7UTB

KPC-2 CARBAPENEMASE IN COMPLEX WITH THE BORONIC ACID INHIBITOR MB_076


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.38 Å
  • R-Value Free: 0.170 
  • R-Value Work: 0.148 
  • R-Value Observed: 0.149 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history


Literature

Boronic Acid Transition State Inhibitors as Potent Inactivators of KPC and CTX-M beta-Lactamases: Biochemical and Structural Analyses.

Alsenani, T.A.Rodriguez, M.M.Ghiglione, B.Taracila, M.A.Mojica, M.F.Rojas, L.J.Hujer, A.M.Gutkind, G.Bethel, C.R.Rather, P.N.Introvigne, M.L.Prati, F.Caselli, E.Power, P.van den Akker, F.Bonomo, R.A.

(2023) Antimicrob Agents Chemother 67: e0093022-e0093022

  • DOI: https://doi.org/10.1128/aac.00930-22
  • Primary Citation of Related Structures:  
    7UTB

  • PubMed Abstract: 

    Design of novel β-lactamase inhibitors (BLIs) is one of the currently accepted strategies to combat the threat of cephalosporin and carbapenem resistance in Gram-negative bacteria. B oronic a cid t ransition s tate i nhibitors (BATSIs) are competitive, reversible BLIs that offer promise as novel therapeutic agents. In this study, the activities of two α-amido-β-triazolylethaneboronic acid transition state inhibitors (S02030 and MB_076) targeting representative KPC (KPC-2) and CTX-M (CTX-M-96, a CTX-M-15-type extended-spectrum β-lactamase [ESBL]) β-lactamases were evaluated. The 50% inhibitory concentrations (IC 50 s) for both inhibitors were measured in the nanomolar range (2 to 135 nM). For S02030, the k 2 / K for CTX-M-96 (24,000 M -1 s -1 ) was twice the reported value for KPC-2 (12,000 M -1 s -1 ); for MB_076, the k 2 / K values ranged from 1,200 M -1 s -1 (KPC-2) to 3,900 M -1 s -1 (CTX-M-96). Crystal structures of KPC-2 with MB_076 (1.38-Å resolution) and S02030 and the in silico models of CTX-M-96 with these two BATSIs show that interaction in the CTX-M-96-S02030 and CTX-M-96-MB_076 complexes were overall equivalent to that observed for the crystallographic structure of KPC-2-S02030 and KPC-2-MB_076. The tetrahedral interaction surrounding the boron atom from S02030 and MB_076 creates a favorable hydrogen bonding network with S70, S130, N132, N170, and S237. However, the changes from W105 in KPC-2 to Y105 in CTX-M-96 and the missing residue R220 in CTX-M-96 alter the arrangement of the inhibitors in the active site of CTX-M-96, partially explaining the difference in kinetic parameters. The novel BATSI scaffolds studied here advance our understanding of structure-activity relationships (SARs) and illustrate the importance of new approaches to β-lactamase inhibitor design.


  • Organizational Affiliation

    Department of Biochemistry, Case Western Reserve University School of Medicine, Cleveland, Ohio, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Carbapenem-hydrolyzing beta-lactamase KPC266Klebsiella pneumoniaeMutation(s): 0 
Gene Names: blakpckpc1
EC: 3.5.2.6
UniProt
Find proteins for Q9F663 (Klebsiella pneumoniae)
Explore Q9F663 
Go to UniProtKB:  Q9F663
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9F663
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
OC0 (Subject of Investigation/LOI)
Query on OC0

Download Ideal Coordinates CCD File 
B [auth A][(1~{R})-1-[2-[(5-azanyl-1,3,4-thiadiazol-2-yl)sulfanyl]ethanoylamino]-2-(4-carboxy-1,2,3-triazol-1-yl)ethyl]-$l^{3}-oxidanyl-bis(oxidanyl)boron
C9 H13 B N7 O6 S2
QYCRGDXARHKIHF-YFKPBYRVSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.38 Å
  • R-Value Free: 0.170 
  • R-Value Work: 0.148 
  • R-Value Observed: 0.149 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 51.716α = 90
b = 66.673β = 90
c = 73.143γ = 90
Software Package:
Software NamePurpose
XDSdata reduction
Aimlessdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Not funded--

Revision History  (Full details and data files)

  • Version 1.0: 2022-12-14
    Type: Initial release
  • Version 1.1: 2023-01-18
    Changes: Database references
  • Version 1.2: 2023-02-08
    Changes: Database references
  • Version 1.3: 2023-10-25
    Changes: Data collection, Refinement description