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 (
    6748, 3226, 3218, 6754, 6745, 6752, 6712, 
    6738, 6703, 5032, 3346, 3342, 3345, 
    3341, 5035, 3340, 3344, 3339, 3347, 
    5936, 5378, 3338, 6290, 8813, 6741, 
    5028, 5030, 6739, 5029, 5194, 5957, 
    5040, 5036, 5461, 10221, 6702, 5034, 
    6753, 5042, 8784
  ) 
  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 0.00150

JSON explain

{
  "query_block": {
    "select_id": 1,
    "cost_info": {
      "query_cost": "29.36"
    },
    "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": 43,
        "rows_produced_per_join": 8,
        "filtered": "19.99",
        "index_condition": "(`softwarepirmam_hewadelivard_cscart_4`.`cscart_product_prices`.`product_id` in (6748,3226,3218,6754,6745,6752,6712,6738,6703,5032,3346,3342,3345,3341,5035,3340,3344,3339,3347,5936,5378,3338,6290,8813,6741,5028,5030,6739,5029,5194,5957,5040,5036,5461,10221,6702,5034,6753,5042,8784))",
        "cost_info": {
          "read_cost": "28.50",
          "eval_cost": "0.86",
          "prefix_cost": "29.36",
          "data_read_per_join": "206"
        },
        "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)))"
      }
    }
  }
}