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 (
    12693, 11795, 2629, 11122, 2633, 2655, 
    11124, 2653, 2654, 11123, 2219, 2572, 
    2614, 2613, 15131, 2786, 2789, 2790, 
    11133, 11809, 2787, 2784, 2791, 2785
  ) 
  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 0.02013

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": 4.805454731,
          "attached_condition": "cscart_product_prices.lower_limit <=> 1 and cscart_product_prices.product_id in (12693,11795,2629,11122,2633,2655,11124,2653,2654,11123,2219,2572,2614,2613,15131,2786,2789,2790,11133,11809,2787,2784,2791,2785) and cscart_product_prices.usergroup_id in (0,1)"
        }
      }
    }
  }
}