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 (
    16324, 13173, 13183, 13160, 13167, 16326, 
    13182, 54669, 13164, 13153, 13158, 
    13152, 13161, 13163, 13159, 16330, 
    13178, 13175, 13157, 13172, 13168, 
    13176, 13162, 13149, 13180, 13185, 
    13181, 13186, 13188, 13165, 13174, 
    13187, 13190, 13169, 13184, 13146, 
    13192, 13179, 13191, 13151, 13171, 
    13154, 13147, 13150, 13148, 13166
  ) 
  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 0.00136

JSON explain

{
  "query_block": {
    "select_id": 1,
    "cost_info": {
      "query_cost": "32.21"
    },
    "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": 46,
        "rows_produced_per_join": 9,
        "filtered": "20.00",
        "index_condition": "(`cscartdb`.`cscart_product_prices`.`product_id` in (16324,13173,13183,13160,13167,16326,13182,54669,13164,13153,13158,13152,13161,13163,13159,16330,13178,13175,13157,13172,13168,13176,13162,13149,13180,13185,13181,13186,13188,13165,13174,13187,13190,13169,13184,13146,13192,13179,13191,13151,13171,13154,13147,13150,13148,13166))",
        "cost_info": {
          "read_cost": "31.29",
          "eval_cost": "0.92",
          "prefix_cost": "32.21",
          "data_read_per_join": "220"
        },
        "used_columns": [
          "product_id",
          "price",
          "percentage_discount",
          "lower_limit",
          "usergroup_id"
        ],
        "attached_condition": "((`cscartdb`.`cscart_product_prices`.`lower_limit` = 1) and (`cscartdb`.`cscart_product_prices`.`usergroup_id` in (0,1)))"
      }
    }
  }
}