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 (
    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_product_prices.lower_limit = 1 
  AND cscart_product_prices.usergroup_id IN (0, 1) 
GROUP BY 
  cscart_product_prices.product_id

Query time 0.00062

JSON explain

{
  "query_block": {
    "select_id": 1,
    "table": {
      "table_name": "cscart_product_prices",
      "access_type": "range",
      "possible_keys": ["usergroup", "product_id", "lower_limit", "usergroup_id"],
      "key": "product_id",
      "key_length": "3",
      "used_key_parts": ["product_id"],
      "rows": 30,
      "filtered": 93.46080017,
      "index_condition": "cscart_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)",
      "attached_condition": "cscart_product_prices.lower_limit = 1 and cscart_product_prices.usergroup_id in (0,1)"
    }
  }
}