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 (
    406851, 447289, 403492, 409045, 411798, 
    455469, 403314, 459175, 412726, 446945, 
    419788, 441409, 421788, 429875, 408990, 
    457492, 402535, 424481, 421915, 427033, 
    425013, 423301, 403335, 416458, 413195, 
    452439, 456232, 409981, 422412, 444874, 
    411736, 410485
  ) 
  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 0.00164

JSON explain

{
  "query_block": {
    "select_id": 1,
    "cost": 0.132572317,
    "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": 64,
          "cost": 0.11207368,
          "filtered": 50,
          "attached_condition": "cscart_product_prices.lower_limit = 1 and cscart_product_prices.product_id in (406851,447289,403492,409045,411798,455469,403314,459175,412726,446945,419788,441409,421788,429875,408990,457492,402535,424481,421915,427033,425013,423301,403335,416458,413195,452439,456232,409981,422412,444874,411736,410485) and cscart_product_prices.usergroup_id in (0,1)"
        }
      }
    ]
  }
}