4NK3

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.213 
  • R-Value Work: 0.174 
  • R-Value Observed: 0.176 

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Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


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

  • DOI: https://doi.org/10.1016/j.bmcl.2013.12.101
  • Primary Citation of 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.


  • Organizational Affiliation

    Department of Medicinal Chemistry, Merck Research Labs, Rahway, NJ 07065, USA. Electronic address: [email protected].


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Beta-lactamase375Pseudomonas aeruginosa PAO1Mutation(s): 1 
Gene Names: ampCPA4110
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
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP24735
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
MK7
Query on MK7

Download Ideal Coordinates CCD File 
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 
  • R-Value Work: 0.174 
  • R-Value Observed: 0.176 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 44.751α = 90
b = 72.127β = 90
c = 106.039γ = 90
Software Package:
Software NamePurpose
ADSCdata collection
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling
REFMACphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

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