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 (
    40303, 40302, 40301, 40300, 40299, 40298, 
    40297, 79897, 39728, 39507, 39506, 
    39377, 39398, 39447, 39332, 39319, 
    39318, 39313, 39267, 39266, 39265, 
    39264, 39263, 39260, 39259, 39641, 
    39255, 39247, 39246, 39225, 39224, 
    39223, 39184, 39183, 39270, 39147, 
    39393, 39391, 39390, 39389, 39387, 
    39385, 39383, 39382, 39381, 39644, 
    39144, 39143, 39142, 39141, 39140, 
    39139, 39138, 39137, 39136, 39135, 
    39134, 39133, 39132, 39131, 39130, 
    39129, 39128, 39127, 39069, 39068, 
    39067, 39066, 39065, 39064, 79921, 
    39118, 39117, 39116, 39115, 39034, 
    70800, 70799, 70798, 70797
  ) 
  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 0.00089

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