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 (
    68534, 68533, 68459, 68363, 68362, 68360, 
    68358, 68357, 68135, 68065, 68064, 
    67902, 67896, 67685, 67684, 66983, 
    68359, 67955, 68319, 68312, 67848, 
    67845, 67839, 67686, 67683, 66841, 
    66840, 66839, 67958, 68200, 67770, 
    67769, 67768, 67767, 67766, 67765, 
    67764, 67763, 67762, 67761
  ) 
  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 0.00053

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