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 (
    5504, 5384, 5506, 6018, 6749, 5385, 5464, 
    6185, 6735, 6114, 5647, 6713, 6146, 
    6187, 6742, 5651, 6086, 6299, 6307, 
    6371, 5508, 6081, 8812, 6740, 6705, 
    6144, 6254, 6433, 6755, 6228, 6192, 
    6227, 6356, 6083, 6230, 6710, 6275, 
    6277, 6393, 6426, 6258, 6428, 8800, 
    6255, 6394, 6229, 6256, 8576, 6189, 
    6257, 6259, 6145, 6332, 6362, 8577, 
    6278, 5644, 6226, 6279, 6392, 6297, 
    6354, 6331, 6337, 6395, 6423, 6427, 
    6364, 8569, 6190, 6276, 6303, 6359, 
    6429, 6280, 6260, 6305, 6330, 6434, 
    6355
  ) 
  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 0.00277

JSON explain

{
  "query_block": {
    "select_id": 1,
    "cost_info": {
      "query_cost": "56.01"
    },
    "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": 80,
        "rows_produced_per_join": 15,
        "filtered": "19.99",
        "index_condition": "(`softwarepirmam_hewadelivard_cscart_4`.`cscart_product_prices`.`product_id` in (5504,5384,5506,6018,6749,5385,5464,6185,6735,6114,5647,6713,6146,6187,6742,5651,6086,6299,6307,6371,5508,6081,8812,6740,6705,6144,6254,6433,6755,6228,6192,6227,6356,6083,6230,6710,6275,6277,6393,6426,6258,6428,8800,6255,6394,6229,6256,8576,6189,6257,6259,6145,6332,6362,8577,6278,5644,6226,6279,6392,6297,6354,6331,6337,6395,6423,6427,6364,8569,6190,6276,6303,6359,6429,6280,6260,6305,6330,6434,6355))",
        "cost_info": {
          "read_cost": "54.41",
          "eval_cost": "1.60",
          "prefix_cost": "56.01",
          "data_read_per_join": "383"
        },
        "used_columns": [
          "product_id",
          "price",
          "percentage_discount",
          "lower_limit",
          "usergroup_id"
        ],
        "attached_condition": "((`softwarepirmam_hewadelivard_cscart_4`.`cscart_product_prices`.`lower_limit` = 1) and (`softwarepirmam_hewadelivard_cscart_4`.`cscart_product_prices`.`usergroup_id` in (0,1)))"
      }
    }
  }
}