In molecular docking aspect, what is the difference between the Ligand and Cofactor? Can a Cofactor be used like a ligand for docking with the target?


Ligand is an umbrella term for non-covalently bound anything. A cofactor, substrate, or allosteric regulator could be a ligand. This is a biochemical definition ligand, don't confuse it with a formal chemistry definition of ligand.

What's generally important about cofactors is they're not protein, but they're essential to the protein's biological activity. They could be a metal ion, organic complex, a vitamin, etc. Organic complexes that act as cofactors are also known as coenzymes. Cofactors that bind tightly or become covalently bound are called prosthetic groups. The protein without the required cofactors is called an apoenzyme, and with it's cofactors is called the holoenzyme.

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  • $\begingroup$ @Kendall I read this article before, but I expect answer in 'Molecular Docking' aspect. I mean, whether the cofactor can also be considered as ligand for docking? Does removing the cofactor affects nature of the docking? $\endgroup$ – ak-SE Feb 16 '16 at 18:58
  • $\begingroup$ Apoenzymes largely don't attain their catalytic effect due to conformational changes or active site changes that cofactors induce upon binding in forming a holoenzyme. This means that sometimes there will be two docking states: one for the cofactor/coenyme, and if there is a conformational change another docking state for the substrate. In short though, it depends. $\endgroup$ – CKM Feb 16 '16 at 19:07
  • $\begingroup$ Kendall So, In molecular docking of ligands... Should the cofactors must also be included? $\endgroup$ – ak-SE Feb 16 '16 at 19:14
  • $\begingroup$ You need to know what you're modeling. If you're modeling the docking of a cofactor to an apoenzyme, that's a different study than the binding of a substrate to a holoenzyme. Since apoenzymes lack catalytic activity, you wouldn't want to model binding of a substrate to an apoenzyme, however, so you would probably be modeling the interactions with a holoenzyme (which has cofactors bound). The design of your study and what your goals are will dramatically affect that question. $\endgroup$ – CKM Feb 16 '16 at 19:19

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