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 (
    406480, 437686, 423559, 424334, 460558, 
    456062, 432907, 404813, 447269, 409338, 
    403991, 456256, 420163, 453916, 414087, 
    424432, 428079, 401029, 456055, 445068, 
    418346, 407735, 436615, 428503, 417977, 
    418226, 423333, 449562, 401443, 449507, 
    433832, 409821, 434815, 418429, 428304, 
    454998, 401192, 420138, 420200, 411483, 
    433250, 448259, 456498, 453797, 440607, 
    427308, 452175, 444603, 434992, 435134, 
    446266, 428321, 423625, 436076, 428627, 
    446847, 439096, 440647, 439207, 451256, 
    460133, 459641, 419106, 460861, 423479, 
    433559, 440573, 421300, 443507, 438971, 
    404180, 445058, 441079, 442454, 460859, 
    414365, 440075, 444561, 438377, 430757, 
    425044, 446929, 406357, 435303, 435650, 
    455895, 409755, 444595, 456183, 430020, 
    405721, 408755, 406722, 444839, 428245, 
    418635
  ) 
  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 0.00261

JSON explain

{
  "query_block": {
    "select_id": 1,
    "cost": 0.396590684,
    "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": 192,
          "cost": 0.3346388,
          "filtered": 50,
          "attached_condition": "cscart_product_prices.lower_limit = 1 and cscart_product_prices.product_id in (406480,437686,423559,424334,460558,456062,432907,404813,447269,409338,403991,456256,420163,453916,414087,424432,428079,401029,456055,445068,418346,407735,436615,428503,417977,418226,423333,449562,401443,449507,433832,409821,434815,418429,428304,454998,401192,420138,420200,411483,433250,448259,456498,453797,440607,427308,452175,444603,434992,435134,446266,428321,423625,436076,428627,446847,439096,440647,439207,451256,460133,459641,419106,460861,423479,433559,440573,421300,443507,438971,404180,445058,441079,442454,460859,414365,440075,444561,438377,430757,425044,446929,406357,435303,435650,455895,409755,444595,456183,430020,405721,408755,406722,444839,428245,418635) and cscart_product_prices.usergroup_id in (0,1)"
        }
      }
    ]
  }
}