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 (
    1769, 3739, 3740, 3741, 3742, 5415, 5416, 
    5417, 5418, 5419, 5420, 5421, 5422, 
    5423, 5424, 5425, 5426, 5427, 5428, 
    5429, 5430, 5431, 5432, 5433, 5434, 
    5435, 5436, 5437, 5438, 5439, 5440, 
    5441, 5442, 5443, 5444, 5445, 5446, 
    5447, 5448, 5449, 5450, 5451, 5452, 
    5453, 5454, 5455, 5456, 5457
  ) 
  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 0.00122

JSON explain

{
  "query_block": {
    "select_id": 1,
    "cost_info": {
      "query_cost": "34.06"
    },
    "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": 49,
        "rows_produced_per_join": 9,
        "filtered": "20.00",
        "index_condition": "(`gaseus`.`cscart_product_prices`.`product_id` in (1769,3739,3740,3741,3742,5415,5416,5417,5418,5419,5420,5421,5422,5423,5424,5425,5426,5427,5428,5429,5430,5431,5432,5433,5434,5435,5436,5437,5438,5439,5440,5441,5442,5443,5444,5445,5446,5447,5448,5449,5450,5451,5452,5453,5454,5455,5456,5457))",
        "cost_info": {
          "read_cost": "33.08",
          "eval_cost": "0.98",
          "prefix_cost": "34.06",
          "data_read_per_join": "235"
        },
        "used_columns": [
          "product_id",
          "price",
          "percentage_discount",
          "lower_limit",
          "usergroup_id"
        ],
        "attached_condition": "((`gaseus`.`cscart_product_prices`.`lower_limit` = 1) and (`gaseus`.`cscart_product_prices`.`usergroup_id` in (0,1)))"
      }
    }
  }
}