CTX-M-15 in complex with FPI-1602

Experimental Data Snapshot

  • Resolution: 2.70 Å
  • R-Value Free: 0.227 
  • R-Value Work: 0.187 
  • R-Value Observed: 0.189 

wwPDB Validation   3D Report Full Report

Ligand Structure Quality Assessment 

This is version 1.4 of the entry. See complete history


Structural and Kinetic Characterization of Diazabicyclooctanes as Dual Inhibitors of Both Serine-beta-Lactamases and Penicillin-Binding Proteins.

King, A.M.King, D.T.French, S.Brouillette, E.Asli, A.Alexander, J.A.Vuckovic, M.Maiti, S.N.Parr, T.R.Brown, E.D.Malouin, F.Strynadka, N.C.Wright, G.D.

(2016) ACS Chem Biol 11: 864-868

  • DOI: https://doi.org/10.1021/acschembio.5b00944
  • Primary Citation of Related Structures:  
    5FA7, 5FAO, 5FAP, 5FAQ, 5FAS, 5FAT, 5FGZ

  • PubMed Abstract: 

    Avibactam is a diazabicyclooctane β-lactamase inhibitor possessing outstanding but incomplete efficacy against multidrug-resistant Gram-negative pathogens in combination with β-lactam antibiotics. Significant pharmaceutical investment in generating derivatives of avibactam warrants a thorough characterization of their activity. We show here through structural and kinetic analysis that select diazabicyclooctane derivatives display effective but varied inhibition of two clinically important β-lactamases (CTX-M-15 and OXA-48). Furthermore, these derivatives exhibit considerable antimicrobial activity (MIC ≤ 2 μg/mL) against clinical isolates of Pseudomonas aeruginosa, Escherichia coli, and Enterobacter spp. Imaging of cell phenotype along with structural and biochemical experiments unambiguously demonstrate that this activity, in E. coli, is a result of targeting penicillin-binding protein 2. Our results suggest that structure-activity relationship studies for the purpose of drug discovery must consider both β-lactamases and penicillin-binding proteins as targets. We believe that this approach will yield next-generation combination or monotherapies with an expanded spectrum of activity against currently untreatable Gram-negative pathogens.

  • Organizational Affiliation

    The Department of Biochemistry and Molecular Biology and Centre for Blood Research, University of British Columbia . 2350 Health Sciences Mall, Vancouver, British Columbia V6T 1Z3, Canada.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Beta-lactamaseA [auth B],
B [auth A]
263Escherichia coliMutation(s): 0 
Gene Names: 
blaUOE-1blabla CTX-M-15bla_1bla_2bla_3blaCTX-M-15blaCTX-M15CTX-M-15ECONIH1_02760ECONIH1_27135ERS085368_04262ERS085370_01802ERS085377_05268ERS139214_01914ERS139238_04648ERS139238_04652ERS150880_04508HUS2011_pI0012pCTXM15_EC8_00003SK84_05077SK86_03319bla CTXM-15blaCTX-MA9X72_26855ACN68_29740AWP47_17965BANRA_05422BJI68_26810C2121_004650C2121_005381CO706_01125CY655_16075E3O05_17770E5P22_18740E5P33_09365E5P39_23850E5P41_23530E5P42_20460E5P43_23600E5P44_23710E5P45_23695E5P46_23480E5P47_23815E5P48_23485E5P49_23765E5P50_24275E5P51_02965EA435_19100EBP16_19885EBP16_24990ELT22_08720ELT25_03215ELT31_23875ELT40_25155ELT41_23005ELT44_26705ELT46_06805ELT48_21595ELT48_27155ELT49_23685ELT54_13870ELT60_26675ELT61_26075ELU83_06515ELU96_05460ELU97_00005ELV01_27290ELV02_26600ELV03_26255ELV04_25750ELV07_26450ELV11_23415ELV13_26970ELV16_12500ELV21_22135ELV23_26085ELX76_26235ELX76_27770ELX79_26345ELY36_26165EXX13_27820F0L67_27800F9B07_28185FEJ01_19840FEJ01_27020G3565_28475G5603_26845G9448_24215GQW07_24060GQW07_26690GRO95_23990GRO95_26745HL601_21620HL601_27220HMJ82_28240HMJ82_29040IH772_23850RCS105_pI0076RCS46_P0095RCS53_P0006RCS57_p0080RCS59_P0138RCS67_P0011SAMEA4363221_00081SAMEA4370330_00042SAMEA4370365_00031SAMEA4370386_00071SAMEA4370473_00021

Find proteins for Q9EXV5 (Escherichia coli)
Explore Q9EXV5 
Go to UniProtKB:  Q9EXV5
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9EXV5
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on 602

Download Ideal Coordinates CCD File 
C [auth B],
D [auth A]
[[(3~{R},6~{S})-6-[(azetidin-3-ylcarbonylamino)carbamoyl]-1-methanoyl-piperidin-3-yl]amino] hydrogen sulfate
C11 H19 N5 O7 S
Experimental Data & Validation

Experimental Data

  • Resolution: 2.70 Å
  • R-Value Free: 0.227 
  • R-Value Work: 0.187 
  • R-Value Observed: 0.189 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 63.12α = 90
b = 61.83β = 103.98
c = 73.07γ = 90
Software Package:
Software NamePurpose
xia2data reduction
Aimlessdata scaling

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment 

Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
Canadian Institutes of Health Research (CIHR)Canada--
Canadian Foundation for InnovationCanada--
Canada research Chair ProgramsCanada--
Howard Hughes Medical Institute (HHMI)United States--

Revision History  (Full details and data files)

  • Version 1.0: 2016-01-20
    Type: Initial release
  • Version 1.1: 2016-04-27
    Changes: Database references
  • Version 1.2: 2017-09-20
    Changes: Author supporting evidence, Derived calculations
  • Version 1.3: 2019-11-20
    Changes: Author supporting evidence
  • Version 1.4: 2023-09-27
    Changes: Data collection, Database references, Refinement description