Help finding proteins in the PDB...

[Ray Crawford <iguana "-at-" one.net>]

 Howdy all!!!
  I had a question about the contents of the PDB.  I?m currently doing an
 examination of a macromolecular docking program and I am looking for various
 ligand/protein complex test cases.  Ideally I would like to find two proteins
 which have 5-10 experimentally determined structures, each with different
 ligands
 (ie Dihydrofolate Reductase with 5-10 different experimentally determined
 ligands
 in the active site).  The two examples I was thinking about were:
 1.) a protein with an active-site-surface cleft such as cyclophilin A.
 2.) a protein with a partially or completely enclosed pocket like the retonioc
 acid binding protein RXRg.
 So far, I have looked at two examples -- ~10 experimentally determined HIV
 protease complexes (which have not been deposited in the PDB) and 4 cyclophilin
 A
 complexes.  The problem with the HIV protease case is that the active site is
 too
 darn symmetrical and I think that it is not a fair test of the program?s
 ?docking? ability ? there are too many ?good? orientations for the ligand (i.e.,
 the program finds plausible binding modes but they are all WAY off from the
 experimental binding mode).  CypA, on the other hand,  is a perfect example of a
 cleft binding site but there are only 4 structures of small, drug-like molecules
 experimentally determined in the PDB (and they are all dipeptides which, I might
 add, the program nails right on?) ? I think that this example is too easy.
  So, my question is two-fold.  Do you all think I am neglecting any important
 ?binding modes? by limiting my examination to surface clefts and enclosed
 pockets, and does any one know of any proteins in the PDB (or coordinate sets
 you
 would be willing to share?) that fit these criteria?
  Thanks,
   Ray Crawford
   Research Associate
   The Procter & Gamble Co.