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 (
    48374, 48373, 48372, 48371, 48370, 48369, 
    48368, 48367, 48366, 48365, 48364, 
    48363, 48362, 48361, 48360, 48359, 
    48358, 48357, 48356, 48355, 48354, 
    48353, 48352, 48351, 70736, 70735, 
    70734, 70733, 48051, 48033, 48032, 
    48031, 47866, 48025, 47884, 47883, 
    47851, 47885, 48028, 47854, 47850, 
    47849, 47813, 47723, 90955, 90954, 
    90953, 90952, 90951, 90950, 90949, 
    47810, 48013, 47836, 47815, 47814, 
    47808, 47689, 47818, 47778, 47777, 
    47776, 47775, 47763, 47762, 47761, 
    47760, 47639, 47744, 47743, 47742, 
    47746, 47604, 47603, 47602, 47601, 
    47600, 47599, 47598, 47597
  ) 
  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 0.00102

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