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 (
    5618, 5676, 5661, 5634, 5619, 6216, 2458, 
    2457, 2456, 2455, 2454, 2451, 2450, 
    6164, 2443, 2448, 2447, 2446, 2445, 
    2444, 85065, 85064, 78818, 78817, 2441, 
    2440, 2439, 5885, 2442, 78201, 5897, 
    2434, 2435, 2437, 2438, 2436, 6059, 
    2433, 2432, 2431, 2430, 6189, 6130, 
    6129, 6126, 6125, 6124, 6123, 6122, 
    5940, 2428, 2427, 2426, 2425, 6183, 
    2422, 2423, 2421, 2420, 2424, 2419, 
    2418, 2416, 2414, 6181, 5985, 77579, 
    6321, 26680, 6174, 6306, 2408, 2412, 
    2413, 2411, 2410, 2409, 2407, 6186, 
    103458
  ) 
  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 0.00092

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