Figure 2: Comparison of binding mode of compounds 1 and 2 to HIV-1 PR. | Nature Communications

Figure 2: Comparison of binding mode of compounds 1 and 2 to HIV-1 PR.

From: Triggering HIV polyprotein processing by light using rapid photodegradation of a tight-binding protease inhibitor

Figure 2

(a) Two views of the HIV-1 PR-1 complex (PDB code 4U7Q). The protein is shown in cartoon representation with a transparent surface, while the inhibitor atoms are represented by spheres. The coumarin moiety protrudes from the enzyme active site cavity. (b) Superposition of 1 (pink carbon atoms) and RTV (ritonavir; grey carbon atoms) bound in the HIV-1 PR active site. (c) Superposition of 1 with 2 (in green, PDB code 4U7V) bound to HIV-1 PR (PDB code 1HXW (ref. 28)). (b,c) Residues interacting with 1, 2 and RTV are indicated in the corresponding colours for individual enzyme subsites. Residues forming polar interactions are highlighted in bold italics. To identify non-polar interactions, the cut-off for distance between any atom of residue and any atom of inhibitor was 4 Å. For polar interaction, the cut-off for distance between hydrogen bond donor and acceptor was 3.5 Å. Active site aspartates are shown in stick representation.

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