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 (
    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, 6958, 6960, 6968, 6961, 6964, 
    6957, 6956, 6954, 6955, 3500, 3501, 
    3431, 6948, 3499, 3914, 3913, 3455, 
    3466, 3454, 3456, 3449, 3461
  ) 
  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 0.00105

JSON explain

{
  "query_block": {
    "select_id": 1,
    "cost_info": {
      "query_cost": "34.06"
    },
    "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": 49,
        "rows_produced_per_join": 9,
        "filtered": "20.00",
        "index_condition": "(`gaseus`.`cscart_product_prices`.`product_id` in (6963,6952,6953,3484,3487,3485,3486,6969,3434,6947,3424,3911,3422,3910,3421,3909,3420,3423,3912,3430,3429,3437,3436,3438,6959,3425,6958,6960,6968,6961,6964,6957,6956,6954,6955,3500,3501,3431,6948,3499,3914,3913,3455,3466,3454,3456,3449,3461))",
        "cost_info": {
          "read_cost": "33.08",
          "eval_cost": "0.98",
          "prefix_cost": "34.06",
          "data_read_per_join": "235"
        },
        "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)))"
      }
    }
  }
}