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 (
    14641, 14640, 14637, 14635, 14634, 14633, 
    14632, 14631, 14630, 14629, 14628, 
    14627, 14626, 14481, 14480, 14482, 
    24684, 24683, 14436, 14434, 14438, 
    14437, 14411, 16539, 14409, 14410, 
    14101, 14138, 14137, 31447, 31446, 
    31445, 31444, 31443, 31442, 31441, 
    31440, 31439, 31438, 31437
  ) 
  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 0.00046

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