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 (
    5690, 5691, 5692, 5693, 5694, 5695, 5696, 
    5697, 5698, 5699, 5700, 5701, 5702, 
    5703, 5704, 5705, 5706, 5707, 5708, 
    5709, 5710, 5711, 5712, 5713, 5714, 
    5715, 5716, 5717, 5718, 5719, 5720, 
    5721, 1479, 1480, 1481, 1482, 1483, 
    5188, 5189, 5190, 5191, 5192, 5193, 
    1467, 1468, 1469, 1470, 1471
  ) 
  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 0.00098

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 (5690,5691,5692,5693,5694,5695,5696,5697,5698,5699,5700,5701,5702,5703,5704,5705,5706,5707,5708,5709,5710,5711,5712,5713,5714,5715,5716,5717,5718,5719,5720,5721,1479,1480,1481,1482,1483,5188,5189,5190,5191,5192,5193,1467,1468,1469,1470,1471))",
        "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)))"
      }
    }
  }
}