But both the structure share very little sequence similarity. Their length also vary.
Perhaps reading this article will help you
https://doi.org/10.1016/j.csbj.2021.04.048
I would simply superimpose (sequence guided if possible but with manual adjustments when overall sequences similarity is low) the target structure with protein ligand complexes with similar folds and use the ligand position from the complex as a rough starting position for docking. However, if the ligand binding site residues from the overlayed complex do not have reasonable conserved properties in the corresponding target site from the overlay, I would throw that complex away.
Use structural superposition (https://en.wikipedia.org/wiki/Structural_alignment) rather than sequence alignment, e.g. in PyMol using the "super" command ( https://pymolwiki.org/index.php/Super ) rather than "align" . Check Proteopedia for links to various servers and programs doing structural superposition ( https://proteopedia.org/wiki/index.php/Structure_superposition_tools )
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