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 (
    5503, 5504, 5163, 5153, 1419, 1420, 1421, 
    3157, 5132, 5133, 5134, 5135, 1452, 
    5161, 1442, 5151, 6734, 6733, 6729, 
    6710, 1721, 1722, 1723, 1724, 1725, 
    1726, 1727, 1728, 1729, 1730, 1731, 
    1732, 1733, 1734, 1735, 1736, 1737, 
    1738, 1739, 1740, 1741, 1742, 1743, 
    1744, 1745, 1746, 1747, 1748
  ) 
  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 0.00097

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 (5503,5504,5163,5153,1419,1420,1421,3157,5132,5133,5134,5135,1452,5161,1442,5151,6734,6733,6729,6710,1721,1722,1723,1724,1725,1726,1727,1728,1729,1730,1731,1732,1733,1734,1735,1736,1737,1738,1739,1740,1741,1742,1743,1744,1745,1746,1747,1748))",
        "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)))"
      }
    }
  }
}