Fig 9. In-silico comparison of the 3D models of PmV.

(A) Superimposed catalytic domains of two Pf_PmV 3D models. The one we used in this work (blue ribbon) (PDB file in S1 File) and the one derived from modelling Pf_PmV to the recently published structure of Pv_PmV in complex with WEHI-842 (red ribbon) [39] (PDB file in S3 File). 3D models of PmV were obtained by Phyre 2 homology modelling software using as templates either pro-plasmepsin of Plasmodium vivax (PDB code 1MIQ) (blue ribbon) or the recently published Pv_PmV in complex with WEHI-842 (PDB code 4ZL4) (red ribbon) [39]. The two 3D models were then superimposed, aligning the alpha Carbons of the peptidic backbones. The two catalytic aspartates and the β-sheet flap, that form the aspartic protease catalytic groove, are indicated. (B) In-silico comparison between (S)-1 bound to each of the two 3D models. 3D representation of (S)-1-PmV complex was obtained by Phyre 2 homology modelling software. The (S)-1-PmV complex to the model used in this work is in blue, while the complex to the model derived from Pv_PmV is in red. Compound 1 is represented as solid ‘balls and sticks’ while PmV active aspartates of the catalytic pocket are as wireframe. For sake of clarity, only Compound 1 (indicating the principal residues, R1 and L3), Asp118 and Asp365 are shown. The superimposition of the full 3D models is available in S3 Fig.