The $1 billion dollar cost per drug is risk adjusted, so it includes all failed attempts at clinical trials and compounds that didn't make it through pre-trial screening.

Edit: The $1 billion number is meaningless outside the context of large pharmaceutical companies. The cost for phase 3 trials is in the tens or hundreds of millions of dollars so the floor is a wide range and there have been instances of companies getting incredibly lucky and developing a drug for much less than a full billion.