SELECT 
  cscart_ult_product_prices.product_id, 
  MIN(
    IF(
      cscart_ult_product_prices.percentage_discount = 0, 
      cscart_ult_product_prices.price, 
      cscart_ult_product_prices.price - (
        cscart_ult_product_prices.price * cscart_ult_product_prices.percentage_discount
      )/ 100
    )
  ) AS price 
FROM 
  cscart_ult_product_prices 
WHERE 
  cscart_ult_product_prices.product_id IN (
    5390, 5388, 5387, 5386, 5389, 5384, 5385, 
    6685, 6759, 6712, 6677, 6697, 6736, 
    6693, 6761, 6762, 6681, 6710, 6701, 
    6689, 6737, 6763, 6760, 6709
  ) 
  AND cscart_ult_product_prices.lower_limit = 1 
  AND cscart_ult_product_prices.company_id = 1 
  AND cscart_ult_product_prices.usergroup_id IN (0, 0, 1) 
GROUP BY 
  cscart_ult_product_prices.product_id

Query time 0.00038

JSON explain

{
  "query_block": {
    "select_id": 1,
    "filesort": {
      "sort_key": "cscart_ult_product_prices.product_id",
      "temporary_table": {
        "table": {
          "table_name": "cscart_ult_product_prices",
          "access_type": "ALL",
          "possible_keys": [
            "usergroup",
            "product_id",
            "company_id",
            "lower_limit",
            "usergroup_id"
          ],
          "rows": 44,
          "filtered": 54.54545593,
          "attached_condition": "cscart_ult_product_prices.lower_limit = 1 and cscart_ult_product_prices.company_id = 1 and cscart_ult_product_prices.product_id in (5390,5388,5387,5386,5389,5384,5385,6685,6759,6712,6677,6697,6736,6693,6761,6762,6681,6710,6701,6689,6737,6763,6760,6709) and cscart_ult_product_prices.usergroup_id in (0,0,1)"
        }
      }
    }
  }
}