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A few examples of pockets and binding sites identified using CAST:
Staphyloccocal nulcease

The binding pocket (green) of staphyloccocal nuclease (1snc). The ligand (red) occupies the binding site. Each of the rest of the pockets and cavities are colored differently (left). The ligand binding site is colored in bright green (mouth perimeter atoms) and green (interior atoms).

Pockets and cavities can be seen in corresponding alpha shapes (right). The surface of pocket mouth openings are formed by blue Delaunay triangles, the interior surface of pockets and cavities are formed by gold Delaunay triangles.

For more details see Liang, et al, 1998.

Visualized by VMD and Raster3D with scripts generated by CAST, and by ALVIS.

Bacteriochlorophyll A protein

The ligand binding site (green) of bacteriochlorophyll A protein (3bcl). It is occupied by seven bacteriochlorophyll A molecules (yellow).

Visualization by RasMol with scripts generated by CAST.

FK506 binding protein

Unoccupied Pocket near Active Site:

FK506 binding protein(1fkf).  The ivory pocket is the active site, where the ligand FK506 molecule (red, an immunesuppresant) binds.  This is the largest pocket found on this molecule.  An anciliary pocekt (green), the second largest, is found near the active site and is unoccupied.  It provides extra binding surface for enhance binding affinity and specificity in ligand design, as demonstrated by the SAR (Structure Activity Relationship) by NMR method from Fesik group at Abbott lab.

Visualization by RasMol with scripts generated by CAST.

HIV-1 protease

The binding pocket (green) of HIV-1 protease (1hte).  The ligand Gr12397(yellow) occupies the binding site.


Visualization by RasMol with scripts generated by CAST.

For more details see Liang, et al, 1998.

Membrane protein: reaction center of bacterialphotosynthesis

Membrane Protein: Bacterial Reaction Center

A pocket of the membrane protein reaction center from Rhodbactor sphaeroides  as identified by CAST.  Based on chemical complementation experiments, the corresponding pocket in photosystem II of higher plants is thought to be where the proton acceptor for redox-active tyrosine D imidazole is located.
 





For more detals, see:
  • Kim SY, Liang J, Barry B. 1997.  Chemical complementation identifies a protein acceptor for redox-active tyrosine D in photosystem II.  Proc. Natl. Acad. Sci. USA, 94:14406-14411

Visualization by RasMol with scripts generated by CAST.