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 (
    6903, 6911, 6993, 7438, 7415, 7422, 7439, 
    7443, 6880, 6996, 9523, 7172, 9520, 
    8132, 8133, 9372, 9413, 9521, 9522, 
    9368, 9374, 9375, 9624, 8793, 9414, 
    9415, 9419, 9420, 9426, 9427, 9524, 
    9416, 9417, 9418, 9469, 8791, 8794, 
    9373, 8413, 8790, 8792
  ) 
  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 0.00100

JSON explain

{
  "query_block": {
    "select_id": 1,
    "cost_info": {
      "query_cost": "28.71"
    },
    "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": 41,
        "rows_produced_per_join": 8,
        "filtered": "19.99",
        "index_condition": "(`softwarepirmam_hewadelivard_cscart_4`.`cscart_product_prices`.`product_id` in (6903,6911,6993,7438,7415,7422,7439,7443,6880,6996,9523,7172,9520,8132,8133,9372,9413,9521,9522,9368,9374,9375,9624,8793,9414,9415,9419,9420,9426,9427,9524,9416,9417,9418,9469,8791,8794,9373,8413,8790,8792))",
        "cost_info": {
          "read_cost": "27.89",
          "eval_cost": "0.82",
          "prefix_cost": "28.71",
          "data_read_per_join": "196"
        },
        "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)))"
      }
    }
  }
}