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1446: Y1 Receptor Ligand Docking

Closed since over 8 years ago

Intermediate Overall

Summary

Created
October 31, 2017
Expires
Max points
100
Description

This is a follow-on puzzle of Puzzle 1441: Y1 Receptor Homology Modeling. In the previous puzzle, we asked you to model the structure of the human Y1 neuropeptide receptor. In this puzzle, we'd like you to determine how a known binder of Y1 interacts with that model.

We're starting you off with the top scoring structure from puzzle 1441, made by reefyrob and LociOiling.
We've placed BIBP-3226 into the homology model, in the approximate location of the binding pocket between the transmembrane helicies.
BIBP-3226 is a potent antagonist for Y1, and is speculated to bind in this general location.
For this puzzle, we'd like you to find the best location and best interactions of BIBP-3226 to Y1.

As proteins sometimes rearrange slightly around a small molecule, we've allowed for some flexibility in the protein,
but as we'd like for you to focus on how the ligand binds, you'll get a penalty if the protein moves too far from the starting model.

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Comments

Susume Lv 1

I hope you'll give us this puzzle again in a few weeks, now that we know the ligand can change shape and are starting to build tools to make that happen.

LociOiling Lv 1

Here are the atom numbers applied to the ligand.

[img_assist nid=2004447 title=Puzzle 1446 ligand with numbered atoms. desc=Puzzle 1446, segment 320 atom numbers. link=node align=left width=640 height=514]

Susume Lv 1

How important is it to get rid of voids around the ligand vs forming bonds? I never play with voids on, and when I checked them near the end of the puzzle I realized I have huge voids even though I have good bonds.