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 (
    3564, 3482, 3581, 3574, 3583, 3579, 3476, 
    3569, 3870, 3562, 3543, 3856, 3585, 
    3503, 3488, 2119, 3577, 3899, 3544, 
    3502, 3823, 3884, 3575, 3539, 3541, 
    2120, 3576, 3469, 3584, 3487, 3808, 
    3868, 3472, 3514, 3580, 3473, 3479, 
    3572, 3866, 3570, 3582, 3489, 3567, 
    3861, 3561, 3504, 3475, 3565, 3573, 
    3568, 3563, 3547, 3513, 3586, 3542, 
    3571, 3566, 3474, 3538, 3540, 3587
  ) 
  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 0.00214

JSON explain

{
  "query_block": {
    "select_id": 1,
    "cost_info": {
      "query_cost": "42.71"
    },
    "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": 61,
        "rows_produced_per_join": 12,
        "filtered": "19.99",
        "index_condition": "(`softwarepirmam_hewadelivard_cscart_4`.`cscart_product_prices`.`product_id` in (3564,3482,3581,3574,3583,3579,3476,3569,3870,3562,3543,3856,3585,3503,3488,2119,3577,3899,3544,3502,3823,3884,3575,3539,3541,2120,3576,3469,3584,3487,3808,3868,3472,3514,3580,3473,3479,3572,3866,3570,3582,3489,3567,3861,3561,3504,3475,3565,3573,3568,3563,3547,3513,3586,3542,3571,3566,3474,3538,3540,3587))",
        "cost_info": {
          "read_cost": "41.49",
          "eval_cost": "1.22",
          "prefix_cost": "42.71",
          "data_read_per_join": "292"
        },
        "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)))"
      }
    }
  }
}