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 (
    5348, 5349, 5350, 5351, 5352, 2832, 2833, 
    2834, 2835, 6417, 6418, 6419, 6420, 
    6421, 2823, 2824, 2825, 2826, 6408, 
    6409, 6410, 6411, 6412, 2827, 2828, 
    2829, 2830, 2831, 6413, 6414, 6415, 
    6416, 2928, 2929, 2930, 2931, 2932, 
    6513, 6514, 6515, 6516, 3032, 6609, 
    3028, 3029, 3030, 3031, 6605
  ) 
  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 0.00104

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 (5348,5349,5350,5351,5352,2832,2833,2834,2835,6417,6418,6419,6420,6421,2823,2824,2825,2826,6408,6409,6410,6411,6412,2827,2828,2829,2830,2831,6413,6414,6415,6416,2928,2929,2930,2931,2932,6513,6514,6515,6516,3032,6609,3028,3029,3030,3031,6605))",
        "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)))"
      }
    }
  }
}