Fig 1.
Schematic diagram of avibactam inhibition and deacylation pathways of KPC-2.
Table 1.
Data collection and refinement statistics for SHV-1 and KPC-2 soaked with avibactam.
Fig 2.
Electron density of avibactam bound to the active site of KPC-2.
A, |Fo|-|Fc| electron density difference density is depicted for the ligand (contoured at 3.25σ). The covalently-bound avibactam is shown in blue stick model. Prior to the map calculation, the model with the avibactam ligand removed has been subjected to 10 cycles of Refmac crystallographic refinement. B, close-up view of the electron density around the N1 atom of avibactam with 3 different models of avibactam: avibactam refined with the N1 in the S enantiomer conformation (same colors as in A), avibactam refined with the N1 in the planar conformation (all atoms in magenta), and avibactam refined with the N1 in the R enantiomer conformation (all atoms in green). By changing the refined chirality of the N1 atom, the resulting model yields a different position for the C7 atom of avibactam thus distorting the planarity of the adjacent carbonyl moiety (involving avibactam atoms N1, C7, O, and S70 atom OG). As a measure of this carbonyl planarity, the OG atom distance from the plane defined by avibactam atoms N1, C7, and O is 0.15, 0.56, and 0.86 Å for the S, planar, and R enantiomer conformation of N1, respectively.
Fig 3.
Electron density of avibactam bound to the active site of SHV-1.
|Fo|-|Fc| electron density difference density is depicted for the ligand (contoured at 3.25σ). The covalently-bound avibactam is shown in blue stick model. The map was calculated similar to that in Fig 2.
Fig 4.
Interactions of avibactam in the active site of KPC-2.
Avibactam is shown with green carbon atoms. Hydrogen bonds are depicted as dashed lines (cut-off distance is 3.2Å). The deacylation water is present (labeled W#1). Additional waters are labeled W#2–3.
Fig 5.
Avibactam in the active site of SHV-1.
Interactions of avibactam (shown with green carbon atoms) in the active site of SHV-1. Hydrogen bonds are depicted as dashed lines. The deacylation water is present (labeled W#1). Additional waters are labeled W#2–4.
Fig 6.
Superposition of complexes of KPC-2 and SHV-1 bound with avibactam.
Superimposed are KPC-2 (cyan carbon atoms) and SHV-1 (grey carbon atoms). The nitrogen N1 is labelled ‘1’ and ‘1’” for KPC-2 and SHV-1, respectively, to indicate the differences in the chirality and direction of the lone pair electrons that nitrogen in the 2 different structures. The oxygen of the sulfate moiety of avibactam bound to KPC-2 is indicated by a ‘*’. The deacylation water, W#1, and sulfate hydrogen-bonding water in KPC-2, W#2, are indicated as well. The following active site residues were used for the superpositioning: SHV-1 residues 233–238, 68–84, 121–140, 167–172 onto the equivalent residues of KPC-2; root-mean-square-deviation is 0.51Å for 48 Cα atoms.
Fig 7.
Superposition of complexes of KPC-2 and CTX-M-15 bound with avibactam.
Superimposed are CTX-M-15 (grey carbons atoms) and KPC-2 (cyan carbon atoms). The deacylation water, W#1, is labelled. Key distance differences listed in Table 2 are indicated by dashed lines. These distance differences involve the avibactam N6 atom pointing towards the avibactam C7 atom in CTX-M-15 (listed in black) whereas in KPC-2 this avibactam N6 atom is pointing away thus being situated at a larger distance (listed in green). In addition, the avibactam N6 hydrogen bond with S130 in CTX-M-1 is depicted as well; this is not present in KPC-2.
Table 2.
Comparison of avibactam inhibition kinetics and avibactam active site interaction.