SELECT 
  cscart_product_prices.product_id, 
  MIN(
    IF(
      cscart_product_prices.percentage_discount = 0, 
      cscart_product_prices.price, 
      cscart_product_prices.price - (
        cscart_product_prices.price * cscart_product_prices.percentage_discount
      )/ 100
    )
  ) AS price 
FROM 
  cscart_product_prices 
WHERE 
  cscart_product_prices.product_id IN (
    398, 1981, 1716, 40446, 31637, 5278, 
    855, 1277, 5786, 47020, 47023, 41339, 
    47022, 31635, 1580, 3876, 1975, 48980, 
    120, 43824, 40443, 27353, 37850, 2873, 
    3577, 2854, 1538, 3713, 41590, 40149, 
    6369, 2290
  ) 
  AND cscart_product_prices.lower_limit = 1 
  AND cscart_product_prices.usergroup_id IN (0, 1) 
GROUP BY 
  cscart_product_prices.product_id

Query time 0.01387

JSON explain

{
  "query_block": {
    "select_id": 1,
    "nested_loop": [
      {
        "table": {
          "table_name": "cscart_product_prices",
          "access_type": "range",
          "possible_keys": [
            "usergroup",
            "product_id",
            "lower_limit",
            "usergroup_id"
          ],
          "key": "product_id",
          "key_length": "3",
          "used_key_parts": ["product_id"],
          "rows": 32,
          "filtered": 99.9960556,
          "index_condition": "cscart_product_prices.product_id in (398,1981,1716,40446,31637,5278,855,1277,5786,47020,47023,41339,47022,31635,1580,3876,1975,48980,120,43824,40443,27353,37850,2873,3577,2854,1538,3713,41590,40149,6369,2290)",
          "attached_condition": "cscart_product_prices.lower_limit = 1 and cscart_product_prices.usergroup_id in (0,1)"
        }
      }
    ]
  }
}