I think you want to know whether a comparison between the Km of the substrate and the Ki of the inhibitor is a valid way of assessing the quality of an inhibitor for the target enzyme. If so, then my answer is that I don't think it is a meaningful comparison. However, if the inhibitor is an alternate substrate for the enzyme, then you could compare kcat/Km for the 2 compounds.

The Ki of an inhibitor (equivalent to Kd) is, all by itself, an excellent way of stating the potency of an inhibitor and of comparing inhibitors to each other. Frequently, one measures the IC50 rather than the Ki, but that is equally useful because the IC50 is usually directly proportional to (and higher than) the Ki. The Cheng-Prusoff equation expresses this proportionality.

What do you mean by "prove that the inhibitor is not effective as natural ligand"?

Km is a constant defined operationally as a combination of kinetic rate constants:

Km=(k-1 + k2)/k1

In certain situations (k2

Yes, as long as the Km and Ki were determined using the same enzyme under the same assay conditions.

And after reading Adam's response, I should say I was thinking of comparing the Ki for HIV-1 protease inhibitors (which are typically transition state peptidomimetics) to the Km for the HIV-1 protease substrate which was used for designing the inhibitor.

I think you want to know whether a comparison between the Km of the substrate and the Ki of the inhibitor is a valid way of assessing the quality of an inhibitor for the target enzyme. If so, then my answer is that I don't think it is a meaningful comparison. However, if the inhibitor is an alternate substrate for the enzyme, then you could compare kcat/Km for the 2 compounds.

The Ki of an inhibitor (equivalent to Kd) is, all by itself, an excellent way of stating the potency of an inhibitor and of comparing inhibitors to each other. Frequently, one measures the IC50 rather than the Ki, but that is equally useful because the IC50 is usually directly proportional to (and higher than) the Ki. The Cheng-Prusoff equation expresses this proportionality.