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 (
    306, 316, 307, 311, 514, 515, 516, 427, 
    319, 320, 531, 322, 325, 326, 410, 327, 
    323, 324, 328, 329, 330, 535, 333, 390, 
    280, 689, 281, 283, 641, 309, 691, 693
  ) 
  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 0.00094

JSON explain

{
  "query_block": {
    "select_id": 1,
    "filesort": {
      "sort_key": "cscart_product_prices.product_id",
      "temporary_table": {
        "table": {
          "table_name": "cscart_product_prices",
          "access_type": "range",
          "possible_keys": [
            "usergroup",
            "product_id",
            "lower_limit",
            "usergroup_id"
          ],
          "key": "usergroup_id",
          "key_length": "6",
          "used_key_parts": ["usergroup_id", "product_id"],
          "rows": 64,
          "filtered": 100,
          "index_condition": "cscart_product_prices.product_id in (306,316,307,311,514,515,516,427,319,320,531,322,325,326,410,327,323,324,328,329,330,535,333,390,280,689,281,283,641,309,691,693) and cscart_product_prices.usergroup_id in (0,1)",
          "attached_condition": "cscart_product_prices.lower_limit = 1"
        }
      }
    }
  }
}