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 (
    12709, 12644, 2801, 15148, 3217, 2265, 
    2509, 13837, 2512, 2574, 2565, 15388, 
    12935, 2621, 11119, 2560, 2664, 2684, 
    2665, 2663, 2279, 2514, 2511, 2513
  ) 
  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 0.00779

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": "ref",
          "possible_keys": [
            "usergroup",
            "product_id",
            "lower_limit",
            "usergroup_id"
          ],
          "key": "lower_limit",
          "key_length": "3",
          "used_key_parts": ["lower_limit"],
          "ref": ["const"],
          "rows": 6449,
          "filtered": 4.783926964,
          "attached_condition": "cscart_product_prices.lower_limit <=> 1 and cscart_product_prices.product_id in (12709,12644,2801,15148,3217,2265,2509,13837,2512,2574,2565,15388,12935,2621,11119,2560,2664,2684,2665,2663,2279,2514,2511,2513) and cscart_product_prices.usergroup_id in (0,1)"
        }
      }
    }
  }
}