Load the 1XDN files (receptor.pdb and ligand.pdb) into BINANA to answer this and the following questions.

What type of interaction does ASN92 form with the ligand?

Question

Load the 1XDN files (receptor.pdb and ligand.pdb) into BINANA to answer this and the following questions.

What type of interaction does ASN92 form with the ligand?

BlackTom AI · Accepted Answer

The prompt asks: 'What type of interaction does ASN92 form with the ligand?' and provides an answer of 'Hydrogen bond' but does not list any answer options.

Because no alternative choices are given, I cannot compare hydrogen bonding to other potential interactions (e.g., ionic, hydrophobic, van der Waals) within the provided options. Nevertheless, I can reason about why a hydrogen bond is a plausible interaction for ASN92 with a ligand in BINANA analyses.

First, consider the residue ASN (asparagine) side chain: it contains an amide group with a carbonyl oxygen (C=O) and an amide nitrogen (NH2). The carbonyl oxygen is a hydrogen-bond acceptor, while the amide NH can donate a hydrogen bond. In protein–ligand interfaces, asparagine often participates in hydrogen bonding with ligand atoms such as amines, heteroatoms, or carbonyls, aligning the ligand so that donors and acceptors on the ligand can form a stabilizing network.

Second, in BINANA or similar docking/pose-analysis tools, a reported interaction involving ASN92 with a ligand is frequently identified as a hydrogen bond when there is an appropriate geometric alignment: a donor hydrogen on the ligand targeting the ASN acceptor, or a donor on ASN's amide NH forming a bond to a ligand acceptor, with favorable distance (roughly 2.7–3.5 Å) and angle criteria.

Third, without alternative options to contrast, we can still assess why other interaction types might be less likely in this specific context: ionic interactions require charged groups; if ASN92 or the ligand lacks the necessary charge separation in the pose, an ionic interaction would be unlikely. Hydrophobic contacts would require nonpolar surfaces in close proximity, which is less consistent with the polar, hydrogen-bond-capable side chain of asparagine. Van der Waals interactions are ubiquitous but typically weaker and less specific than a directional hydrogen bond when a donor–acceptor pair is properly aligned.

In summary, given ASN92’s amide-containing side chain can both donate and accept hydrogen bonds, and assuming the ligand presents an appropriate donor or acceptor in proximity, a hydrogen bond is a plausible and common interaction type between ASN92 and the ligand in BINANA analyses.

Note: If there were multiple answer choices, I would evaluate each one against known ASN92 chemistry and common BINANA criteria, explaining why hydrogen bonding stands out for this residue–ligand pair and why other interactions would be less consistent with the observed geometry and chemistry.

2254 BIOSC 1544 SEC1000 Homework: BINANA

Load the 1XDN files (receptor.pdb and ligand.pdb) into BINANA to answer this and the following questions. What type of interaction does ASN92 form with the ligand?

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