Table 7 Ligand-amino acid interactions with DNA gyrase of E. coli (PDB: ID 7P2M).
No | Protein | Ligand | Hydrophilic interactions | Hydrophobic contacts | No. of H-bonds | No. of total bonds | Affinity kcal mol−1 | ||
|---|---|---|---|---|---|---|---|---|---|
Residue (H-bond) | Length | Residue (bond type) | Length | ||||||
1 | DNA Gyrase of E.coli (PDB: ID 7P2M) | 7 | Asp73, (H- Bond) | 1.99 | Ile94, (alkyl) | 5.18 | 1 | 10 | − 8.90 |
Ile94, (alkyl) | 4.95 | ||||||||
Val120, (alkyl) | 5.46 | ||||||||
Thr165, (Unfavorable) | 1.91 | ||||||||
Val43, (alkyl) | 5.32 | ||||||||
Val167, (alkyl) | 5.05 | ||||||||
Val120, (alkyl) | 5.15 | ||||||||
Glu50, ((pi-Cation) | 4.36 | ||||||||
Arg76, ((pi-Cation) | 3.34 | ||||||||
2 | 9 | Asp73, (H- Bond) Asp73, (H- Bond) | 2.11 2.60 | Val120, (alkyl) | 4.01 | 2 | 8 | − 8.0 | |
Ile78, (alkyl) | 4.86 | ||||||||
Ile78, (alkyl | 5.08 | ||||||||
Asn46, (Pi-Pi T shaped) | 4.56 | ||||||||
Thr165, (pi-Sigma) | 3.82 | ||||||||
Gly77, (C-H bond) | 3.15 | ||||||||
11 | Asp73, (H- Bond) Asp73, (H- Bond) | 2.11 2.59 | Val120, (alkyl) | 4.02 | 2 | 8 | − 7.7 | ||
Ile78, (alkyl) | 4.86 | ||||||||
Ile78, (alkyl | 5.07 | ||||||||
Asn46, (Pi-Pi T shaped) | 4.55 | ||||||||
Thr165, (pi-Sigma) | 3.82 | ||||||||
Gly77, (C-H bond) | 3.14 | ||||||||
15 | Gly77, (H- Bond) Thr165, (H- Bond) | 1.80 2.41 | Ile78, (alkyl) | 5.03 | 2 | 8 | − 8.0 | ||
Ile94, (alkyl) | 3.61 | ||||||||
Ile94, (alkyl | 4.62 | ||||||||
Pro79, (alkyl) | 4.02 | ||||||||
Glu50, (pi-Cation) | 3.87 | ||||||||
Arg76, (pi-Cation) | 3.60 | ||||||||
3 | Ciprofloxacin | – | – | Asn46, (Unfavorable) | 1.81 | 0 | 7 | − 6.6 | |
Ile94, (alkyl) | 5.20 | ||||||||
Ile78, (alkyl) | 4.61 | ||||||||
Ile78, (alkyl | 3.87 | ||||||||
Asn46, (Pi-Pi T shaped) | 4.73 | ||||||||
Ile78, (pi-Sigma) | 3.87 | ||||||||
Asp73, (C-H bond) | 3.70 | ||||||||
