4NK3 | pdb_00004nk3

Amp-c beta-lactamase (pseudomonas aeruginosa) in complex with mk-7655

• PDB DOI: https://doi.org/10.2210/pdb4NK3/pdb

• Classification: HYDROLASE/HYDROLASE INHIBITOR
• Organism(s): Pseudomonas aeruginosa PAO1
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2013-11-12 Released: 2014-02-19 
• Deposition Author(s): Scapin, G., Lu, J., Fitzgerald, P.M.D., Sharma, N.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 
  0.213 (Depositor), 0.211 (DCC) 
• R-Value Work: 
  0.174 (Depositor), 0.172 (DCC) 
• R-Value Observed: 
  0.176 (Depositor) 

Literature

Discovery of MK-7655, a beta-lactamase inhibitor for combination with Primaxin().

Blizzard, T.A., Chen, H., Kim, S., Wu, J., Bodner, R., Gude, C., Imbriglio, J., Young, K., Park, Y.W., Ogawa, A., Raghoobar, S., Hairston, N., Painter, R.E., Wisniewski, D., Scapin, G., Fitzgerald, P., Sharma, N., Lu, J., Ha, S., Hermes, J., Hammond, M.L.

(2014) Bioorg Med Chem Lett 24: 780-785

• PubMed: 24433862 
• DOI: https://doi.org/10.1016/j.bmcl.2013.12.101
• Primary Citation Related Structures: 
  4NK3


• PubMed Abstract: 
  

  β-Lactamase inhibitors with a bicyclic urea core and a variety of heterocyclic side chains were prepared and evaluated as potential partners for combination with imipenem to overcome class A and C β-lactamase mediated antibiotic resistance. The piperidine analog 3 (MK-7655) inhibited both class A and C β-lactamases in vitro. It effectively restored imipenem's activity against imipenem-resistant Pseudomonas and Klebsiella strains at clinically achievable concentrations. A combination of MK-7655 and Primaxin® is currently in phase II clinical trials for the treatment of Gram-negative bacterial infections.

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Organizational Affiliation: 
• Department of Medicinal Chemistry, Merck Research Labs, Rahway, NJ 07065, USA. Electronic address: [e-mail].
Department of Medicinal Chemistry, Merck Research Labs, Rahway, NJ 07065, USA.
Department of Infectious Diseases, Merck Research Labs, Rahway, NJ 07065, USA.
Department of Medicinal Chemistry, Merck Research Labs, Rahway, NJ 07065, USA; Department of Infectious Diseases, Merck Research Labs, Rahway, NJ 07065, USA.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 41.37 kDa 
• Atom Count: 3,151 
• Modeled Residue Count: 361 
• Deposited Residue Count: 375 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Beta-lactamase	A	375	Pseudomonas aeruginosa PAO1	Mutation(s): 1  Gene Names: ampC, PA4110 EC: 3.5.2.6
UniProt
Find proteins for P24735 (Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1)) Explore P24735  Go to UniProtKB:  P24735

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
MK7	B [auth A]	(2S,5R)-1-formyl-N-(piperidin-4-yl)-5-[(sulfooxy)amino]piperidine-2-carboxamide C12 H22 N4 O6 S VGHMECNLFQGIJM-MNOVXSKESA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free:  0.213 (Depositor), 0.211 (DCC) 
• R-Value Work:  0.174 (Depositor), 0.172 (DCC) 
• R-Value Observed: 0.176 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 44.751	α = 90
b = 72.127	β = 90
c = 106.039	γ = 90

Software Package:

Software Name	Purpose
ADSC	data collection
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling
REFMAC	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2014-02-19 
Deposition Author(s): Scapin, G., Lu, J., Fitzgerald, P.M.D., Sharma, N.

Revision History  

• Version 1.0: 2014-02-19
  Type: Initial release
  
• Version 1.1: 2024-11-27
  Changes: Data collection, Database references, Derived calculations, Structure summary