Inhibition of PDK1 kinase activity is one of the targets in developing cancer drug. In the present study, a docking calculation for ligand-PDK1 kinase complexes was carried out using the Autodock program. Experimental binding modes of 9 available lignad-PDK1 structures were reproduced. The binding energies of these complexes were correlated well with experimental IC50 values except 2 ligands. Toward designing better inhibitors, we have carried out docking calculation for a number of derivatives of the inhibitors of low IC50 value, UCN (in nM range) and BIM8. The calculations for several derivatives gave lower binding energy, suggesting that they are better inhibitors. The rationals of the calculated binding energies are discussed. In addition, calculations for a series of celebrex-based compounds were also carried out. Their correlations with experimental available IC50 values are discussed as well.