TABLE 2.
Detail of binding energy interpreted using AutoDock Vina software along with brief description of key active site residues involved in binding
| β-Lactamase variant | Attribute | Data for: |
||||
|---|---|---|---|---|---|---|
| D2573 | D2148 | D63 | Cefotaxime | Avibactam | ||
| KPC-2 | Binding energy | –9.1 | –8.6 | –8.1 | –7.3 | –7.2 |
| H bond | Ser70, Ser130, Ser170, Arg220, Thr235, Thr237 | Ser70, Asn132, Asn170, Thr235 | Ser70, Lys73, Ser130, Asn132, Glu166, Asn170, Thr237 | Ser70, Ser130, Thr215, Arg220, Thr235, Thr237 | Ser70, Trp105, Ser130, Asn132, Glu166, Thr237 | |
| Hydrophobic bond | Trp105, Leu167, Thr216 | Trp105, Leu167 | Trp105 | Trp105 | ||
| Other bond | His219 (Pi sulfur bond) | |||||
| CTXM -15 | Binding energy | –9.2 | –9.1 | –8.6 | –8.4 | –6.9 |
| H bond | Ser70, Asn104, Ser130, Thr235, Ser237 | Asn104, Asn132, Asn170, Thr235, Ser237 | Ser70, Ser130, Asn132, Thr235, Gly236 | Ser70, Asn132, Lys234, Thr235, Ser237, Pro268, Ala270 | Ser70, Ser130, Asn132, Lys234, Ser237, Thr235 | |
| Hydrophobic bond | Tyr 105, Pro167 | Tyr105, Gly238-Gly239 | Arg274 | |||
| SHV-1 | Binding energy | –8.0 | –7.5 | –7.2 | –7.2 | –6.8 |
| H bond | Ser70, Asn132, Ala237 | Ser70, Ser130, Thr167, Ala237 | Ser70, Ser130, Asn132, Asn170, Thr235 | Ser70, Ser130, Asn132, Thr167, Asn170, Lys234 | Ser70, Ser130, Asn132, Asn170, Thr235 | |
| Hydrophobic bond | Glu168, Ala237 | Tyr105 | Val216, Ala237 | Ala237 | Ala237 | |
| Other bond | Glu168 (electrostatic bond), Glu240 (Electrostatic bond) | Glu240 (electrostatic bond) | Glu240 (electrostatic bond) | |||
| TEM-1 | Binding energy | –8.2 | –8.2 | –8.3 | –8.0 | –7.3 |
| H bond | Ser70, Lys73, Ser130, Asn132 | Ser70, Asn132, Asn170, Ser235, Arg244 | Ser70, Ser130, Asn132, Asn170, Val216, Ser235, Arg244 | Ser70, Ser130, Pro167, Asn170, Ser235, Ala237, Gly238, Arg244 | Lys 73, Ser130, Asn132, Arg244 | |
| Hydrophobic bond | Tyr105, Ala237 | Val216, Ala237, Ala237-Gly238, Gly238-Glu240 | Val216, Ala237, Ala237-Gly238, | Tyr105, Ala237 | Tyr105, Val216, Ala237 | |
| Other bond | Glu104 (electrostatic bond), Glu166 (electrostatic bond) | Tyr105 (Pi-sulfur bond) | ||||
| NDM-1 | Binding energy | –8.8 | –9.5 | –8.1 | –6.7 | –6.3 |
| H bond | Gly36, His250 | Asn220, Ser251, His189 | His122, Gln123, Asp124, Lys211, Asn220 | Gln123, Glu152, His189, Lys211, Asn220, His250 | Lys211, Gly219 | |
| Hydrophobic bond | ILE35, Ala215, His250 | Ile35, Lys211, Ala215, Lys216, His250 | His122, His250 | Ile35, His122, His250 | ILE35, Val73, His250 | |
| Other bond | Zn1: Zn2 (electrostatic bond), Asp124 (electrostatic bond), Asp212 (electrosatic bond) | Zn2 (electrostatic bond) | Zn2 (electrostatic bond), His122 (electrostatic bond), Asp124 (electrostatic bond) | Zn1 (metal acceptor bond), Trp93 (Pi-sulfur bond) | Zn1: Zn2 (metal acceptor bond), His189 | |
| Amp-C | Binding energy | –9.7 | –9.9 | –8.5 | –8.9 | –6.9 |
| H bond | Gln 146, Asn 179, Thr343, Asn373 | Tyr177, Asn179, Thr 343, Asn 373 | Ser90, Arg175, Tyr177, Gly313, Thr343, Asn373 | Ser 90, Asn 179, Gly313, Thr316, Lys342, Thr343, Ser345, Asn373, Glu 299, Asn 314 | Ser 90, Asn 179, Ser345, Asn 373 | |
| Hydrophobic bond | Ala 319, Met 318, Tyr177, Tyr 249, Ala319 | Ala319, Tyr249 | Tyr 177, Ala 319 | Tyr 177, Thr249, Ala 319 | Tyr 177, Ala 319 | |
| Other bond | Glu 299 (electrostatic bond) | Glu 299 (electrostatic bond) | Tyr 177 | |||