Table 1 |
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|
Descriptors of chemical space consisting of sc-PDB-derived ligands and ACD-SC-derived ordinary molecules and corresponding loadings (Varimax normalized) for the first two factors* |
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| Descriptors |
Characterization |
Factor loadings |
Software |
|
|
|
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| 1 |
2 |
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|
|
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| AREA |
Total molecular surface area |
0.974 |
0.103 |
Sybyl |
| PSA |
Polar molecular surface area |
0.255 |
0.892 |
|
| PV |
Polar molecular volume |
0.501 |
0.741 |
|
| VOL |
Total molecular volume |
0.991 |
0.062 |
|
| MOLWEIGHT |
Molecular weight |
0.958 |
0.206 |
|
| Acceptor |
H-bond acceptor counts |
0.464 |
0.799 |
|
| Donor |
H-bond donor counts |
0.376 |
0.817 |
|
| BondCount |
Total bond counts |
0.972 |
0.060 |
|
| Chiral |
Counts of chiral center |
0.367 |
0.617 |
|
| Hydrophobe |
Hydrophobic fragment counts |
0.767 |
-0.417 |
|
| RingCount |
Ring counts |
0.686 |
-0.069 |
|
| RotBonds |
Number of rotatable bonds |
0.630 |
0.428 |
|
| HeavyAtoms |
Number of non-H atoms |
0.978 |
0.149 |
|
|
|
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| Carbons |
Number of carbons atoms |
0.943 |
-0.228 |
Perl |
| Oxygens |
Number of oxygen atoms |
0.425 |
0.793 |
|
| Nitrogens |
Number of nitrogen atoms |
0.475 |
0.324 |
|
| Sulfurs |
Number of sulfur atoms |
0.141 |
-0.009 |
|
| Phosphorus |
Number of phosphorus atoms |
0.162 |
0.617 |
|
| Halides |
Number of halide atoms |
0.076 |
-0.170 |
|
| DoubleBonds |
Number of double bonds |
0.527 |
0.378 |
|
| TripleBonds |
Number of triple bonds |
-0.009 |
-0.109 |
|
|
|
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| RadOfGyration |
Radius of gyration |
0.888 |
0.004 |
Cerius 2 |
| ShadowXY |
Surface area projections |
0.967 |
0.076 |
|
| ShadowXZ |
0.951 |
0.053 |
||
| ShadowYZ |
0.877 |
0.093 |
||
| ShadowXYfrac |
-0.610 |
-0.027 |
||
| ShadowXZfrac |
-0.421 |
-0.002 |
||
| ShadowYZfrac |
-0.289 |
0.039 |
||
| Shadownu |
0.268 |
-0.117 |
||
| ShadowXlength |
0.849 |
-0.008 |
||
| ShadowYlength |
0.798 |
0.075 |
||
| ShadowZlength |
0.756 |
0.059 |
||
| Density |
Density |
-0.089 |
0.354 |
|
| PMImag |
Principal moment of inertia |
0.819 |
0.134 |
|
| AlogP |
Log of the partition coefficient using Ghose and Crippen's method. |
0.425 |
-0.727 |
|
| AlogP98 |
Log of the partition coefficient, atom-type value, using latest parameters. |
0.365 |
-0.852 |
|
| Fh2o |
Desolvation free energy for water |
-0.479 |
-0.762 |
|
| Foct |
Desolvation free energy for octanol |
-0.578 |
-0.617 |
|
| LogP |
Log of the partition coefficient. |
-0.022 |
-0.892 |
|
| MR |
Molar refractivity using Hopfinger's method. |
0.835 |
-0.110 |
|
| MolRef |
Molar refractivity using linear additive method based on AlogP atom types |
0.986 |
-0.033 |
|
| JX |
Balaban indices |
-0.567 |
0.027 |
|
| Kappa1 |
Kappa topological indices |
0.969 |
0.189 |
|
| Kappa2 |
0.926 |
0.026 |
||
| Kappa3 |
0.691 |
0.033 |
||
| Kappa1AM |
0.958 |
0.220 |
||
| Kappa2AM |
0.901 |
0.050 |
||
| Kappa3AM |
0.630 |
0.046 |
||
| PHI |
Molecular flexibility index |
0.800 |
0.078 |
|
| SC0 |
Subgraph topological counts |
0.980 |
0.147 |
|
| SC1 |
0.973 |
0.125 |
||
| SC2 |
0.943 |
0.186 |
||
| SC3P |
0.904 |
0.141 |
||
| SC3C |
0.749 |
0.389 |
||
| SC3CH |
0.016 |
-0.086 |
||
| CHI0 |
Kier and Hall Chi connectivity indices |
0.974 |
0.190 |
|
| CHI1 |
0.983 |
0.115 |
||
| CHI2 |
0.958 |
0.210 |
||
| CHI3P |
0.939 |
0.136 |
||
| CHI3C |
0.655 |
0.484 |
||
| CHI3CH |
0.015 |
-0.087 |
||
| CHIV0 |
0.990 |
0.076 |
||
| CHIV1 |
0.971 |
0.120 |
||
| CHIV2 |
0.913 |
0.137 |
||
| CHIV3P |
0.838 |
0.096 |
||
| CHIV3C |
0.476 |
0.148 |
||
| CHIV3CH |
0.016 |
-0.088 |
||
| Wiener |
Wiener topological index |
0.854 |
0.186 |
|
| logZ |
Logarithm of Hosoya topological index |
-0.220 |
-0.131 |
|
| Zagreb |
Zagreb topological index |
0.958 |
0.162 |
|
|
|
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|
*The first factor explains 52.8% of the variance and the second explains 12.7%. Factors with high loadings (>0.9 for first factors and >0.8 for second factors) are shown in bold. |
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|
Ji et al. Genome Biology 2007 8:R176 doi:10.1186/gb-2007-8-8-r176 |
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