SELECT 
  category_id, 
  parent_id 
FROM 
  cscart_categories 
WHERE 
  parent_id IN(
    3124, 3116, 3117, 3122, 3121, 3118, 3119, 
    3126, 3125, 3120, 3127, 3123, 3129, 
    3131, 3133
  ) 
  AND category_id != 414

Query time 0.00052

JSON explain

{
  "query_block": {
    "select_id": 1,
    "cost_info": {
      "query_cost": "10.96"
    },
    "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": 16,
      "rows_produced_per_join": 16,
      "filtered": "100.00",
      "index_condition": "(`s2cart`.`cscart_categories`.`parent_id` in (3124,3116,3117,3122,3121,3118,3119,3126,3125,3120,3127,3123,3129,3131,3133))",
      "cost_info": {
        "read_cost": "9.36",
        "eval_cost": "1.60",
        "prefix_cost": "10.96",
        "data_read_per_join": "56K"
      },
      "used_columns": [
        "category_id",
        "parent_id"
      ],
      "attached_condition": "(`s2cart`.`cscart_categories`.`category_id` <> 414)"
    }
  }
}