Assets within a retirement account are not subject to capital gains treatment, so the purchase price of the shares is irrelevant. The purchase price is not used in calculating the taxable amount of the distribution.
The details you provided suggest that the distribution is from a traditional IRA and that the IRA/SEP/SIMPLE box is also marked on the Form 1099-R provided by the payer. If so, the entire distribution is taxable unless you have basis in nondeductible traditional IRA contributions. If you have basis in nondeductible traditional IRA contributions, TurboTax uses Form 8606 to calculate the nontaxable and taxable amounts of the IRA distribution.
