Which factor indicates that X has a tighter binding affinity to the protein than Y?

The binding affinity of a ligand to a protein is commonly quantified using the dissociation constant, denoted as Kd. The Kd value reflects the concentration of the ligand at which half of the protein binding sites are occupied. A lower Kd value indicates that a ligand binds more tightly to the protein, as it requires a lower concentration of the ligand to achieve this occupancy.

In practical terms, a lower Kd signifies that more interactions are occurring between the ligand and the protein, resulting in a stronger association. Thus, if X has a lower Kd than Y, this means that X binds more tightly to the protein than Y does.

The relationship of Kd to binding affinity is critical in biochemistry, as it allows researchers to compare the effectiveness of different ligands. A higher Kd indicates weaker binding, while a lower Kd indicates stronger binding, which is the key reason why the answer is focused on the significance of Kd values in determining binding affinity.