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 (
    12684, 12714, 13260, 13267, 13176, 13162, 
    13169, 13232, 13225, 13190, 13183, 
    13239, 13204, 13197, 13246, 13218, 
    13211, 13253, 13302, 13303, 13308, 
    13309, 13306, 13307, 13310, 13311, 
    13312, 13313, 13304, 13305, 12349, 
    12364, 12259, 12504, 12524, 12379, 
    13319, 1154, 3315, 6843, 3318, 3687, 
    5076, 6840, 4691, 3071, 513, 3505
  ) 
  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,
    "cost_info": {
      "query_cost": "67.21"
    },
    "grouping_operation": {
      "using_filesort": false,
      "table": {
        "table_name": "cscart_product_prices",
        "access_type": "range",
        "possible_keys": [
          "usergroup",
          "product_id",
          "lower_limit",
          "usergroup_id"
        ],
        "key": "usergroup",
        "used_key_parts": [
          "product_id",
          "usergroup_id",
          "lower_limit"
        ],
        "key_length": "9",
        "rows_examined_per_scan": 96,
        "rows_produced_per_join": 96,
        "filtered": "100.00",
        "index_condition": "((`test2_gaseus`.`cscart_product_prices`.`lower_limit` = 1) and (`test2_gaseus`.`cscart_product_prices`.`product_id` in (12684,12714,13260,13267,13176,13162,13169,13232,13225,13190,13183,13239,13204,13197,13246,13218,13211,13253,13302,13303,13308,13309,13306,13307,13310,13311,13312,13313,13304,13305,12349,12364,12259,12504,12524,12379,13319,1154,3315,6843,3318,3687,5076,6840,4691,3071,513,3505)) and (`test2_gaseus`.`cscart_product_prices`.`usergroup_id` in (0,1)))",
        "cost_info": {
          "read_cost": "57.61",
          "eval_cost": "9.60",
          "prefix_cost": "67.21",
          "data_read_per_join": "2K"
        },
        "used_columns": [
          "product_id",
          "price",
          "percentage_discount",
          "lower_limit",
          "usergroup_id"
        ]
      }
    }
  }
}