SELECT 
  category_id, 
  parent_id 
FROM 
  cscart_categories 
WHERE 
  parent_id IN(
    3416, 3420, 3421, 3422, 3424, 3425, 3426, 
    3427, 3428, 3429, 3431, 3432, 3433, 
    3434, 3435, 3436, 3437, 3439, 3440, 
    3441, 3442, 3443, 3444, 3445, 3451, 
    3453, 3454, 3455, 3456, 3457, 3458, 
    3459, 3460, 3461, 3462, 3463, 3464, 
    3465, 3466, 3468
  ) 
  AND category_id != 414

Query time 0.00062

JSON explain

{
  "query_block": {
    "select_id": 1,
    "cost_info": {
      "query_cost": "28.01"
    },
    "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": 40,
      "rows_produced_per_join": 40,
      "filtered": "100.00",
      "index_condition": "(`s2cart`.`cscart_categories`.`parent_id` in (3416,3420,3421,3422,3424,3425,3426,3427,3428,3429,3431,3432,3433,3434,3435,3436,3437,3439,3440,3441,3442,3443,3444,3445,3451,3453,3454,3455,3456,3457,3458,3459,3460,3461,3462,3463,3464,3465,3466,3468))",
      "cost_info": {
        "read_cost": "24.01",
        "eval_cost": "4.00",
        "prefix_cost": "28.01",
        "data_read_per_join": "141K"
      },
      "used_columns": [
        "category_id",
        "parent_id"
      ],
      "attached_condition": "(`s2cart`.`cscart_categories`.`category_id` <> 414)"
    }
  }
}