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 (
    480519, 596382, 697795, 1108774, 386215, 
    589116, 1732209, 590365, 589122, 611344, 
    524885, 590294, 590359, 503738, 611343, 
    1114057, 611248, 1108257, 1232917, 
    589813, 697874, 592084, 612918, 1232953, 
    592827, 589079, 596346, 697492, 1233035, 
    594419, 1108259, 696364, 697773, 588450, 
    1108367, 594204
  ) 
  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 0.00691

JSON explain

{
  "query_block": {
    "select_id": 1,
    "cost_info": {
      "query_cost": "79.90"
    },
    "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": 72,
        "rows_produced_per_join": 72,
        "filtered": "100.00",
        "cost_info": {
          "read_cost": "72.70",
          "eval_cost": "7.20",
          "prefix_cost": "79.90",
          "data_read_per_join": "1K"
        },
        "used_columns": [
          "product_id",
          "price",
          "percentage_discount",
          "lower_limit",
          "usergroup_id"
        ],
        "attached_condition": "((`maniamall_cscart`.`cscart_product_prices`.`lower_limit` = 1) and (`maniamall_cscart`.`cscart_product_prices`.`product_id` in (480519,596382,697795,1108774,386215,589116,1732209,590365,589122,611344,524885,590294,590359,503738,611343,1114057,611248,1108257,1232917,589813,697874,592084,612918,1232953,592827,589079,596346,697492,1233035,594419,1108259,696364,697773,588450,1108367,594204)) and (`maniamall_cscart`.`cscart_product_prices`.`usergroup_id` in (0,1)))"
      }
    }
  }
}

Result