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 (
    5474, 5475, 5476, 5477, 5478, 5479, 5480, 
    5481, 5482, 5483, 5484, 5485, 5486, 
    5487, 5488, 5489, 5490, 5491, 5492, 
    5493, 5494, 5495, 5496, 5497, 5498, 
    5499, 5500, 5501, 5502, 5503, 5504, 
    5163, 5153, 1419, 1420, 1421, 3157, 
    5132, 5133, 5134, 5135, 1452, 5161, 
    1442, 5151, 6734, 6733, 6729
  ) 
  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 0.00126

JSON explain

{
  "query_block": {
    "select_id": 1,
    "cost_info": {
      "query_cost": "33.61"
    },
    "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": 48,
        "rows_produced_per_join": 9,
        "filtered": "20.00",
        "index_condition": "(`gaseus`.`cscart_product_prices`.`product_id` in (5474,5475,5476,5477,5478,5479,5480,5481,5482,5483,5484,5485,5486,5487,5488,5489,5490,5491,5492,5493,5494,5495,5496,5497,5498,5499,5500,5501,5502,5503,5504,5163,5153,1419,1420,1421,3157,5132,5133,5134,5135,1452,5161,1442,5151,6734,6733,6729))",
        "cost_info": {
          "read_cost": "32.65",
          "eval_cost": "0.96",
          "prefix_cost": "33.61",
          "data_read_per_join": "230"
        },
        "used_columns": [
          "product_id",
          "price",
          "percentage_discount",
          "lower_limit",
          "usergroup_id"
        ],
        "attached_condition": "((`gaseus`.`cscart_product_prices`.`lower_limit` = 1) and (`gaseus`.`cscart_product_prices`.`usergroup_id` in (0,1)))"
      }
    }
  }
}