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 (
    48813, 45029, 46155, 47878, 47614, 48560, 
    40524, 48836, 44758, 49290, 40713, 
    45241, 41440, 3616, 43477, 2044, 43856, 
    47871, 48551, 49001, 47615, 47612, 
    47870, 48938, 41431, 35685, 41434, 
    41432, 48939, 2042, 48550, 321
  ) 
  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 0.00134

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": 33,
          "filtered": 99.9960556,
          "index_condition": "cscart_product_prices.product_id in (48813,45029,46155,47878,47614,48560,40524,48836,44758,49290,40713,45241,41440,3616,43477,2044,43856,47871,48551,49001,47615,47612,47870,48938,41431,35685,41434,41432,48939,2042,48550,321)",
          "attached_condition": "cscart_product_prices.lower_limit = 1 and cscart_product_prices.usergroup_id in (0,1)"
        }
      }
    ]
  }
}