Maybe you can store all the pairs sorted in a hash:

use strict;
use warnings;
use Data::Dumper;

my %data = ();
while (<DATA>){
  chomp;
  $data{join (' ',sort {$a cmp $b} split / /,$_)} = 1;
}
 print Dumper \%data;

__DATA__
ENSP000010 ENSP000011
ENSP000020 ENSP000050
ENSP000011 ENSP000010
ENSP000050 ENSP000020
[download]

Outputs:

VAR1 = {
          'ENSP000020 ENSP000050' => 1,
          'ENSP000010 ENSP000011' => 1
        };
[download]

citromatik