Multiple realities
(covers information from several alternate timelines)

Second Street was a road in San Francisco.

By 2024, the street was part of Sanctuary District A. After the SFPD had "pacified" the Sanctuary Processing Center during the Bell Riots, the police moved off as there was still trouble on Second Street. (DS9: "Past Tense, Part II")

In the alternate reality of 2259, Starfleet Headquarters was located on this street. (Star Trek Into Darkness)

The location was derived from a of Starfleet Headquarters on directory made by Jorge Almeida for the film. [1] The directory can be seen in the background in the scene where Kirk enters Headquarters on his way to the Daystrom Conference Room.
There is an actual Second Street in San Francisco today, in the SoMa neighborhood. If this is the same street, then the alternate reality Headquarters would be in a completely different part of the city from other locations seen hosting Starfleet Headquarters, which all appeared near the Golden Gate.
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