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 (
    6417, 6416, 5607, 5605, 5606, 5699, 5703, 
    5701, 5700, 5697, 5702, 5698, 7249, 
    7247, 7243, 7248, 7246, 7244, 7242, 
    7245, 6692, 6702, 6703, 6704, 6705, 
    6707, 6708, 6706, 5704, 1294, 1297, 
    1301, 1298, 1299, 1300, 1296, 1295, 
    3576, 3585, 3584, 3575, 7601, 7602, 
    6709, 3146, 3752, 3145, 5096
  ) 
  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 0.00080

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 (6417,6416,5607,5605,5606,5699,5703,5701,5700,5697,5702,5698,7249,7247,7243,7248,7246,7244,7242,7245,6692,6702,6703,6704,6705,6707,6708,6706,5704,1294,1297,1301,1298,1299,1300,1296,1295,3576,3585,3584,3575,7601,7602,6709,3146,3752,3145,5096))",
        "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)))"
      }
    }
  }
}