5A5Z | pdb_00005a5z

Approved Drugs Containing Thiols as Inhibitors of Metallo-beta- lactamases: Strategy To Combat Multidrug-Resistant Bacteria

• PDB DOI: https://doi.org/10.2210/pdb5A5Z/pdb

• Classification: HYDROLASE
• Organism(s): Klebsiella pneumoniae
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2015-06-23 Released: 2015-07-08 
• Deposition Author(s): Klingler, F.M., Wichelhaus, T.A., Frank, D., Cuesta-Bernal, J., El-Delik, J., Mueller, H.F., Sjuts, H., Goettig, S., Koenigs, A., Pogoryelov, D., Proschak, E.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.60 Å
• R-Value Free: 
  0.252 (Depositor), 0.260 (DCC) 
• R-Value Work: 
  0.208 (Depositor), 0.210 (DCC) 
• R-Value Observed: 
  0.210 (Depositor) 

Starting Model: experimental

Re-refinement Note

A newer entry is available that reflects an alternative modeling of the original data: 5NBK

Literature

Approved Drugs Containing Thiols as Inhibitors of Metallo-beta-lactamases: Strategy To Combat Multidrug-Resistant Bacteria.

Klingler, F.M., Wichelhaus, T.A., Frank, D., Cuesta-Bernal, J., El-Delik, J., Muller, H.F., Sjuts, H., Gottig, S., Koenigs, A., Pos, K.M., Pogoryelov, D., Proschak, E.

(2015) J Med Chem 58: 3626-3630

• PubMed: 25815530 
• DOI: https://doi.org/10.1021/jm501844d
• Primary Citation of Related Structures:  
  5A5Z


• PubMed Abstract: 
  

  Resistance to β-lactam antibiotics can be mediated by metallo-β-lactamase enzymes (MBLs). An MBL inhibitor could restore the effectiveness of β-lactams. We report on the evaluation of approved thiol-containing drugs as inhibitors of NDM-1, VIM-1, and IMP-7. Drugs were assessed by a novel assay using a purchasable fluorescent substrate and thermal shift. Best compounds were tested in antimicrobial susceptibility assay. Using these orthogonal screening methods, we identified drugs that restored the activity of imipenem.

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Organizational Affiliation: 

§Institute of Medical Microbiology and Infection Control, Paul-Ehrlich-Straße 40, 60596 Frankfurt, Germany.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 generated by PISA (software)

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 54.26 kDa 
• Atom Count: 3,614 
• Modelled Residue Count: 472 
• Deposited Residue Count: 502 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
BETA-LACTAMASE NDM-1	A, B [auth C]	251	Klebsiella pneumoniae	Mutation(s): 0  EC: 3.5.2.6
UniProt
Find proteins for C7C422 (Klebsiella pneumoniae) Explore C7C422  Go to UniProtKB:  C7C422

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
WJZ	E [auth A], H [auth C]	TIOPRONIN C5 H9 N O3 S YTGJWQPHMWSCST-VKHMYHEASA-N
ZN	C [auth A], D [auth A], F [auth C], G [auth C]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.60 Å
• R-Value Free:  0.252 (Depositor), 0.260 (DCC) 
• R-Value Work:  0.208 (Depositor), 0.210 (DCC) 
• R-Value Observed: 0.210 (Depositor) 

Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 108.047	α = 90
b = 108.047	β = 90
c = 92.571	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XSCALE	data scaling
PHENIX	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2015-07-08 
Deposition Author(s): Klingler, F.M., Wichelhaus, T.A., Frank, D., Cuesta-Bernal, J., El-Delik, J., Mueller, H.F., Sjuts, H., Goettig, S., Koenigs, A., Pogoryelov, D., Proschak, E.

Revision History  

• Version 1.0: 2015-07-08
  Type: Initial release
  
• Version 1.1: 2019-02-27
  Changes: Data collection, Database references, Experimental preparation, Other
• Version 1.2: 2024-01-10
  Changes: Data collection, Database references, Derived calculations, Other, Refinement description