IMHO, while explaining binding affinity from a structure is fun, it does
not prove anything.  Assuming that I understand your situation
correctly, you can (relatively) easily find out from experiment which
pocket has higher affinity.  Just do soaks with different ligand
concentrations - the expectation is that the weaker binding site will
become partially occupied first.

On Tue, 2013-11-19 at 04:58 +0000, Xiaodi Yu wrote:
> Hi Wei:
> 
> Based on the structure, you can calculate the binding surface between
> the protein and the ligand. Maybe the two binding pockets will give
> you two different numbers. And the larger one usually can have the
> higher binding affinity.  You also can analyse how the ligand
> interacts with the protein though hydrophobic or electrostatic
> interaction , etc?  the last, you may also compare the b factors of
> the ligand or the protein binding pocket regions after you refining
> the structure. These things may give you some hints about which
> binding site is more strong.
> 
> Dee
> 
> 
> ______________________________________________________________________
> Date: Mon, 18 Nov 2013 22:45:58 -0500
> From: [log in to unmask]
> Subject: Re: [ccp4bb] distinguish ligand binding sites within a
> protein
> To: [log in to unmask]
> 
> Thank you so much for the suggestions, Tomas! Yes, my ligand is a
> small molecule. I have the crystal structure of the ligands bound to
> the protein, do I still need to computationally dock the ligand to the
> two pockets, can I calculate the parameters of binding directly using
> the crystal structure? 
> 
> Best,
> Wei 
> 
> 
> 
> On Mon, Nov 18, 2013 at 9:03 PM, Tomas Malinauskas
> <[log in to unmask]> wrote:
>         Dear Wei Shi,
>         is your ligand a small molecule? If it is a small molecule, I
>         would
>         try to computationally dock the small molecule to two pockets
>         separately using AutoDock, and look at the estimated free
>         energies of
>         binding.
>         Best wishes,
>         Tomas
>         
>         On Mon, Nov 18, 2013 at 8:55 PM, Wei Shi
>         <[log in to unmask]> wrote:
>         > Hi all,
>         > I got the crystal structure of a transcription factor, and
>         every monomer
>         > binds two molecules of the same ligand in different binding
>         pockets. And I
>         > also did the ITC experiment, titrating the ligand into the
>         protein, and got
>         > a U-shaped curve. The binding affinity for the first binding
>         site is higher
>         > than the second binding site.
>         > I am wondering whether I could computationally determine
>         from the
>         > protein-ligand complex structure that which binding site has
>         higher affinity
>         > for the ligand and correlate the binding sites with the
>         parameters I got
>         > from ITC experiment.
>         > Thank you so much!
>         >
>         > Best,
>         > Wei
>         
> 
> 

-- 
Edwin Pozharski, PhD, Assistant Professor
University of Maryland, Baltimore
----------------------------------------------
When the Way is forgotten duty and justice appear;
Then knowledge and wisdom are born along with hypocrisy.
When harmonious relationships dissolve then respect and devotion arise;
When a nation falls to chaos then loyalty and patriotism are born.
------------------------------   / Lao Tse /