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 (
    41279, 6059, 6060, 6058, 6061, 6063, 
    6062, 6057, 6056, 6552, 6553, 40421, 
    40507, 40506
  ) 
  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 0.14486

JSON explain

{
  "query_block": {
    "select_id": 1,
    "filesort": {
      "sort_key": "cscart_product_prices.product_id",
      "temporary_table": {
        "nested_loop": [
          {
            "table": {
              "table_name": "cscart_product_prices",
              "access_type": "ref",
              "possible_keys": [
                "usergroup",
                "product_id",
                "lower_limit",
                "usergroup_id"
              ],
              "key": "lower_limit",
              "key_length": "3",
              "used_key_parts": ["lower_limit"],
              "ref": ["const"],
              "rows": 25327,
              "filtered": 1.546716571,
              "attached_condition": "cscart_product_prices.lower_limit <=> 1 and cscart_product_prices.product_id in (41279,6059,6060,6058,6061,6063,6062,6057,6056,6552,6553,40421,40507,40506) and cscart_product_prices.usergroup_id in (0,1)"
            }
          }
        ]
      }
    }
  }
}