SELECT 
  category_id, 
  parent_id 
FROM 
  cscart_categories 
WHERE 
  parent_id IN(
    1039, 1051, 1040, 1052, 1043, 1048, 1041, 
    1053, 1055, 1054, 1044, 1050, 1045, 
    1047, 1042, 1049, 1046
  ) 
  AND category_id != 414

Query time 0.00030

JSON explain

{
  "query_block": {
    "select_id": 1,
    "cost_info": {
      "query_cost": "11.91"
    },
    "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": 17,
      "rows_produced_per_join": 17,
      "filtered": "100.00",
      "index_condition": "(`s2cart`.`cscart_categories`.`parent_id` in (1039,1051,1040,1052,1043,1048,1041,1053,1055,1054,1044,1050,1045,1047,1042,1049,1046))",
      "cost_info": {
        "read_cost": "10.21",
        "eval_cost": "1.70",
        "prefix_cost": "11.91",
        "data_read_per_join": "60K"
      },
      "used_columns": [
        "category_id",
        "parent_id"
      ],
      "attached_condition": "(`s2cart`.`cscart_categories`.`category_id` <> 414)"
    }
  }
}