3S1Y | pdb_00003s1y

AMP-C BETA-LACTAMASE (PSEUDOMONAS AERUGINOSA) in complex with a beta-lactamase inhibitor

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.40 Å
  • R-Value Free: 
    0.202 (Depositor), 0.222 (DCC) 
  • R-Value Work: 
    0.181 (Depositor), 0.203 (DCC) 
  • R-Value Observed: 
    0.182 (Depositor) 

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Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted S1YClick on this verticalbar to view details

This is version 1.3 of the entry. See complete history. 


Literature

Side chain SAR of bicyclic Beta-lactamase inhibitors (BLIs). 2. N-Alkylated and open chain analogs of MK-8712

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

(2011) Bioorg Med Chem Lett 21: 4267-4270

  • DOI: https://doi.org/10.1016/j.bmcl.2011.05.065
  • Primary Citation of Related Structures:  
    3S1Y, 3S22

  • PubMed Abstract: 

    The bridged monobactam β-lactamase inhibitor MK-8712 (1) effectively inhibits class C β-lactamases. Side chain N-alkylated and ring-opened analogs of 1 were prepared and evaluated for combination with imipenem to overcome class C β-lactamase mediated resistance. Although some analogs were more potent inhibitors of AmpC, none exhibited better synergy with imipenem than 1.

    • Organizational Affiliation: 

    Departments of Medicinal Chemistry, Merck Research Labs, Rahway, NJ 07065, USA. helen_chen@merck.com


Macromolecules
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Beta-lactamase371Pseudomonas aeruginosaMutation(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
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP24735
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.40 Å
  • R-Value Free:  0.202 (Depositor), 0.222 (DCC) 
  • R-Value Work:  0.181 (Depositor), 0.203 (DCC) 
  • R-Value Observed: 0.182 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 43.253α = 90
b = 69.696β = 90
c = 101.667γ = 90
Software Package:
Software NamePurpose
StructureStudiodata collection
MERLOTphasing
REFMACrefinement
X-GENdata reduction
X-GENdata scaling

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted S1YClick on this verticalbar to view details

View more in-depth experimental data
Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2011-06-29
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2013-06-26
    Changes: Database references
  • Version 1.3: 2024-10-30
    Changes: Data collection, Database references, Derived calculations, Structure summary