CITY HALL — Bio-tech firm Agensys on Wednesday cleared a major hurdle in its bid to build its headquarters on a City Hall-owned lot near Bergamot Station, avoiding heavy criticism of its proposal during a hearing before the Planning Commission.

The proposed building, a 153,000 square-foot office complex at 1800 Stewart St., in recent weeks became a battle ground for bicycle activists who argued the plan should include a bike path to connect the soon-to-be light rail stop to Michigan Avenue.

Agensys, which specializes in therapeutic antibody research and development in cancer patients, resisted the idea, saying there was no safe way to incorporate the bike route.

On Wednesday, the bike path issue was front and center, but even the route’s staunchest supporters said they were convinced there was no feasible way it could be included and turned their attention to other ways the project may be able to benefit bicyclists.

While disappointed, Barbara Filet, a member of the bicycle advocacy group Spoke, said she was pleased the commission recommended augmenting the company’s contribution to bicycle infrastructure improvements in the neighborhood.

Agensys has already offered to pay $70,350 to enhance bike access to Bergamot Station as part of its proposed development agreement with City Hall.

In a unanimous vote, the commission on Wednesday recommended that the City Council either increase that amount or find other ways for the company to do more to improve bike connectivity.

Additional money could be used to study other ways to build a bike link between Bergamot Station and a possible future bike path on Michigan Avenue, officials said.

“It’s a good project and they’re a great employer,” Planning Commissioner Ted Winterer said after the meeting. “They’ve worked very hard to listen to the council, the Planning Commission and the community to significantly improve their project … it would just be great for them to make a gesture towards bicycling so the package is complete.”

Planning Commission Chairman Jim Ries acknowledged the bike path was the trickiest issue to resolve in the Agensys project but said he believed the company’s proposal is a net benefit to Santa Monica even without the path.

“It’s a difficult situation to be in because we want this company to stay here. They’re under a tight time frame and there does not seem to be a lot of practical solutions to this issue,” he said.

Agensys has proposed offering “public benefits” that include a pedestrian walkway that will connect to Bergamot Station, a cafe that will be open to the public, a sculpture garden and a transportation demand management program.

The company’s proposal is next set to come before the City Council on Sept. 14. Dale Goldsmith, an attorney representing Agensys, has said the company needs to secure development approval from City Hall by Sept. 28 in order to move ahead with its plans.

Councilman Kevin McKeown, who had earlier urged Agensys to find a way to include a pathway for bikes in its plans, on Thursday indicated the development agreement would have little trouble receiving the council’s approval.

“I look forward to welcoming Agensys to a permanent home in Santa Monica,” he said on Thursday, “and doing so in a way that provides very real improved bike connections from the Bergamot Station area to the rest of the city.”

Kent Strumpell, also a member of Spoke, said the fact that the bicycle path became the central issue for officials considering the Agensys proposal was a sign that cycling advocates are gaining increased local influence.

The episode was also a learning experience, he said.

“What went down in this situation looks to us like an unfortunate oversight that bicycling was not raised as a key issue early enough and got left off the table,” he said. “The key thing for us is for bicycling to be integrated at the very earliest project stage so we don’t miss these opportunities in the future.”

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