SELECT 
  category_id, 
  parent_id 
FROM 
  cscart_categories 
WHERE 
  parent_id IN(
    539, 538, 536, 531, 529, 528, 530, 537, 
    540, 545, 548, 547, 544, 532, 543, 542, 
    549, 550, 546, 541, 533, 551, 534, 535, 
    552, 557, 554, 553, 555, 556, 559, 558, 
    562, 563, 560, 561
  ) 
  AND category_id != 414

Query time 0.00041

JSON explain

{
  "query_block": {
    "select_id": 1,
    "cost_info": {
      "query_cost": "25.21"
    },
    "table": {
      "table_name": "cscart_categories",
      "access_type": "range",
      "possible_keys": [
        "PRIMARY",
        "parent",
        "p_category_id"
      ],
      "key": "parent",
      "used_key_parts": [
        "parent_id"
      ],
      "key_length": "3",
      "rows_examined_per_scan": 36,
      "rows_produced_per_join": 36,
      "filtered": "100.00",
      "index_condition": "(`s2cart`.`cscart_categories`.`parent_id` in (539,538,536,531,529,528,530,537,540,545,548,547,544,532,543,542,549,550,546,541,533,551,534,535,552,557,554,553,555,556,559,558,562,563,560,561))",
      "cost_info": {
        "read_cost": "21.61",
        "eval_cost": "3.60",
        "prefix_cost": "25.21",
        "data_read_per_join": "127K"
      },
      "used_columns": [
        "category_id",
        "parent_id"
      ],
      "attached_condition": "(`s2cart`.`cscart_categories`.`category_id` <> 414)"
    }
  }
}