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 (
    41007, 41010, 5447, 4365, 47605, 31901, 
    23166, 47606, 5469, 4468, 4358, 46273, 
    5464, 5474, 1744, 4464, 41008, 1753, 
    41009, 1743, 4364, 1761, 4466, 47261, 
    47594, 4359, 5481, 5459, 31866, 4357, 
    47853, 4467
  ) 
  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 0.00238

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": 32,
          "filtered": 99.9960556,
          "index_condition": "cscart_product_prices.product_id in (41007,41010,5447,4365,47605,31901,23166,47606,5469,4468,4358,46273,5464,5474,1744,4464,41008,1753,41009,1743,4364,1761,4466,47261,47594,4359,5481,5459,31866,4357,47853,4467)",
          "attached_condition": "cscart_product_prices.lower_limit = 1 and cscart_product_prices.usergroup_id in (0,1)"
        }
      }
    ]
  }
}