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 (
    38980, 38979, 38978, 38977, 38950, 38949, 
    39126, 38968, 38962, 38961, 38960, 
    38959, 38958, 38957, 38956, 38955, 
    38954, 38953, 38952, 38951, 38930, 
    39545, 39544, 39543, 39542, 39541, 
    39540, 39539, 39538, 39537, 39536, 
    39535, 39534, 39533, 39532, 39531, 
    39530, 39529, 39528, 39527, 39526, 
    39525, 39524, 39523, 39522, 39521, 
    39492, 39491, 39490, 39489, 39488, 
    39487, 39486, 39485, 39484, 39483, 
    39482, 39481, 39480, 39479, 39478, 
    39477, 39476, 39475, 39474, 39473, 
    39357, 39356, 39355, 39354, 39353, 
    39352, 39351, 39350, 39349, 39348, 
    39347, 39346, 39345, 39344
  ) 
  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 0.00098

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