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 (
    2721, 2202, 2625, 2678, 2824, 2776, 2826, 
    2775, 2777, 2823, 13441, 13762, 11667, 
    11666, 11668, 11665, 13106, 15112, 
    13839, 13838, 13140, 13828, 12505, 
    13829, 13830, 15426, 2567, 2557, 2569, 
    2556
  ) 
  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 0.01249

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": 6.525276184,
          "attached_condition": "cscart_product_prices.lower_limit <=> 1 and cscart_product_prices.product_id in (2721,2202,2625,2678,2824,2776,2826,2775,2777,2823,13441,13762,11667,11666,11668,11665,13106,15112,13839,13838,13140,13828,12505,13829,13830,15426,2567,2557,2569,2556) and cscart_product_prices.usergroup_id in (0,1)"
        }
      }
    }
  }
}