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 (
    5097, 5098, 5099, 5100, 5101, 5102, 5103, 
    5104, 5105, 5106, 2760, 2761, 2762, 
    2763, 2764, 6348, 6349, 6350, 6351, 
    2756, 2757, 2758, 2759, 6343, 6344, 
    6345, 6346, 6347, 2818, 2819, 2820, 
    2821, 2822, 6404, 6405, 6406, 6407, 
    2933, 2934, 2935, 2936, 6517, 6518, 
    6519, 6520, 6521, 2510, 2511
  ) 
  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 0.00099

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 (5097,5098,5099,5100,5101,5102,5103,5104,5105,5106,2760,2761,2762,2763,2764,6348,6349,6350,6351,2756,2757,2758,2759,6343,6344,6345,6346,6347,2818,2819,2820,2821,2822,6404,6405,6406,6407,2933,2934,2935,2936,6517,6518,6519,6520,6521,2510,2511))",
        "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)))"
      }
    }
  }
}