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PostPosted: Wed Jun 17, 2015 2:40 pm 
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Hello,

I'm trying to produce a ligand-protein docking protocol by using the crystal structure of a protein. The idea being that i can then apply this protocol to homology protein models i have generated using MODELLER and various ligands from zinc/chemspider etc...

The only issue i seem to have is that in the crystal structure the ligand interacts with the FE of the heme cofactor (nitrogen in the triazole ring occupys the sixth position of the octahedral geometry of FE. However, when running Autodock Vina the ligand docks similarly to the known crystal structure except for a the interaction with the heme. The nitrogen that i'm expecting to interact with FE points towards a side chain in the protein structure (although the distance to this side chain is relatively large).

How can i get the triazole ring and the HEME cofactor to interact as they should? I have included a picture of my docking attempt (left) and the crystal structure (right).

Any help would be greatly appreciated.

Many thanks

Thomas


Attachments:
File comment: Left is docking example; Right is crystal structure
ignoring_heme.tiff
ignoring_heme.tiff [ 194.33 KiB | Viewed 1169 times ]
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