SELECT 
  category_id, 
  parent_id 
FROM 
  cscart_categories 
WHERE 
  parent_id IN(
    2709, 2778, 2922, 2934, 2945, 2959, 2974, 
    2981, 3004, 3012, 3037, 3430, 3048, 
    3181, 3190, 3191, 3200, 3220, 3236, 
    3237, 3242, 3243, 3244, 3250, 3366, 
    3413
  ) 
  AND category_id != 414

Query time 0.00061

JSON explain

{
  "query_block": {
    "select_id": 1,
    "cost_info": {
      "query_cost": "44.31"
    },
    "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": 84,
      "rows_produced_per_join": 84,
      "filtered": "100.00",
      "index_condition": "(`s2cart`.`cscart_categories`.`parent_id` in (2709,2778,2922,2934,2945,2959,2974,2981,3004,3012,3037,3430,3048,3181,3190,3191,3200,3220,3236,3237,3242,3243,3244,3250,3366,3413))",
      "cost_info": {
        "read_cost": "35.91",
        "eval_cost": "8.40",
        "prefix_cost": "44.31",
        "data_read_per_join": "297K"
      },
      "used_columns": [
        "category_id",
        "parent_id"
      ],
      "attached_condition": "(`s2cart`.`cscart_categories`.`category_id` <> 414)"
    }
  }
}