
• Column 69: mean_C**SX6_S - Mean value of the mass proportion of the carbon atoms raised to a power equal to Carbon atoms chain skewness.
• Column 70: mean_H_rel**MM_3D - Mean value of the relative ratio of Hydrogens atoms raised to a power equal to the length of the molecules of the compound along the 3D axes.
• Column 71: mean_H_rel**allAtoms_rel_3D - Mean value of the relative ratio of Hydrogen atoms raised to a power equal to the relative ratio of the molecule size along the 3D axes.
• Column 72: mean_H**SX6_S - Mean value of the mass proportion of the Hydrogen atoms raised to a power equal to the molecule skewness along the 3D axes.