9% for around $120,000 lease is within range.
You are not getting ripped off on the commission at $1 per square foot per year..
I did the math though. you stated the the commissions are 9% of the total lease for a 5,000 square foot office building?! If so, the annual rent is about $55,000 or $11.00 per square foot per year or 90 cents per foot per month. That sounds extremely low for a class "C" office building in San Francisco. If I was the tenant at that rent I would want to give my agent a bonus and a thank you gift!
If I was the landlord, I'd ask for an explanation of why the rent was so low.