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 (
    2686, 2568, 15042, 14456, 2188, 13664, 
    12195, 14044, 15057, 12955, 2645, 2646, 
    2333, 2331, 2330, 2792, 2793, 11131, 
    2794, 11132, 2798, 2795, 2797, 11890
  ) 
  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 0.02019

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": 4.513635159,
          "attached_condition": "cscart_product_prices.lower_limit <=> 1 and cscart_product_prices.product_id in (2686,2568,15042,14456,2188,13664,12195,14044,15057,12955,2645,2646,2333,2331,2330,2792,2793,11131,2794,11132,2798,2795,2797,11890) and cscart_product_prices.usergroup_id in (0,1)"
        }
      }
    }
  }
}