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 (
    40437, 40451, 49487, 49539, 47084, 40442, 
    40446, 40443, 40449, 40448, 40447, 
    40444, 40436, 40450, 40438, 40441, 
    40439, 40434, 40440, 634, 48826, 294, 
    48772, 39612, 36304, 635, 636, 48827, 
    31953
  ) 
  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 0.00651

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": 29,
          "filtered": 99.9960556,
          "index_condition": "cscart_product_prices.product_id in (40437,40451,49487,49539,47084,40442,40446,40443,40449,40448,40447,40444,40436,40450,40438,40441,40439,40434,40440,634,48826,294,48772,39612,36304,635,636,48827,31953)",
          "attached_condition": "cscart_product_prices.lower_limit = 1 and cscart_product_prices.usergroup_id in (0,1)"
        }
      }
    ]
  }
}