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 (
    809, 5139, 5133, 5132, 5131, 5140, 6256, 
    6257, 6267, 6259, 6224, 6226, 6238, 
    6246, 6235, 6242, 6740, 6244, 6239, 
    6241, 6237, 6208, 6247, 6738, 6255, 
    6243, 6240, 6737, 6206, 6252, 6260, 
    6258, 6207, 6209, 6741, 6266, 6250, 
    6269, 6236, 6268, 4238, 2756, 4239, 
    3913, 3910, 4619, 3916, 3898
  ) 
  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 0.00069

JSON explain

{
  "query_block": {
    "select_id": 1,
    "cost_info": {
      "query_cost": "33.61"
    },
    "grouping_operation": {
      "using_filesort": false,
      "table": {
        "table_name": "cscart_product_prices",
        "access_type": "range",
        "possible_keys": [
          "usergroup",
          "product_id",
          "lower_limit",
          "usergroup_id"
        ],
        "key": "product_id",
        "used_key_parts": [
          "product_id"
        ],
        "key_length": "3",
        "rows_examined_per_scan": 48,
        "rows_produced_per_join": 9,
        "filtered": "19.12",
        "index_condition": "(`dbggbern`.`cscart_product_prices`.`product_id` in (809,5139,5133,5132,5131,5140,6256,6257,6267,6259,6224,6226,6238,6246,6235,6242,6740,6244,6239,6241,6237,6208,6247,6738,6255,6243,6240,6737,6206,6252,6260,6258,6207,6209,6741,6266,6250,6269,6236,6268,4238,2756,4239,3913,3910,4619,3916,3898))",
        "cost_info": {
          "read_cost": "32.69",
          "eval_cost": "0.92",
          "prefix_cost": "33.61",
          "data_read_per_join": "220"
        },
        "used_columns": [
          "product_id",
          "price",
          "percentage_discount",
          "lower_limit",
          "usergroup_id"
        ],
        "attached_condition": "((`dbggbern`.`cscart_product_prices`.`lower_limit` = 1) and (`dbggbern`.`cscart_product_prices`.`usergroup_id` in (0,1)))"
      }
    }
  }
}