How would you describe the interaction between Lys167 and the ligand?

Question

BlackTom AI · Accepted Answer

The provided data for this question is incomplete: the answer options list is empty, so there aren’t multiple choices to evaluate against. Nevertheless, the given answer indicates that the interaction between Lys167 and the ligand is a hydrogen bond.

Why a hydrogen bond is plausible: Lysine has a terminal amino group (–NH3+ at physiological pH) that can act as a hydrogen bond donor to electronegative atoms like oxygen or nitrogen in the ligand. If the ligand presents a suitable hydrogen-bond acceptor, such as a carbonyl oxygen, an amide nitrogen, or an ether/ester oxygen, a hydrogen bond can form between the lysine side chain and the ligand.

Key considerations to support this interpretation:
- Donor capability: The protonated amine on Lys167 can donate a hydrogen to an acceptor on the ligand.
- Geometric alignment: For a hydrogen bond to be present, the donor–acceptor distance is typically around 2.7–3.5 Å, and the angle is favorable (nearly linear O–H···N or N–H···O). If the ligand positions itself within the binding pocket to satisfy these geometric constraints, a hydrogen bond is feasible.
- Alternative interactions: Lysine can also engage in ionic (electrostatic) interactions with negatively charged groups, or participate in water-mediated hydrogen bonds. If the text specifically identifies a hydrogen bond, it suggests a direct (or possibly water-bridged) H-bond involvement rather than purely ionic contact.

Limitations due to missing options: Since there are no other answer choices to compare, we cannot critique or contrast the hydrogen-bond explanation with, for example, ionic interactions, hydrophobic contacts, or covalent bonding. In a typical question, you would evaluate each option's plausibility within the binding context and explain why other interactions would be less likely given the surrounding residues and ligand chemistry.

In summary, describing the interaction as a hydrogen bond aligns with the common role of a lysine side chain in liganding roles, provided there is an appropriate hydrogen-bond acceptor on the ligand and correct geometric arrangement within the binding site.

2254 BIOSC 1544 SEC1000 Homework: Protein/ligand interactions

How would you describe the interaction between Lys167 and the ligand?

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