This study contains the synthesis, spectral analysis, and the enzyme inhibition effects of the Pd-based complexes bearing both 2-aminopyridine andN-heterocyclic carbene (NHC) ligands. The NHC ligand in the Pd-based complexes contains the 3-cyanobenzyl group. All new complexes were synthesized from (NHC)PdBr2(pyridine) complexes and 2-aminopyridine. These new complexes were characterized by using elemental analysis,H-1 NMR,C-13 NMR, and FT-IR spectroscopy techniques. Furthermore, inhibitor effects of these complexes were also tested toward some metabolic enzymes such as carbonic anhydrase and xanthine oxidase enzymes. The IC50 range for hCA I, hCA II, and XO were determined as 0.325-0.707, 0.238-0.636, and 0.576-1.693 mu M, respectively. These data showed that Pd(II)-NHC complexes bearing 2-aminopyridine may be potent inhibitors of hCA and XO enzymes. Besides these applications, molecular docking was performed by using CDOCKER tool as a part of Discovery studio 2019, not only to determine the binding mode of synthesized inhibitors, but also to determine the correlation between the CDOCKER score values and IC50 values. We found a good correlation (R-2 = 0.7403) between IC50 and the CDOCKER score of the inhibitors for XO. These findings could be a reference to start the development of effective medicine for XO.