SELECT 
  category_id, 
  parent_id 
FROM 
  cscart_categories 
WHERE 
  parent_id IN(
    516, 501, 494, 480, 299, 476, 289, 495, 
    500, 499, 496, 497, 298, 304, 498, 478, 
    286, 502, 305, 493, 288, 454, 456, 455, 
    460, 269, 287, 166, 223, 274, 311, 461, 
    271, 204, 242, 229, 222, 251, 210, 168, 
    198, 307, 212, 176, 178, 448, 190, 224, 
    246, 270, 309, 182, 175, 230, 220, 252, 
    197, 211, 213, 185, 169, 243, 191, 247, 
    475, 209, 217, 225, 193, 199, 215, 221, 
    214, 231, 208, 179, 249, 253, 226, 186, 
    218, 174, 244, 194, 200, 180, 232, 202, 
    227, 248, 187, 181, 195, 177, 196, 188, 
    254, 189, 245, 479, 250, 165, 170, 171, 
    172, 201, 481, 512, 263, 513, 519, 526
  ) 
  AND category_id != 264

Query time 0.01181

JSON explain

{
  "query_block": {
    "select_id": 1,
    "cost": 0.02424812,
    "nested_loop": [
      {
        "table": {
          "table_name": "cscart_categories",
          "access_type": "index",
          "possible_keys": ["PRIMARY", "parent", "p_category_id"],
          "key": "parent",
          "key_length": "3",
          "used_key_parts": ["parent_id"],
          "loops": 1,
          "rows": 120,
          "cost": 0.02424812,
          "filtered": 100,
          "attached_condition": "cscart_categories.parent_id in (516,501,494,480,299,476,289,495,500,499,496,497,298,304,498,478,286,502,305,493,288,454,456,455,460,269,287,166,223,274,311,461,271,204,242,229,222,251,210,168,198,307,212,176,178,448,190,224,246,270,309,182,175,230,220,252,197,211,213,185,169,243,191,247,475,209,217,225,193,199,215,221,214,231,208,179,249,253,226,186,218,174,244,194,200,180,232,202,227,248,187,181,195,177,196,188,254,189,245,479,250,165,170,171,172,201,481,512,263,513,519,526) and cscart_categories.category_id <> 264",
          "using_index": true
        }
      }
    ]
  }
}