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 (
    431086, 431212, 431369, 431402, 430785, 
    430833, 430987, 431300, 430724, 430941, 
    431081, 431377, 431384, 430733, 431181, 
    431229, 431472, 430956, 431253, 431454, 
    430721, 431387, 431225, 431431, 430682, 
    430951, 431438, 431450, 430716, 431382, 
    431446, 431468, 431401, 431412, 431430, 
    430945, 431143, 431215, 431058, 431170, 
    431294, 431312, 431367, 431460, 430731, 
    431036, 431224, 431259, 431276, 431310, 
    430777, 431332, 431396, 431296, 431298, 
    431414, 431014, 431172, 431207, 431471, 
    431479, 431180, 431233, 431442, 431189, 
    431413, 431455, 431213, 431278, 431351, 
    430970, 430996, 431095, 431299, 431483, 
    431496, 431059, 431075, 431391, 431478, 
    431282, 431436, 431265, 431435, 431489, 
    431232, 431477, 430728, 431449, 431214, 
    431448, 430986, 431379, 431331, 431375, 
    431221, 431323, 431492, 431388, 431475
  ) 
  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 0.00290

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 (431086,431212,431369,431402,430785,430833,430987,431300,430724,430941,431081,431377,431384,430733,431181,431229,431472,430956,431253,431454,430721,431387,431225,431431,430682,430951,431438,431450,430716,431382,431446,431468,431401,431412,431430,430945,431143,431215,431058,431170,431294,431312,431367,431460,430731,431036,431224,431259,431276,431310,430777,431332,431396,431296,431298,431414,431014,431172,431207,431471,431479,431180,431233,431442,431189,431413,431455,431213,431278,431351,430970,430996,431095,431299,431483,431496,431059,431075,431391,431478,431282,431436,431265,431435,431489,431232,431477,430728,431449,431214,431448,430986,431379,431331,431375,431221,431323,431492,431388,431475)) and (`webmarco`.`cscart_product_prices`.`usergroup_id` in (0,1)))"
      }
    }
  }
}