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 (
    86692, 86670, 86611, 86610, 86609, 86608, 
    87120, 86648, 87460, 87459, 87458, 
    87112, 86644, 86643, 86541, 87352, 
    87351, 87350, 87349, 87348, 87347, 
    87346, 87345, 87344, 87343, 87342, 
    87341, 87240, 87239, 87238, 87237, 
    87236, 87235, 87234, 87233, 87232, 
    87231, 87230, 87229, 87228
  ) 
  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 0.00067

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