Bcl-Xl is a member of the Bcl-2 family. This family consists of pro-apoptotic and anti-apoptotic members. Bcl-Xl (in the image) ,an anti-apoptotic protein, binds pro-apoptotic proteins like BAK and BAD thus regularly inhibit program cell death. Many cancer cells overexpress at least one of the anti-apoptotic members of this family ,thus escaping a needed apoptosis . Therefore, these proteins are important targets for the development of new anti-cancer drugs.
The PDB file 2yxj shows the structure of Bcl-Xl and ABT 737. ABT 737 is a potent inhibitor of Bcl-Xl (Kd = 1nM). It binds Bcl-xl in the same position as BAK does as can be seen in 1bxl.
Interestingly the interface of Bcl-Xl is almost symmetric. There are Arg 100 and Arg 139.
Glu96 and Glu129.
Two which include Phe191 Val141 and
Ala93 for one, and the other patch includes Phe146 Val126 and Leu108. A look at the picture shows that there are hydrophobic patches (in gray) "above" and "below" the ligand ,negatively charged residues "above-right" and "below-left" of the ligand and positively charges on the "right" and "left" of it.
This symmetry can be exploited, a symmetric molecule can bind the same interface in two different ways thus increasing the "chance" of binding which means better binding affinity.
