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 (
    12684, 12714, 13260, 13267, 12349, 12364, 
    12259, 12504, 12524, 12379, 6843, 6840, 
    6841, 6846, 13274, 13286, 13280, 13292, 
    6962, 6966, 6967, 6965, 6963, 6952, 
    6953, 3484, 3487, 3485, 3486, 6969, 
    3434, 6947, 3424, 3911, 3422, 3910, 
    3421, 3909, 3420, 3423, 3912, 3430, 
    3429, 3437, 3436, 3438, 6959, 3425
  ) 
  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 0.00125

JSON explain

{
  "query_block": {
    "select_id": 1,
    "cost_info": {
      "query_cost": "60.16"
    },
    "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": 107,
        "rows_produced_per_join": 21,
        "filtered": "19.99",
        "index_condition": "(`test2_gaseus`.`cscart_product_prices`.`product_id` in (12684,12714,13260,13267,12349,12364,12259,12504,12524,12379,6843,6840,6841,6846,13274,13286,13280,13292,6962,6966,6967,6965,6963,6952,6953,3484,3487,3485,3486,6969,3434,6947,3424,3911,3422,3910,3421,3909,3420,3423,3912,3430,3429,3437,3436,3438,6959,3425))",
        "cost_info": {
          "read_cost": "58.02",
          "eval_cost": "2.14",
          "prefix_cost": "60.16",
          "data_read_per_join": "513"
        },
        "used_columns": [
          "product_id",
          "price",
          "percentage_discount",
          "lower_limit",
          "usergroup_id"
        ],
        "attached_condition": "((`test2_gaseus`.`cscart_product_prices`.`lower_limit` = 1) and (`test2_gaseus`.`cscart_product_prices`.`usergroup_id` in (0,1)))"
      }
    }
  }
}