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 (
    69285, 69284, 69283, 69282, 69281, 69280, 
    69279, 69278, 69277, 69276, 69275, 
    69274, 69273, 69272, 69271, 69270, 
    69269, 69268, 69267, 69266, 69265, 
    69264, 69263, 69262, 69261, 69260, 
    69259, 69258, 69128, 68673, 68672, 
    68671, 68670, 68669, 68668, 69121, 
    68664, 68460, 68380, 68611
  ) 
  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 0.00056

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