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 (
    431070, 431397, 431433, 431255, 431389, 
    431268, 431398, 430783, 431432, 431443, 
    431305, 431306, 430775, 431399, 431493, 
    431386, 431417, 430784, 430967, 431444, 
    431272, 435512, 431016, 431416, 431484, 
    430776, 431254, 431490, 435513, 430763, 
    431371, 431461, 431216, 431318, 431319, 
    431271, 435515, 431269, 431372, 431373, 
    431173, 435514, 430729, 431267, 431270, 
    387051, 435516, 435517, 435518, 432250
  ) 
  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 0.00397

JSON explain

{
  "query_block": {
    "select_id": 1,
    "cost_info": {
      "query_cost": "140.16"
    },
    "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": 100,
        "rows_produced_per_join": 100,
        "filtered": "100.00",
        "cost_info": {
          "read_cost": "120.16",
          "eval_cost": "20.00",
          "prefix_cost": "140.16",
          "data_read_per_join": "6K"
        },
        "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 (431070,431397,431433,431255,431389,431268,431398,430783,431432,431443,431305,431306,430775,431399,431493,431386,431417,430784,430967,431444,431272,435512,431016,431416,431484,430776,431254,431490,435513,430763,431371,431461,431216,431318,431319,431271,435515,431269,431372,431373,431173,435514,430729,431267,431270,387051,435516,435517,435518,432250)) and (`webmarco`.`cscart_product_prices`.`usergroup_id` in (0,1)))"
      }
    }
  }
}