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 (
    3161, 3719, 3720, 5142, 5143, 5144, 6730, 
    6731, 3158, 3159, 3160, 2102, 2039, 
    1985, 1472, 1484, 5613, 1428, 1478, 
    1466, 1873, 1460, 1449, 3743, 1454, 
    1444, 1422, 1765, 3734, 1418, 3136, 
    2040, 2041, 2042, 2043, 2044, 2045, 
    2046, 2047, 2048, 2049, 2050, 2051, 
    2052, 2053, 2054, 2055, 2056
  ) 
  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 0.00104

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 (3161,3719,3720,5142,5143,5144,6730,6731,3158,3159,3160,2102,2039,1985,1472,1484,5613,1428,1478,1466,1873,1460,1449,3743,1454,1444,1422,1765,3734,1418,3136,2040,2041,2042,2043,2044,2045,2046,2047,2048,2049,2050,2051,2052,2053,2054,2055,2056))",
        "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)))"
      }
    }
  }
}