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 (
    1716, 1717, 1718, 1719, 1720, 3733, 3735, 
    3736, 3737, 3738, 5371, 5372, 5373, 
    5374, 5375, 5376, 5377, 5378, 5379, 
    5380, 5381, 5382, 5383, 5384, 5385, 
    5386, 5387, 5388, 5389, 5390, 5391, 
    5392, 5393, 5394, 5395, 5396, 5397, 
    5398, 5399, 5400, 5401, 5402, 5403, 
    5404, 5405, 5406, 5407, 5408
  ) 
  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 0.00116

JSON explain

{
  "query_block": {
    "select_id": 1,
    "cost_info": {
      "query_cost": "33.61"
    },
    "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": 48,
        "rows_produced_per_join": 9,
        "filtered": "20.00",
        "index_condition": "(`gaseus`.`cscart_product_prices`.`product_id` in (1716,1717,1718,1719,1720,3733,3735,3736,3737,3738,5371,5372,5373,5374,5375,5376,5377,5378,5379,5380,5381,5382,5383,5384,5385,5386,5387,5388,5389,5390,5391,5392,5393,5394,5395,5396,5397,5398,5399,5400,5401,5402,5403,5404,5405,5406,5407,5408))",
        "cost_info": {
          "read_cost": "32.65",
          "eval_cost": "0.96",
          "prefix_cost": "33.61",
          "data_read_per_join": "230"
        },
        "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)))"
      }
    }
  }
}