The $3 million that Isis Pharmaceuticals (Nasdaq: ISIS) got yesterday as part of its expanded drug development pact with GlaxoSmithKline (NYSE: GSK) doesn't sound like that much.

And financially it isn't; Isis ended the first quarter with nearly $427 million in cash. The extra cash isn't going extend the runway of the cash-burning biotech by all that much.

Nevertheless, investors should be happy about the payment. The partnership struck last year is proceeding along nicely. Isis has already discovered one candidate, ISIS-TTRRx, that is ready to enter a phase 1 clinical trial. The $3 million this week was to add another disease program to the five that were ongoing. Glaxo seems to like the progress Isis is making.

All told, Isis could get $1.5 billion for the six drugs for rare and infectious diseases it's developing for Glaxo. And Isis only has to usher them through phase 2 development. After that, Glaxo will take over development, and Isis can sit back and collect milestone and up to double-digit royalties on sales -- assuming of course that the drugs work and get past the regulatory authorities.

Isis drug technology uses antisense to turn genes off. The drugs interfere with an intermediary in the process between genes on DNA and the disease-causing proteins that the genes code for.

Isis also has pacts with Bristol-Myers Squibb (NYSE: BMY), Eli Lilly (NYSE: LLY), Teva (Nasdaq: TEVA) and others. The most advanced drug, mipomersen -- which it's developing with Genzyme, now Sanofi (NYSE: SNY) -- will be submitted to the FDA this year.

Mipomersen is clearly more important to Isis' short-term future, but the pact with Glaxo shouldn't be overlooked as a long-term driver of value for shareholders.

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Fool contributor Brian Orelli, Ph.D., doesn't own shares of any company mentioned in this article. The Motley Fool has a disclosure policy.