I have a mac with a custom PHP 5 install that built from about a year ago. I remember it took all Sunday and I had to compile about 20 times to get it right. The MySQL I have is
You're going to need to compile it by hand, instead of via PECL. You'll need to know where your MySQL install is. I don’t know about the Entropy packages, but the builds provided by MySQL (which I recommend) install into /usr/local/mysql
.
$ pecl download pdo_mysql
$ tar xzf PDO_MYSQL-1.0.2.tgz
$ cd PDO_MYSQL-1.0.2
$ phpize
$ ./configure --with-pdo-mysql=/usr/local/mysql
$ make && sudo make install
And that should get you to the point where you can configure it.
FYI; the MySQL PDO driver is included in the php 5.2.9 and 5.3 builds from Marc Liyanage's entropy.ch