Similar code with Hibernate ORM 4.3.10 runs without problems.
MysqlDataSource ds = new MysqlDataSource();
ds.setUrl("jdbc:mysql://localhost/test2?user=root");
new SchemaUpdate(new StandardServiceRegistryBuilder()
.applySetting(Environment.DATASOURCE, ds).build(), new Configuration().addAnnotatedClass(My.class)).execute(true, true);