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 (
    5485, 5479, 5420, 5518, 5441, 5434, 5590, 
    5417, 5541, 5406, 5407, 5493, 5526, 
    5484, 5412, 5583, 5680, 5416, 5482, 
    5544, 5589, 5600, 5487, 5418, 5421, 
    5499, 5521, 5532, 5597, 5455, 5512, 
    5560, 5562, 5588, 5669, 5525, 5679, 
    5533, 5974, 5579, 5584, 5481, 5489, 
    5428, 5524, 5591, 5511, 5419, 5495, 
    5423, 5424, 5480, 5486, 5657, 5546, 
    5543, 5440, 5547, 5548, 9547, 5438, 
    5443, 5476, 5542, 5592, 5585, 5649, 
    5447, 5529, 5439, 5659, 5602, 5496, 
    5656, 5475, 5433, 5498, 5603, 5432, 
    5514
  ) 
  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 0.00182

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 (5485,5479,5420,5518,5441,5434,5590,5417,5541,5406,5407,5493,5526,5484,5412,5583,5680,5416,5482,5544,5589,5600,5487,5418,5421,5499,5521,5532,5597,5455,5512,5560,5562,5588,5669,5525,5679,5533,5974,5579,5584,5481,5489,5428,5524,5591,5511,5419,5495,5423,5424,5480,5486,5657,5546,5543,5440,5547,5548,9547,5438,5443,5476,5542,5592,5585,5649,5447,5529,5439,5659,5602,5496,5656,5475,5433,5498,5603,5432,5514))",
        "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)))"
      }
    }
  }
}