Deductible built-in gain tax on the S Corporation return

Per IRC section 1366(f)(2), the built-in gain tax is treated as a loss sustained by the S Corporation during such taxable year. The character of the loss is determined by allocating the loss proportionately among the recognized built-in gains that gave rise to the built-in gain tax.
The built-in gain tax attributable to ordinary income property is deducted on the Taxes and licenses line on Form 1120-S, Page 1. The built-in gain tax attributable to short-term or long-term capital gain property is reported on Schedule D as a subtraction from the total short-term or long-term capital gain.

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