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 (
    3748, 3749, 3750, 3751, 5505, 5506, 5507, 
    5508, 5509, 5510, 5511, 5512, 5513, 
    5514, 5515, 5516, 5517, 5518, 5519, 
    5520, 5521, 5522, 5523, 5524, 5525, 
    5526, 5527, 5528, 5529, 5530, 5531, 
    5532, 5533, 5534, 5535, 5536, 5537, 
    5538, 5539, 5540, 5541, 5542, 5543, 
    5544, 5545, 5546, 5547, 5548
  ) 
  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 0.00113

JSON explain

{
  "query_block": {
    "select_id": 1,
    "cost_info": {
      "query_cost": "33.61"
    },
    "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": 48,
        "rows_produced_per_join": 9,
        "filtered": "20.00",
        "index_condition": "(`gaseus`.`cscart_product_prices`.`product_id` in (3748,3749,3750,3751,5505,5506,5507,5508,5509,5510,5511,5512,5513,5514,5515,5516,5517,5518,5519,5520,5521,5522,5523,5524,5525,5526,5527,5528,5529,5530,5531,5532,5533,5534,5535,5536,5537,5538,5539,5540,5541,5542,5543,5544,5545,5546,5547,5548))",
        "cost_info": {
          "read_cost": "32.65",
          "eval_cost": "0.96",
          "prefix_cost": "33.61",
          "data_read_per_join": "230"
        },
        "used_columns": [
          "product_id",
          "price",
          "percentage_discount",
          "lower_limit",
          "usergroup_id"
        ],
        "attached_condition": "((`gaseus`.`cscart_product_prices`.`lower_limit` = 1) and (`gaseus`.`cscart_product_prices`.`usergroup_id` in (0,1)))"
      }
    }
  }
}