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 (
    11485, 10960, 10201, 397, 10188, 10353, 
    10355, 1655, 388, 395, 10163, 9871
  ) 
  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 0.00049

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 24 Using index condition

Result

product_id price
388 910.000000
395 2329.000000
397 1446.000000
1655 2089.000000
9871 1435.000000
10163 2629.000000
10188 1160.000000
10201 1446.000000
10353 1460.000000
10355 1360.000000
10960 3500.000000
11485 3000.000000