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 (
    421, 427, 408, 1971, 382, 418, 1959, 1930, 
    400, 1960, 424, 1961, 1931, 381, 1529, 
    401, 1465, 1962, 1933, 1935, 1958, 428, 
    415, 391, 1729, 406, 439, 390, 1969, 
    393, 394, 396, 397, 398, 399, 422, 1964, 
    434, 383, 412, 1927, 419, 430, 324, 1965, 
    1966, 432, 1973, 429, 1968, 384, 1963, 
    1934, 395, 420, 385, 405, 410, 413, 1970, 
    417, 1937, 414, 425, 407, 389, 402, 1972, 
    388, 426, 409, 1974, 404, 387, 386, 416, 
    441, 1957
  ) 
  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 0.00149

JSON explain

{
  "query_block": {
    "select_id": 1,
    "cost_info": {
      "query_cost": "204.01"
    },
    "grouping_operation": {
      "using_filesort": false,
      "table": {
        "table_name": "cscart_product_prices",
        "access_type": "range",
        "possible_keys": [
          "usergroup",
          "product_id",
          "lower_limit",
          "usergroup_id"
        ],
        "key": "product_id",
        "used_key_parts": [
          "product_id"
        ],
        "key_length": "3",
        "rows_examined_per_scan": 90,
        "rows_produced_per_join": 17,
        "filtered": "19.98",
        "index_condition": "(`eshopuga_upgr_4122`.`cscart_product_prices`.`product_id` in (421,427,408,1971,382,418,1959,1930,400,1960,424,1961,1931,381,1529,401,1465,1962,1933,1935,1958,428,415,391,1729,406,439,390,1969,393,394,396,397,398,399,422,1964,434,383,412,1927,419,430,324,1965,1966,432,1973,429,1968,384,1963,1934,395,420,385,405,410,413,1970,417,1937,414,425,407,389,402,1972,388,426,409,1974,404,387,386,416,441,1957))",
        "cost_info": {
          "read_cost": "200.41",
          "eval_cost": "3.60",
          "prefix_cost": "204.01",
          "data_read_per_join": "431"
        },
        "used_columns": [
          "product_id",
          "price",
          "percentage_discount",
          "lower_limit",
          "usergroup_id"
        ],
        "attached_condition": "((`eshopuga_upgr_4122`.`cscart_product_prices`.`lower_limit` = 1) and (`eshopuga_upgr_4122`.`cscart_product_prices`.`usergroup_id` in (0,1)))"
      }
    }
  }
}