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 (
    13407, 13439, 13440, 13441, 13442, 13443, 
    13499, 13444, 13445, 13408, 13446, 
    13447, 13448, 13409, 13504, 13410, 
    13449, 13450, 13411, 13412, 13413, 
    13414, 13415, 13451
  ) 
  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 0.00074

JSON explain

{
  "query_block": {
    "select_id": 1,
    "cost": 0.06190128,
    "nested_loop": [
      {
        "table": {
          "table_name": "cscart_product_prices",
          "access_type": "range",
          "possible_keys": [
            "usergroup",
            "product_id",
            "lower_limit",
            "usergroup_id"
          ],
          "key": "usergroup",
          "key_length": "9",
          "used_key_parts": ["product_id", "usergroup_id", "lower_limit"],
          "loops": 1,
          "rows": 48,
          "cost": 0.04656984,
          "filtered": 49.95571136,
          "attached_condition": "cscart_product_prices.lower_limit = 1 and cscart_product_prices.product_id in (13407,13439,13440,13441,13442,13443,13499,13444,13445,13408,13446,13447,13448,13409,13504,13410,13449,13450,13411,13412,13413,13414,13415,13451) and cscart_product_prices.usergroup_id in (0,1)"
        }
      }
    ]
  }
}