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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 (
    5516, 5517, 5518, 5519, 5520, 5521, 5522, 
    5523, 5524, 5525, 5526, 5527, 5528, 
    5529, 5530, 5531, 5532, 5533, 5534, 
    5535, 5536, 5537, 5538, 5539
  ) 
  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 0.00036

JSON explain

{
  "query_block": {
    "select_id": 1,
    "message": "no matching row in const table"
  }
}