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 (
    1504, 1494, 6209, 1499, 1489, 1433, 6614, 
    2268, 2269, 2270, 2271, 2336, 2337, 
    2338, 2339, 2412, 2413, 2414, 2415, 
    2416, 2417, 2418, 2419, 2420, 2514, 
    2515, 2516, 2517, 2518, 2604, 2605, 
    2606, 2607, 3840, 3841, 3842, 3843, 
    5867, 5868, 5869, 5870, 5871, 5935, 
    5936, 5937, 5938, 5939, 6012
  ) 
  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 0.00111

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": "20.00",
        "index_condition": "(`gaseus`.`cscart_product_prices`.`product_id` in (1504,1494,6209,1499,1489,1433,6614,2268,2269,2270,2271,2336,2337,2338,2339,2412,2413,2414,2415,2416,2417,2418,2419,2420,2514,2515,2516,2517,2518,2604,2605,2606,2607,3840,3841,3842,3843,5867,5868,5869,5870,5871,5935,5936,5937,5938,5939,6012))",
        "cost_info": {
          "read_cost": "32.65",
          "eval_cost": "0.96",
          "prefix_cost": "33.61",
          "data_read_per_join": "230"
        },
        "used_columns": [
          "product_id",
          "price",
          "percentage_discount",
          "lower_limit",
          "usergroup_id"
        ],
        "attached_condition": "((`gaseus`.`cscart_product_prices`.`lower_limit` = 1) and (`gaseus`.`cscart_product_prices`.`usergroup_id` in (0,1)))"
      }
    }
  }
}