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 (
    5568, 5574, 5571, 5573, 5569, 5567, 5572, 
    5570, 5581
  ) 
  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 0.00032

JSON explain

{
  "query_block": {
    "select_id": 1,
    "table": {
      "table_name": "cscart_ult_product_prices",
      "access_type": "range",
      "possible_keys": [
        "usergroup",
        "product_id",
        "company_id",
        "lower_limit",
        "usergroup_id"
      ],
      "key": "product_id",
      "key_length": "3",
      "used_key_parts": ["product_id"],
      "rows": 9,
      "filtered": 100,
      "index_condition": "cscart_ult_product_prices.product_id in (5568,5574,5571,5573,5569,5567,5572,5570,5581)",
      "attached_condition": "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)"
    }
  }
}