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 (
    431312, 431450, 431036, 431276, 431396, 
    431014, 431298, 431414, 431172, 431233, 
    431296, 431442, 381706, 431207, 431471, 
    431180, 431332, 431479, 431455, 431213, 
    430970, 431496, 430996, 431059, 431278, 
    431413, 431095, 431189, 431299, 431075, 
    431478, 431282, 431483, 431351, 431435, 
    431436, 431489, 430728, 431232, 431391, 
    431448, 431214, 431265, 387048, 431449, 
    430986, 431331, 431323, 431375, 431379, 
    431477, 431492, 431388, 431437, 431475, 
    431485, 381714, 431261, 431374, 431476, 
    431499, 431221, 431258, 431266, 435511, 
    387053, 431462, 430709, 431347, 431441, 
    431366, 431320, 431363, 430774, 431307, 
    431257, 430779, 431179, 431348, 431404, 
    431228, 430668, 430710, 431317, 431277, 
    431473, 431321, 431418, 431445, 431206, 
    431293, 431209, 431389, 431486, 431491, 
    430670, 431400, 431390, 431256, 431443
  ) 
  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 0.00131

JSON explain

{
  "query_block": {
    "select_id": 1,
    "cost_info": {
      "query_cost": "280.31"
    },
    "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": 200,
        "rows_produced_per_join": 200,
        "filtered": "100.00",
        "cost_info": {
          "read_cost": "240.31",
          "eval_cost": "40.00",
          "prefix_cost": "280.31",
          "data_read_per_join": "12K"
        },
        "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 (431312,431450,431036,431276,431396,431014,431298,431414,431172,431233,431296,431442,381706,431207,431471,431180,431332,431479,431455,431213,430970,431496,430996,431059,431278,431413,431095,431189,431299,431075,431478,431282,431483,431351,431435,431436,431489,430728,431232,431391,431448,431214,431265,387048,431449,430986,431331,431323,431375,431379,431477,431492,431388,431437,431475,431485,381714,431261,431374,431476,431499,431221,431258,431266,435511,387053,431462,430709,431347,431441,431366,431320,431363,430774,431307,431257,430779,431179,431348,431404,431228,430668,430710,431317,431277,431473,431321,431418,431445,431206,431293,431209,431389,431486,431491,430670,431400,431390,431256,431443)) and (`webmarco`.`cscart_product_prices`.`usergroup_id` in (0,1)))"
      }
    }
  }
}