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Table 3 Molecular interactions of all six ligands into protein disulfide isomerase

From: Molecular docking studies of dithionitrobenzoic acid and its related compounds to protein disulfide isomerase: computational screening of inhibitors to HIV-1 entry

Molecules Hydrogen bond donor Hydrogen bond acceptor Length of hydrogen bond (Å) Residues involved in van der Waals interaction (Scaling Factor = 1.00 Å) Binding free energy (kcal/mol)
Dithionitrobenzoic acid LIGAND1::MOL1:S1 PDI: A: PHE80: O   ALA34, TRP36, HIS39, CYS40, PRO81 57.26
  PDI:A:CYS37:HG LIGAND1::MOL1:S2 2.029   
  PDI:A:ARG101:HH11 LIGAND1::MOL1:O3 1.721   
NSC695265 LIGAND2::MOL1:H11 PDI:A:CYS37:SG 2.109 ALA34, HIS39, THR68, SER79, PHE80 9.77
  PDI:A:TRP36:HE1: LIGAND2::MOL1:O6 2.131   
Thionitrobenzoic acid 2-nitro-5-thiocyanobenzoic acid PDI:A:CYS37:SG LIGAND3::MOL1:O1 2.109 TRP36, PHE80 9.46
  PDI:A:CYS37:HG LIGAND4::MOL1:O1 1.859 ALA34, TRP36, THR68 72.55
  LIGAND4::MOL1:H7 PDI:A:CYS37:SG 1.887   
  PDI:A:CYS40:HN LIGAND4::MOL1:O4 2.128   
  LIGAND4::MOL1:H5 PDI: A: PHE80: O 1.927   
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