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 (
    5774, 43827, 40312, 48852, 47855, 5565, 
    35470, 48776, 35471, 6544, 48848, 49290, 
    47564, 49397, 49287, 49400, 49289, 
    48946, 49540, 49399, 48939, 49502, 
    49383, 48472, 48475, 49547, 49604, 
    49662, 50297, 50298, 50053, 50179
  ) 
  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 0.00646

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 (5774,43827,40312,48852,47855,5565,35470,48776,35471,6544,48848,49290,47564,49397,49287,49400,49289,48946,49540,49399,48939,49502,49383,48472,48475,49547,49604,49662,50297,50298,50053,50179)",
          "attached_condition": "cscart_product_prices.lower_limit = 1 and cscart_product_prices.usergroup_id in (0,1)"
        }
      }
    ]
  }
}