I have an enzyme structure which utilize NADPH, FAD and amino acid. only FAD is present in the crystal structure, Is redocking important in here for validation?
and when I tried to redock FAD, it is not giving the same orientation in the original structure ( same site but different orientations)?
for the ligands I want to dock, They will be docked at the binding site of the substrate ( amino acid), how to manipulate the docking of the amino acid to be in the right binding site with the best orientation before trying to autodick any other ligands at this site?
and if I need to redock the original substrate, should I draw the structure and get coordinates or there is other preferred way?
Thank you
Are you sure that you have removed FAD present in crystal structure before re-docking of FAD coz it must adopt close conformation to crystal structure in ideal situations. If yes then refine your docking parameters. Usually it depends on docking center and GALS parameters. Examine the cavity carefully and select parameters accordingly.
For docking of ligands at right position your grid box size must be precise and rightly centered.
For substrate redocking crystal structure coordinates can be used (if available) otherwise simple drawing and 3D position superimposition programs can be used i.e HEX.
yes, I definitely removed FAD from the structure before docking.
Can I define the grid box size and position in accordance with similar structure and function crystal structures because I don't have the substrate cocrystallized with the crystal
thank you
You should redock the ligand (FAD) and get the same orientation. If it is not the same, try to minimize the grid box.
For the second question, you can dock your original substrate and look for enzyme mechanism with your specific substrate (so you can know the catalytic amino acids), then dock your compound
@Heba. Yes you can do so but what you can adopt from similar structure is only substrate relative 3D position and AA orientation to define your grid box.
Dear Heba,
Usually, you should indeed be able to dock the natural ligand of in its binding site, and that should serve as a validation.
However, in this case, I'm not sure this is the best course of action.
To start with, FAD is usually a cofactor and its presence might affect the binding of your true ligand (amino acid, or any replacement ligand). In such case, your FAD should be considered as part of the receptor. If your crystal structure is reliable, I'd advise you to keep it. Even if you're doubtful about the quality of your structure, I'd rather refine the position with molecular mechanics (or dynamics) than with docking.
Also, please keep in mind that FAD is more complex than many of the drug-like molecules which are usually handled by autodock. I have not computed logP, but it is definitely outside of Lipinski's rules for MW, H-bond donors and acceptors. Add too that a number of chiral centers. Add on top of that a large number of rotatable bonds... At first glance, I would not expect that kind of ligand to land "spot on" on the X-ray coordinates. Especially if you use default parameters.
If you still want to perform the docking, check that the charges are correctly attributed in the protein and ligand. Check that the hydrogen-bonding network in your binding site is consistent with the way your ligand binds. You should also increase the parameters in your dpf file, in order to somewhat compensate for the complexity of your molecule. So, you might add more g.a. runs, a higher number of maximal operations,...
Good luck....
thank you for answering.
about your third comment, I mis-explain, I need to use the biding site for the substrate which is an amino acid at the main pocket for screening my library.
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