Table 3.
Molecular interactions of the ligands into PON2
| Ligands | H-bond donor | H-bond acceptor | H-bond length (Å) | vdW interaction residues (scaling factor = 1.00 Å) | Binding energy (Kcal/mol) | Docking energy (Kcal/mol) |
|---|---|---|---|---|---|---|
| Homocysteine thiolactone (HCTL) | HCTL::H | Asp168:OD2 | 1.880 | Glu53, Asp54, His114, Ile116, Ser117, Asn167, Asp168, Ile169, Ala171, Asn223, Asn226, Asp268, Asn269 Leu270 Ca 355 | −6.63 | −7.12 |
| HCTL::H | Ile169:O | 1.785 | ||||
| HCTL::H | Ile225:O | 1.944 | ||||
| Thr170:HG1 | HCTL:O | 2.202 | ||||
| Δ Valero lactone (DVL) | Thr170:HG1 | DVL:O | 1.769 | Glu53, Asp54, His114, Ile116, Ser117, Thr118, Asn167, Asp168, Ile169, Asn223, Asn226, Asp268, Asn269, Leu270, Ca 355 | −4.06 | −4.06 |
| Ala171:HN | DVL:O | 2.132 | ||||
| Γ-Thiobutyro lactone (GTBL) | Thr170:HG1 | GTBL:O | 2.004 | Glu53, Asp54, His114, Ile116, Ser117, Thr118, Asn167, Asp168, Ile169, Ala171, Asn223, Asn226, Asp268, Asn269, Leu270, Ca 355 | −3.69 | −3.69 |
| Phenyl acetate (PA) | Thr118:HN | PA:O | 2.062 | Glu53, Asp54, His114, Ile116, Ser117, Asn167, Asp 168, Ile169, Thr170, Asn223, Ile225, Asn226, Asp268, Asn269, Leu270, Ca 355 | −4.73 | −5.38 |
| Ala171: HN | PA:O | 1.947 | ||||
| Thr118:OPA:O | 2.767 | |||||
| 2- Naphthyl acetate (2- NA) | Ile57:HN | 2-NA:O | 2.364 | Glu53, Asp54, Ile55, Asp56, His114, Ile116, Ser117, Thr118, Asn167, Asp 168, Ile169, Thr170, Asn223, Ile225, Asn226, Asp268, Asn269, Leu270, Ser271, Ser334, Ca 355 | −6.34 | −7.08 |
| Ile272:HN | 2-NA:O | 2.066 | ||||
| Benzyl acetate (BA) | Thr170:HG1 | BA:O | 2.062 | Glu53, Asp54, Ile55, Asp56, His114, Ile116, Ser117, Thr118, Asn167, Asp 168, Ile169, Thr170, Asn223, Ile225, Asn226, Asp268, Asn269, Leu270, Ca 355 | −5.21 | −6.16 |
| Ala171:HN | BA:O | 1.911 | ||||
| Paraoxon (PAR) | Lys46:HZ2 | PAR:O | 1.741 | His43, Leu44, Ile45, Met88, Glu93, Lys94, Arg96, Leu341, Tyr351 | −5.56 | −7.95 |
| PAR:H | Pro95:O | 1.923 |