SELECT 
  user_id 
FROM 
  cscart_users 
WHERE 
  `is_root` = 'Y' 
  AND `user_type` = 'V' 
  AND `company_id` = 2 
ORDER BY 
  user_id ASC 
LIMIT 
  1

Query time 0.00011

JSON explain

{
  "query_block": {
    "select_id": 1,
    "nested_loop": [
      {
        "table": {
          "table_name": "cscart_users",
          "access_type": "index",
          "key": "PRIMARY",
          "key_length": "3",
          "used_key_parts": ["user_id"],
          "rows": 1,
          "filtered": 100,
          "attached_condition": "cscart_users.company_id = 2 and cscart_users.is_root = 'Y' and cscart_users.user_type = 'V'"
        }
      }
    ]
  }
}