Hi,
I used Haddock web sever for the docking of a small molecule with DNA duplex. Everything went fine, but when I inspected the generated pdb files, I found one of the thiazole rings of the ligand completely distorted. The sulfur atom formed 4 bonds with all atoms in the ring, which looked as a sphere. Has anyone encountered such a problem?.
Thank you in advance
Best regards
Hasan
This is usually simply a visualization issue - pymol might try to connect atoms that are within a certain distance. Try opening it in a different visualizer.
Thank you for your reply. I used the Discovery Studio , Pymol and Chimera visualizer, however, I faced the same problem. I attached the pdb file for your reference.
Regards,
Hasan
Hasan Yaser Hasan Al Niss
Associate professor
College of Pharmacy
Medicinal Chemistry
T: +97165057427 |
E:
halniss@sharjah.ac.ae
cluster1_1.pdb (59.8 KB)
Looks like only one of the two groups is giving problems.
What was the starting model?
The starting structure is 2MNE. I modified 2mne structure by replacing the pyridine ring of the ligand with a thiazole ring. The modified pdb file is attached.
Hasan Yaser Hasan Al Niss
Associate professor
College of Pharmacy
Medicinal Chemistry
T: +97165057427 |
E:
halniss@sharjah.ac.ae
MGB4_ACTAGT.pdb (67.1 KB)
There is indeed something fishy with the second thiazole ring of each ligand. Must come from the way PRODRG defines the topology - we do not have control on that.
However looking at your input model after deleting the connect statements, I do see before running HADDOCK already something strange in the second thiazole. The geometry must not be good from the start for that one. Any optimisation you can do before docking?
