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 (
    1624, 1625, 5299, 5300, 5301, 5302, 5303, 
    5304, 5305, 5306, 5307, 5308, 5309, 
    5310, 5311, 5312, 5313, 5314, 5315, 
    5316, 5317, 5318, 5319, 5320, 5321, 
    5322, 5323, 5324, 5325, 1627, 1628, 
    1629, 1630, 1631, 1632, 1633, 1634, 
    1635, 1636, 1637, 1638, 1639, 1640, 
    1641, 1642, 1643, 1644, 1645
  ) 
  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 0.00108

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 (1624,1625,5299,5300,5301,5302,5303,5304,5305,5306,5307,5308,5309,5310,5311,5312,5313,5314,5315,5316,5317,5318,5319,5320,5321,5322,5323,5324,5325,1627,1628,1629,1630,1631,1632,1633,1634,1635,1636,1637,1638,1639,1640,1641,1642,1643,1644,1645))",
        "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)))"
      }
    }
  }
}