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. 2015 Mar 31;9:1897–1912. doi: 10.2147/DDDT.S77020

Table 3.

Binding affinities and molecular interaction of the best lead molecules to target Brucella transcription termination factor rho protein was calculated from PyMOL software

S number ZINC ID Binding affinity (kcal/mol) Protein-ligand interactions
Bond distance Bond angle
Protein Ligand
1 ZINC24934545 −10.4 Arg180 CA-N O57P55 2.80 107.38
Arg180 C-O N49C1 2.29 111.49
Thr188 CB-OG1 O40P56 3.26 138.75
Thr188 CB-OG1 O58P56 3.27 97.26
Thr188 CB-OG1 O53C25 2.99 147.81
Asp213 C-O HN8N50 2.90 129.85
Asp213 C-O O38C42 3.18 139.40
Asp213 CG-OD1 O38C42 3.35 88.25
*Arg215 CZ-NH1 O52C16 3.24 110.96
Glu218 CD-OE2 O58P56 3.12 106.91
Phe358 C-O O37C41 3.31 132.17
Phe358 C-O N3C41 3.30 133.70
2 ZINC72319544 −10.4 Thr185 CA-N O38C42 2.80 105.05
Thr185 CB-OG1 O38C42 2.97 113.79
Gly186 CA-N O38C42 2.84 122.00
Lys187 CA-N O38C42 3.11 119.29
Asp213 C-O O57P55 3.52 133.45
*Arg215 CZ-NH2 O43P55 3.28 91.52
*Arg215 CZ-NH2 O47P56 2.99 157.60
*Arg215 CA-N O57P55 3.00 135.60
Phe235 C-O N49C1 2.98 121.93
Phe235 C-O O37C41 3.45 139.39

Note:

*

The anchoring residue for the inhibitor interaction in rho.

Abbreviations: S, serial; ZINC, ZINC Is Not Commercial.