lenacapavir to Cure HIV (II)

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(1)
(a) All viruses have proteinaceous capsid. Some viruses have lipid membrane (which is derived from host cell), whereas other viruses do not (have membrane).
(b) The capsid of a HIV-1 virus forms a closed fullerene cone, whose hexagons or 12 pentagons are NOT made up of carbon atoms at the corner, but (identical) monomers.

(2) In the previous posting titled "lenacapavir to Cure HIV (I),"

Pharmacologic Hyperstabilisation of the HIV-1 Capsid Lattice Induces Capsid Failure. eLife, 13:e83605 (Feb 13, 2024)
https://pubmed.ncbi.nlm.nih.gov/38347802/
(At the upper right corner, click "free" to view the full report)
, whose Figure 1(C) showed lenacapavir as sticks (whose carbon atoms, the most common atoms (which form the backbone), are colored red) in in a "hydrophobic pocket" (colored gray; quoting the text immediately before Figure 1) where capsid's "-l]andmark residues N57 (pale green) and N74 (red-brown) are highlighted."

Figure 1(C) is too closed-up (too zoomed in), for us to get the big picture: Where is the pocket in capsid? Why are N57 and N74 critically positioned?


(3) LINK John R et al,  Clinical Targeting of HIV Capsid Protein with a Long-Acting Small Molecule. Nature, 584: 614 (2020)
https://pubmed.ncbi.nlm.nih.gov/32612233/
provided the answer to the first question.
(a) Published by Gilead, this article talked about experimental drug "GS-6207" which is now lenacapavir. (There is no point to give an experimental drug a formal drug name, as it (experimental drug) may not pass clinical muster.
(b) At the upper right corner, click the tap "FREE Full text PMC." In the new Web page, view Figure 1 g to i.
(i) Figure 1 g displayed a hexamer of (six) monomers -- alternately "colored cyan and gray." Figure 1 g is composed of two panels: the top panel is top view of the hexamers, and the bottom panel, the side view. And one GS-6207 is depicted as several green balls (of carbon atoms) and one redd ball (of oxugen atom). Fugure 1 g had NTD (N-terminal domain) and CTD (C-terminal domain) for each monomer.
(ii) Figure 1 h described, "Space-filling view of GS-6207 in its binding site (X-ray structure)."  Of note, the (surrounding) capsids (one colored cyan and the other Gray) are also represented in space-filling view.
(iii) Figure 1 i is basically the same as Figure 1 h except that, mainly, GS-6207 is sticks.

In both Figure 1 h and i, carbon atom is green (forming the backbone), nitrogen atom is blue, oxygen atom red. and both fluorine and chlorine atoms light green or greenish white. Compare with the chemical structure of lenacapavir in
https://en.wikipedia.org/wiki/Lenacapavir
, one can tell that the lenacapacir (or GS-6207) in the FRONT of Figure 1 i displayed lenacapavir's bottom right quadrant: with three Fluorine atoms connected by a carbon atoms, which is in turn connected to two blue nitrogen atoms, one intermediate carbon atom )from this point on pointing downward), and one more blue nitrogen atom, followed by a pinkish sulfur atom whose three branches are one carbon atom and two red oxygen atoms (one of the two oxygen atoms is blocked from view).

Figure 1 i also have seven ("n=7," as caption said; seven is the total number of hydrogen bonds one lenacapavir establishes with the two adjacent monomers); hydrogen bonds (in "dashed black lines"), two (dashed black lines) connecting GS-6702 with N57 and one with N74. As I explained in the previous positing, the one-letter N stands for amino acid asparagine (the N came from the penultimate letter of asparagine).

Right after Figure 1 was the paragraph of text which stated, "The GS-6207 sulfonamide is the linchpin in a H-bonding network that bridges from CANTD residues N74 and K70 of one subunit [ie, capsid monomer] to CACTD residue N183 of the neighboring subunit [ie, monomer] * * * "


(4) The hydrogen bonds, which stabilizes the interaction between lenacapavir and capsids, are drawn schematically in Figure S1 (S = supplemental)
BESTER Stephanie M et al, Structural and Mechanistic Bases of Viral Resistance to HIV-1 Capsid Inhibitor Lenacapavir. mBio (published by American Society for Microbiology), 13: e0180422 (2022)  
https://www.sciencedirect.com/or ... i/S2150751122003537

Figure S1 answers the second question, posed in the the last sentence of paragraph (2). Figure S1(A) numbered the four rings in one lenacapavir: R1-4.