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 (
    48473, 48713, 48706, 48297, 48920, 48671, 
    48670, 48302, 48276, 48275, 48238, 
    48270, 48271, 48266, 48265, 48264, 
    48263, 48246, 48277, 48247, 48259, 
    48258, 48257, 48256, 48255, 48248, 
    48237, 48236, 48233, 48201, 48103, 
    48102, 48267, 48047, 48192, 48120, 
    48101, 48100, 48099, 48097, 47985, 
    47984, 48078, 48046, 48410, 48409, 
    48408, 48407, 48406, 48405, 48404, 
    48403, 48402, 48401, 48400, 48399, 
    48398, 48397, 48396, 48395, 48394, 
    48393, 48392, 48391, 48390, 48389, 
    48388, 48387, 48386, 48385, 48384, 
    48383, 48382, 48381, 48380, 48379, 
    48378, 48377, 48376, 48375
  ) 
  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 0.00082

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