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What's the difference between the equilibrium binding constant ($K_d$) and Inhibitory Concentration 50 $IC_{50}$? They both seem to mark halfway points. Is the only difference that $K_d$ refers to any binding, whereas $IC_{50}$ refers exclusively to inhibition?

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    $\begingroup$ For a reversible inhibitor, the relationship between Ki and IC(50) will critically depend on the mechanism of inhibition, and IMO IC(50) values are at best misleading (and at worst meaningless). Consider a (reversible) competitive inh: the IC50 value determined at a substrate conc equal to Km will be very different to that determined at, say, a substrate conc equal to 10-times Km. There is a great paper by A. Naqui who explains this very well. For a reversible inh, IC50 only equals Ki if the mechanism of inhibition is non-competitive. $\endgroup$ – user338907 Jul 12 at 17:42
  • $\begingroup$ I have expanded on this topic ( a bit too much perhaps) in the section "Reversible Inhibition & IC50. A Brief Comment" of this old answer. For a much too detailed treatment of reversible inhibition, see this answer $\endgroup$ – user338907 Jul 12 at 17:47
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First, let's review the definitions of $K_d$ and $IC_{50}$.

$K_d$

$K_d$ refers to the dissociation rate at equilibrium and is calculated by $\frac{K_{on}}{K_{off}}$. This is the rate at which the peptide is bound to the target protein ($K_{on}$) divided by the rate at which the peptide unbinds or comes off the target protein ($K_{off}$). So when you look at binding curves, it's the 50% bound/unbound point on the curve (the inflection point).

Kd example graph

$IC_{50}$

$IC_{50}$ indeed refers specifically to the inhibition of binding or inhibition of a function at which 50% of the peptide is bound and 50% is not bound (or 50% of the function is active and 50% is inactive).

Comparison

In some cases $K_{d}$ and $IC_{50}$ may be very similar values even identical, but in other cases $K_{d}$ and $IC_{50}$ values actually differ.

Pragmatically, $K_{d}$ values generally are considered more "constant" and vary less with changes in concentration of the target protein and peptide. They are more independent from the assay set up and type. In contrast, an $IC_{50}$ value can range depending on the assay set up (not considered constant values). For example, the $IC_{50}$ values in Fluorescence Polarization depend heavily on what "probe" molecule was used and the concentrations of the target protein and peptide.

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  • $\begingroup$ (+1) [I am not the downvoter] $\endgroup$ – user338907 Jul 12 at 17:33
  • $\begingroup$ If Kd has dimensions of concentration (Molarity, say), shouldn't Kd be defined as k-off/k-on? (Kd will be the ratio of a first-order rate constant (k-off) divided by a second-order rate constant (k-on), giving overall dimensions of concentration. For example: time^(-1)/( conc^(-1) time^(-1)), giving 1/conc^(-1), which is just conc $\endgroup$ – user338907 Jul 13 at 14:08

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