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 (
    5326, 5316, 5344, 5356, 5359, 5400, 5103, 
    5339, 5350, 6245, 5313, 5399, 5349, 
    5352, 5358, 5201, 5307, 5348, 5337, 
    5338, 5572, 5297, 6253, 5202, 6241, 
    6207, 6220, 6243, 6553, 7516, 11255, 
    11277, 10956, 11280, 10412, 7514, 7521, 
    7515, 7519, 10954
  ) 
  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 0.00185

JSON explain

{
  "query_block": {
    "select_id": 1,
    "cost_info": {
      "query_cost": "34.31"
    },
    "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": 54,
        "rows_produced_per_join": 10,
        "filtered": "19.99",
        "index_condition": "(`softwarepirmam_hewadelivard_cscart_4`.`cscart_product_prices`.`product_id` in (5326,5316,5344,5356,5359,5400,5103,5339,5350,6245,5313,5399,5349,5352,5358,5201,5307,5348,5337,5338,5572,5297,6253,5202,6241,6207,6220,6243,6553,7516,11255,11277,10956,11280,10412,7514,7521,7515,7519,10954))",
        "cost_info": {
          "read_cost": "33.23",
          "eval_cost": "1.08",
          "prefix_cost": "34.31",
          "data_read_per_join": "259"
        },
        "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)))"
      }
    }
  }
}