A directory of the thermodynamic averages determined from these tables and Eq. is given in Table IV. Both DG 0 emergency and DGbind effectively predicted indirubin 3 0 oxime to become a stronger inhibitor than indirubin, and that BAY 11-7821 KT5720 and staurosporine were subsequently greater inhibitors than indirubin 3 0 oxime. Nevertheless, the ranking of inhibitor binding affinities for KT5720 and staurosporine were reversed in comparison to kinetics, with KT5720 predicted to become stronger by 1. 7 kcal mol21 using DGbind. It was reduced to 0. 7 kcal mol21 for DGbind, on inclusion of the loss of ligand VRT entropy upon binding. Accounting for entropy results, not surprisingly, produced the free energy values notably closer in degree with their experimental values. The standing of KT5720 and staurosporine inhibitor potencies assessed using MM GBSA can be accounted for. Given the additional freedom of the KT5720 alkyl chain, we can estimate an upper bound for the substitution reaction loss of KT5720 conformational entropy by attributing an entropy loss of 0. 30 0. 54 kcal mol21 64 to each rotatable sp3 relationship of atoms 16-24. This escalates the KT5720 binding free energy by 1. 8 3. 2 kcal mol21, taking the DGbind price in accordance with staurosporine to at least one. 2 2. 6 kcal mol21 in favor of staurosporine, and in keeping with the rankings from experiment. More, whereas staurosporine does not have any key receptor ligand linking waters, KT5720 was highly bridged by exchanging water molecules together with the receptor. The entropy loss associated with a bound water molecule in protein ligands things is suggested by Dunitz to have an upper bound of 2 kcal mol21 free energy cost at 300 K. 65 For that reason, the general free energy in favor of staurosporine may be increased even further on account of benefits from the loss of bound waters inside the complex. The relevant MM PBSA method and the MM/GBSA method employed here are computationally efficient, end-point free energy which have been trusted to examine protein ligand binding affinities. chk inhibitor 52,66 73 Though they lack the sound theoretical basis of recently developed, computationally demanding total affinity free energy methods,69,74 78 their experience of statistical thermodynamics is established. 79 They should be considered to be approximate, as they mix a molecular mechanics energy function using a continuum electrostatics treatment of solvation effects, they contain solute conformational entropy effects in a approximate manner80 and disregard the solvent molecular structure. For your indirubins, the breakdown of binding free energy contributions revealed that the source of the higher binding affinity of indirubin 3 0 oxime in comparison with indirubin is electrostatic, which may be caused by favorable indirubin 3 0 oxime NOH group interactions.