I did some docking experiments with the human microsomal CYP3A4 extracted from PDB as a holo-structure (heme cofactor)  at 2.05 Å resolution. However, the heme was removed from the protein to release the binding pocket (apo-structure). But you can easily dock your ligands into a holo-structure as well.

hello there!, It is possible to perform docking experiments with the proetin containing haem. The software program Autodock4  will work best. However there might be some slight problems when you want to protonate and energy minismize the entire protein structute containing the haem.  I suggest you first  remove the haem part in the protein 3D, structure, then protonate and energy minimize the protein xture without the haem in it. After doing this, please insert the haem portion and then perform the docking analysis restraining the grid box to cover the entire portion of the protein binding pocking.  This procedure is necessary if you intend to obtain maximum protonation and a correct structure conformation prior to docking. I also suggest you be more precise when asking a question. Thanks for that.

Hello, another option  your define the heme as a part from a pharmacophor, and then dock under consideration from the pharmacophore. You have than a result what the heme included.(You can use your model for further QC calculation TS/Oniom etc.)

worth consideration, the active site in the Cyps is flexible (Volume)  

d-orbitals in MM:

http://www2.warwick.ac.uk/fac/sci/chemistry/research/deeth/deethgroup/research/lfmm/background/