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 (
    431325, 381712, 339825, 431042, 430845, 
    430885, 430976, 431200, 431316, 381711, 
    430756, 430801, 430865, 430887, 430904, 
    430939, 430992, 431003, 431393, 430661, 
    430936, 431238, 431251, 339855, 430753, 
    430836, 431011, 431046, 431061, 431333, 
    430810, 430866, 431029, 431072, 431171, 
    431193, 430932, 431052, 430788, 430809, 
    430905, 430927, 430999, 431192, 431205, 
    431463, 430634, 430749, 430862, 430910, 
    431062, 430870, 430923, 431039, 339726, 
    430794, 431024, 431091, 431314, 431326, 
    431327, 430708, 430714, 431315, 430677, 
    430704, 430853, 430888, 430895, 431028, 
    431098, 431242, 430675, 430687, 430707, 
    430811, 431339, 430641, 430713, 430851, 
    431112, 431365, 430694, 430738, 430782, 
    430827, 430861, 430874, 430937, 431077, 
    431308, 339838, 430947, 431245, 339841, 
    430800, 430852, 430855, 431054, 431129
  ) 
  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 0.00247

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 (431325,381712,339825,431042,430845,430885,430976,431200,431316,381711,430756,430801,430865,430887,430904,430939,430992,431003,431393,430661,430936,431238,431251,339855,430753,430836,431011,431046,431061,431333,430810,430866,431029,431072,431171,431193,430932,431052,430788,430809,430905,430927,430999,431192,431205,431463,430634,430749,430862,430910,431062,430870,430923,431039,339726,430794,431024,431091,431314,431326,431327,430708,430714,431315,430677,430704,430853,430888,430895,431028,431098,431242,430675,430687,430707,430811,431339,430641,430713,430851,431112,431365,430694,430738,430782,430827,430861,430874,430937,431077,431308,339838,430947,431245,339841,430800,430852,430855,431054,431129)) and (`webmarco`.`cscart_product_prices`.`usergroup_id` in (0,1)))"
      }
    }
  }
}