SELECT 
  cscart_ult_product_prices.product_id, 
  MIN(
    IF(
      cscart_ult_product_prices.percentage_discount = 0, 
      cscart_ult_product_prices.price, 
      cscart_ult_product_prices.price - (
        cscart_ult_product_prices.price * cscart_ult_product_prices.percentage_discount
      )/ 100
    )
  ) AS price 
FROM 
  cscart_ult_product_prices 
WHERE 
  cscart_ult_product_prices.product_id IN (
    69618, 69616, 69615, 69459, 69449, 69401, 
    69350, 69507, 69506, 69505, 69503, 
    69447, 69410, 68998, 68698, 67810, 
    67809, 67808, 67807, 67806, 67805, 
    67804, 67803, 67802, 67801, 67800, 
    67799, 67798, 67797, 67796, 67795, 
    67794, 67793, 67792, 67791, 69107, 
    69432, 69348, 69005, 68836
  ) 
  AND cscart_ult_product_prices.lower_limit = 1 
  AND cscart_ult_product_prices.company_id = 1 
  AND cscart_ult_product_prices.usergroup_id IN (0, 0, 1) 
GROUP BY 
  cscart_ult_product_prices.product_id

Query time 0.00055

Explain
id select_type table type possible_keys key key_len ref rows Extra
1 SIMPLE cscart_ult_product_prices range usergroup,product_id,company_id,lower_limit,usergroup_id usergroup 13 1 Using where