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 (
    13316, 13315, 13317, 13318, 1654, 1655, 
    1656, 1657, 1658, 1659, 1660, 1661, 
    1662, 1663, 1664, 1665, 1666, 1667, 
    1668, 1669, 1670, 1671, 2220, 2221, 
    2222, 2223, 5353, 5354, 5355, 5356, 
    5357, 5358, 5359, 5360, 5361, 5362, 
    5363, 5364, 5365, 5366, 5367, 5368, 
    5369, 5370, 5820, 5821, 5822, 5823
  ) 
  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 0.00127

JSON explain

{
  "query_block": {
    "select_id": 1,
    "cost_info": {
      "query_cost": "48.91"
    },
    "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": 82,
        "rows_produced_per_join": 16,
        "filtered": "19.99",
        "index_condition": "(`test2_gaseus`.`cscart_product_prices`.`product_id` in (13316,13315,13317,13318,1654,1655,1656,1657,1658,1659,1660,1661,1662,1663,1664,1665,1666,1667,1668,1669,1670,1671,2220,2221,2222,2223,5353,5354,5355,5356,5357,5358,5359,5360,5361,5362,5363,5364,5365,5366,5367,5368,5369,5370,5820,5821,5822,5823))",
        "cost_info": {
          "read_cost": "47.27",
          "eval_cost": "1.64",
          "prefix_cost": "48.91",
          "data_read_per_join": "393"
        },
        "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)))"
      }
    }
  }
}