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 (
    4390, 4517, 4690, 4326, 4261, 4686, 4383, 
    4705, 4037, 4664, 4703, 4141, 4518, 
    4052, 4077, 4031, 4525, 4114, 4698, 
    4535, 4672, 4386, 3989, 4096, 4382, 
    4074, 4670, 4145, 4453, 4385, 4669, 
    4389, 4655, 4069, 4023, 4510, 4098, 
    4158, 4339, 4515, 4064, 4680, 4040, 
    4671, 3991, 4047, 4388, 4100, 3990, 
    4815, 4684, 4699, 4075, 4048, 4051, 
    4057, 4455, 4113, 4323, 4452, 4036, 
    4260, 4542, 4667, 4097, 4689, 4063, 
    4099, 4262, 4534, 4687, 4033, 4511, 
    4707, 4146, 4034, 4437, 4236, 4826, 
    4359
  ) 
  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 0.00222

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 (4390,4517,4690,4326,4261,4686,4383,4705,4037,4664,4703,4141,4518,4052,4077,4031,4525,4114,4698,4535,4672,4386,3989,4096,4382,4074,4670,4145,4453,4385,4669,4389,4655,4069,4023,4510,4098,4158,4339,4515,4064,4680,4040,4671,3991,4047,4388,4100,3990,4815,4684,4699,4075,4048,4051,4057,4455,4113,4323,4452,4036,4260,4542,4667,4097,4689,4063,4099,4262,4534,4687,4033,4511,4707,4146,4034,4437,4236,4826,4359))",
        "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)))"
      }
    }
  }
}