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 (
    415304, 415296, 415297, 415303, 415291, 
    415290, 415228, 415289, 415308, 415240, 
    427824, 415310, 415305, 427787, 415219, 
    415294, 415302, 415311, 415299, 415242, 
    415300, 415224, 415238, 415217, 415312, 
    415211, 427780, 415241, 415298, 415307, 
    415288, 415232, 427775, 415293, 427786, 
    427782, 427823, 415295, 415306, 415235, 
    427781, 428031, 427738, 427829, 415309, 
    428033, 428032, 427821, 427777, 415292, 
    427779, 427778, 427788, 427826, 427789, 
    415213, 435511, 435512, 435513, 435515, 
    435514, 435516, 435517
  ) 
  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 0.00459

JSON explain

{
  "query_block": {
    "select_id": 1,
    "cost_info": {
      "query_cost": "176.60"
    },
    "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": 126,
        "rows_produced_per_join": 126,
        "filtered": "100.00",
        "cost_info": {
          "read_cost": "151.40",
          "eval_cost": "25.20",
          "prefix_cost": "176.60",
          "data_read_per_join": "7K"
        },
        "used_columns": [
          "product_id",
          "price",
          "percentage_discount",
          "lower_limit",
          "usergroup_id"
        ],
        "attached_condition": "((`webmarco`.`cscart_product_prices`.`lower_limit` = 1) and (`webmarco`.`cscart_product_prices`.`product_id` in (415304,415296,415297,415303,415291,415290,415228,415289,415308,415240,427824,415310,415305,427787,415219,415294,415302,415311,415299,415242,415300,415224,415238,415217,415312,415211,427780,415241,415298,415307,415288,415232,427775,415293,427786,427782,427823,415295,415306,415235,427781,428031,427738,427829,415309,428033,428032,427821,427777,415292,427779,427778,427788,427826,427789,415213,435511,435512,435513,435515,435514,435516,435517)) and (`webmarco`.`cscart_product_prices`.`usergroup_id` in (0,1)))"
      }
    }
  }
}