Table 3 Molecular interactions of all six ligands into protein disulfide isomerase
Molecules | Hydrogen bond donor | Hydrogen bond acceptor | Length of hydrogen bond (Ã…) | Residues involved in van der Waals interaction (Scaling Factor = 1.00 Ã…) | Binding free energy (kcal/mol) |
|---|---|---|---|---|---|
Dithionitrobenzoic acid | LIGAND1::MOL1:S1 | PDI: A: PHE80: O | Â | ALA34, TRP36, HIS39, CYS40, PRO81 | 57.26 |
| Â | PDI:A:CYS37:HG | LIGAND1::MOL1:S2 | 2.029 | Â | Â |
| Â | PDI:A:ARG101:HH11 | LIGAND1::MOL1:O3 | 1.721 | Â | Â |
NSC695265 | LIGAND2::MOL1:H11 | PDI:A:CYS37:SG | 2.109 | ALA34, HIS39, THR68, SER79, PHE80 | 9.77 |
| Â | PDI:A:TRP36:HE1: | LIGAND2::MOL1:O6 | 2.131 | Â | Â |
Thionitrobenzoic acid 2-nitro-5-thiocyanobenzoic acid | PDI:A:CYS37:SG | LIGAND3::MOL1:O1 | 2.109 | TRP36, PHE80 | 9.46 |
| Â | PDI:A:CYS37:HG | LIGAND4::MOL1:O1 | 1.859 | ALA34, TRP36, THR68 | 72.55 |
| Â | LIGAND4::MOL1:H7 | PDI:A:CYS37:SG | 1.887 | Â | Â |
| Â | PDI:A:CYS40:HN | LIGAND4::MOL1:O4 | 2.128 | Â | Â |
| Â | LIGAND4::MOL1:H5 | PDI: A: PHE80: O | 1.927 | Â | Â |
2-nitro-5-sulfo-sulfonyl-benzoic acid | LIGAND5::MOL1:H22 | PDI:A:CYS37:SG | 2.199 | ALA34, TRP36, GLY38, HIS39, PHE80 | 6.19 |
NSC517871 | LIGAND6::MOL1:H9 | PDI:A:CYS37:SG | 2.025 | ALA34, TRP36, HIS39, SER67, THR68, PHE80 | 13.37 |