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 (
    41426, 1050, 2252, 3988, 36297, 2249, 
    41438, 353, 2260, 41018, 41230, 35475, 
    35470, 3984, 47486, 36465, 47608, 36299, 
    41439, 3985, 35471, 45597, 47428, 47614, 
    41440, 3616, 2044, 48551, 47612, 41431, 
    35685, 41434
  ) 
  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 0.00241

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 (41426,1050,2252,3988,36297,2249,41438,353,2260,41018,41230,35475,35470,3984,47486,36465,47608,36299,41439,3985,35471,45597,47428,47614,41440,3616,2044,48551,47612,41431,35685,41434)",
          "attached_condition": "cscart_product_prices.lower_limit = 1 and cscart_product_prices.usergroup_id in (0,1)"
        }
      }
    ]
  }
}