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Table 2 Comparisons of calculated free energies of binding and observed Ki values.

From: Structural and functional definition of the specificity of a novel caspase-3 inhibitor, Ac-DNLD-CHO

Caspase Peptide Inhibitor (Ac-, -CHO) ΔGcalc(predicted) (kcal/mol) a Kiapp (observed) (nM) b RMSD (Å) c
3 DNLD -12.99 0.68 -
  DEVD -13.96 0.288 1.28
  DQTD -12.01 1.27 -
  DMQD -11.39 13.3 -
7 DNLD -11.99 55.7 -
  DEVD -13.59 4.48 1.41
  DQTD -11.69 21.8 -
  DMQD -11.85 >200 -
8 DNLD -10.78 >200 -
  DEVD -13.61 0.597 1.85
  DQTD -11.19 9.75 -
  DMQD -9.67 >200 -
9 DNLD -9.98 >200 -
  DEVD -12.68 1.35 1.46
  DQTD -11.42 14.5 -
  DMQD -9.58 >200 -
  1. a Binding free energies calculated by AutoDock [34].
  2. b Experimentally observed Kiapp values from Table 1.
  3. c RMSD between docked and crystal or constructed structure.
  4. Data points where Kiapp > 200 nM were excluded from the least square fit plot in Fig. 5.