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 (
    41363, 41388, 47610, 4857, 41138, 4868, 
    2640, 41359, 33704, 41014, 4817, 37293, 
    43460, 2639, 3193, 37285, 5757, 41362, 
    49256, 38149, 4821, 4864, 20838, 1518, 
    31943, 41136, 41371, 47605, 2623, 33699, 
    726, 4810
  ) 
  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 0.00210

JSON explain

{
  "query_block": {
    "select_id": 1,
    "nested_loop": [
      {
        "table": {
          "table_name": "cscart_product_prices",
          "access_type": "range",
          "possible_keys": [
            "usergroup",
            "product_id",
            "lower_limit",
            "usergroup_id"
          ],
          "key": "product_id",
          "key_length": "3",
          "used_key_parts": ["product_id"],
          "rows": 33,
          "filtered": 99.9960556,
          "index_condition": "cscart_product_prices.product_id in (41363,41388,47610,4857,41138,4868,2640,41359,33704,41014,4817,37293,43460,2639,3193,37285,5757,41362,49256,38149,4821,4864,20838,1518,31943,41136,41371,47605,2623,33699,726,4810)",
          "attached_condition": "cscart_product_prices.lower_limit = 1 and cscart_product_prices.usergroup_id in (0,1)"
        }
      }
    ]
  }
}