modeling the 5-HT 2a receptor

[tryp2fun]

Yup, and all programs that can generate these images

Pymol, with the plugin for autodock Vina, will do it. They are free if you don't want support.

Pymol: https://www.pymol.org/
Autodock Vina plugin: http://wwwuser.gwdg.de/~dseelig/adplugin.html

 

[anubis23]

Very nice.

https://bitnest.netfirms.com/external.php?id=%0470%02%23%0D%18C%18%1B%01
^
If you really want to go all out lol.

 

[s0rsha]

Your inbox is full, here's the file: http://www.filesonic.com/file/2304851801/5-ht2A_complete.pdb

Yeah there probably are several slightly different binding modes, but I'm pretty sure all of them will have the basic amine bonding to Asp155. I used to specify it as a constraint (really, you'd think the docking software could figure it out itself) or weird things happened! I still didn't manage to reproduce the ligand pose in the file though, and other ligands usually gave poses that didn't agree with experimental data. Hopefully you'll have more luck

Edit: There are a few recent active/agonist bound GPCR crystal structures that you can use as a template to possibly get a better model than the MD derived one:
3QAK - agonist bound adenosine A2A receptor
3P0G - nanobody stabilised active B2AR
2Y03 - agonist bound B1AR
2Y00 - partial agonist bound B1AR

Does anyone happen to be sitting on this still? The original PDF does not paste the correct spacings and also there's a line break that fucks up the format completely... much appreciated!

 

[thizzkid]

This is amazingly cool; as a pharmacology student now, I'm not quite at this level of understanding but this not only gives a really great context with which to try and understand some of the more complex biochem/pharmacodynamic concepts.

One question though, with LSD I can't discern what isomer you have here, but LSD with it's 2 chiral centers and resulting 4-isomers, is there anyway you could image these?.....https://en.wikibooks.org/wiki/Struc...acid_diethylamide#/media/File:LSD_isomers.png

As I understand both iso-LSD isomers are inactive or at least far less active, with this model perhaps the binding residues could show us why.