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 (
    5395, 5396, 5397, 5398, 5399, 5400, 5401, 
    5402, 5403, 5404, 5405, 5406, 5407, 
    5408, 5409, 5410, 5411, 5412, 5413, 
    5414, 6728, 515, 3156, 3676, 5131, 13298, 
    13299, 13300, 13301, 13124, 13125, 
    13126, 13127, 13098, 13105, 13112, 
    13118, 13064, 13071, 13078, 13085, 
    13091, 12464, 12624, 12654, 3834, 3833, 
    2130, 2131, 2132, 2133, 2134, 2135, 
    2136, 2137, 2138, 2139, 2140, 2141, 
    2142, 2143, 2144, 2145, 2146, 2147, 
    2148, 2149, 2150, 2151, 2152, 2153, 
    2154, 2155, 2156, 2157, 2158, 2159, 
    2160, 2161, 2162, 2163, 2164, 2165, 
    2166, 2167, 2168, 2169, 2170, 2171, 
    2172, 2173, 2174, 2175, 2176, 2177, 
    2178
  ) 
  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 0.00237

JSON explain

{
  "query_block": {
    "select_id": 1,
    "cost_info": {
      "query_cost": "114.46"
    },
    "grouping_operation": {
      "using_filesort": false,
      "table": {
        "table_name": "cscart_product_prices",
        "access_type": "range",
        "possible_keys": [
          "usergroup",
          "product_id",
          "lower_limit",
          "usergroup_id"
        ],
        "key": "product_id",
        "used_key_parts": [
          "product_id"
        ],
        "key_length": "3",
        "rows_examined_per_scan": 201,
        "rows_produced_per_join": 40,
        "filtered": "19.99",
        "index_condition": "(`test2_gaseus`.`cscart_product_prices`.`product_id` in (5395,5396,5397,5398,5399,5400,5401,5402,5403,5404,5405,5406,5407,5408,5409,5410,5411,5412,5413,5414,6728,515,3156,3676,5131,13298,13299,13300,13301,13124,13125,13126,13127,13098,13105,13112,13118,13064,13071,13078,13085,13091,12464,12624,12654,3834,3833,2130,2131,2132,2133,2134,2135,2136,2137,2138,2139,2140,2141,2142,2143,2144,2145,2146,2147,2148,2149,2150,2151,2152,2153,2154,2155,2156,2157,2158,2159,2160,2161,2162,2163,2164,2165,2166,2167,2168,2169,2170,2171,2172,2173,2174,2175,2176,2177,2178))",
        "cost_info": {
          "read_cost": "110.44",
          "eval_cost": "4.02",
          "prefix_cost": "114.46",
          "data_read_per_join": "964"
        },
        "used_columns": [
          "product_id",
          "price",
          "percentage_discount",
          "lower_limit",
          "usergroup_id"
        ],
        "attached_condition": "((`test2_gaseus`.`cscart_product_prices`.`lower_limit` = 1) and (`test2_gaseus`.`cscart_product_prices`.`usergroup_id` in (0,1)))"
      }
    }
  }
}