Placeholder image of a protein
Icon representing a puzzle

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.

Top groups

  1. Avatar for HMT heritage 11. HMT heritage 3 pts. 13,567
  2. Avatar for freefolder 12. freefolder 2 pts. 13,564
  3. Avatar for GENE 433 13. GENE 433 1 pt. 13,562
  4. Avatar for Italiani Al Lavoro 14. Italiani Al Lavoro 1 pt. 13,519
  5. Avatar for Team South Africa 15. Team South Africa 1 pt. 13,512
  6. Avatar for Deleted group 16. Deleted group pts. 13,505
  7. Avatar for Russian team 17. Russian team 1 pt. 13,458
  8. Avatar for EricHamber 18. EricHamber 1 pt. 13,331
  9. Avatar for FoldIt@Netherlands 19. FoldIt@Netherlands 1 pt. 13,190
  10. Avatar for xkcd 20. xkcd 1 pt. 6,821
  1. Avatar for TheStaticSloth 21. TheStaticSloth Lv 1 54 pts. 13,596
  2. Avatar for Norrjane 22. Norrjane Lv 1 52 pts. 13,594
  3. Avatar for johnmitch 23. johnmitch Lv 1 50 pts. 13,593
  4. Avatar for Glen B 24. Glen B Lv 1 49 pts. 13,592
  5. Avatar for crpainter 25. crpainter Lv 1 47 pts. 13,591
  6. Avatar for brow42 26. brow42 Lv 1 45 pts. 13,591
  7. Avatar for anthion 27. anthion Lv 1 44 pts. 13,590
  8. Avatar for Jim Fraser 28. Jim Fraser Lv 1 42 pts. 13,589
  9. Avatar for Blipperman 29. Blipperman Lv 1 41 pts. 13,588
  10. Avatar for lamoille 30. lamoille Lv 1 40 pts. 13,587

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.