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 (
    104, 2593, 2711, 2710, 2693, 2709, 2976, 
    2735, 2694, 3187, 2990, 4735, 2991, 
    2989, 863, 1478, 1479, 781, 862, 3175, 
    7926, 1480, 1482, 2446, 1481, 6430, 
    6431, 7254, 7255, 4050, 4051, 4602, 
    4049, 4034, 4048, 4419, 4601, 4422, 
    4418, 4421, 4420, 4423, 4600, 5961, 
    5960, 5958, 5959, 5213
  ) 
  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 0.00051

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 (104,2593,2711,2710,2693,2709,2976,2735,2694,3187,2990,4735,2991,2989,863,1478,1479,781,862,3175,7926,1480,1482,2446,1481,6430,6431,7254,7255,4050,4051,4602,4049,4034,4048,4419,4601,4422,4418,4421,4420,4423,4600,5961,5960,5958,5959,5213))",
        "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)))"
      }
    }
  }
}