7AFZ

L1 metallo-b-lactamase with compound EBL-1306


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.50 Å
  • R-Value Free: 0.168 
  • R-Value Work: 0.152 
  • R-Value Observed: 0.153 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history


Literature

Imitation of beta-lactam binding enables broad-spectrum metallo-beta-lactamase inhibitors.

Brem, J.Panduwawala, T.Hansen, J.U.Hewitt, J.Liepins, E.Donets, P.Espina, L.Farley, A.J.M.Shubin, K.Campillos, G.G.Kiuru, P.Shishodia, S.Krahn, D.Lesniak, R.K.Schmidt Adrian, J.Calvopina, K.Turrientes, M.C.Kavanagh, M.E.Lubriks, D.Hinchliffe, P.Langley, G.W.Aboklaish, A.F.Eneroth, A.Backlund, M.Baran, A.G.Nielsen, E.I.Speake, M.Kuka, J.Robinson, J.Grinberga, S.Robinson, L.McDonough, M.A.Rydzik, A.M.Leissing, T.M.Jimenez-Castellanos, J.C.Avison, M.B.Da Silva Pinto, S.Pannifer, A.D.Martjuga, M.Widlake, E.Priede, M.Hopkins Navratilova, I.Gniadkowski, M.Belfrage, A.K.Brandt, P.Yli-Kauhaluoma, J.Bacque, E.Page, M.G.P.Bjorkling, F.Tyrrell, J.M.Spencer, J.Lang, P.A.Baranczewski, P.Canton, R.McElroy, S.P.Jones, P.S.Baquero, F.Suna, E.Morrison, A.Walsh, T.R.Schofield, C.J.

(2022) Nat Chem 14: 15-24

  • DOI: https://doi.org/10.1038/s41557-021-00831-x
  • Primary Citation of Related Structures:  
    7AFZ

  • PubMed Abstract: 

    Carbapenems are vital antibiotics, but their efficacy is increasingly compromised by metallo-β-lactamases (MBLs). Here we report the discovery and optimization of potent broad-spectrum MBL inhibitors. A high-throughput screen for NDM-1 inhibitors identified indole-2-carboxylates (InCs) as potential β-lactamase stable β-lactam mimics. Subsequent structure-activity relationship studies revealed InCs as a new class of potent MBL inhibitor, active against all MBL classes of major clinical relevance. Crystallographic studies revealed a binding mode of the InCs to MBLs that, in some regards, mimics that predicted for intact carbapenems, including with respect to maintenance of the Zn(II)-bound hydroxyl, and in other regards mimics binding observed in MBL-carbapenem product complexes. InCs restore carbapenem activity against multiple drug-resistant Gram-negative bacteria and have a low frequency of resistance. InCs also have a good in vivo safety profile, and when combined with meropenem show a strong in vivo efficacy in peritonitis and thigh mouse infection models.


  • Organizational Affiliation

    Department of Chemistry, Chemistry Research Laboratory and the Ineos Oxford Institute for Antimicrobial Research, University of Oxford, Oxford, UK. jurgen.brem@chem.ox.ac.uk.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Metallo-beta-lactamase L1271Stenotrophomonas maltophiliaMutation(s): 0 
EC: 3.5.2.6
UniProt
Find proteins for P52700 (Stenotrophomonas maltophilia)
Explore P52700 
Go to UniProtKB:  P52700
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP52700
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.50 Å
  • R-Value Free: 0.168 
  • R-Value Work: 0.152 
  • R-Value Observed: 0.153 
  • Space Group: P 64 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 104.78α = 90
b = 104.78β = 90
c = 98.11γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
PDB_EXTRACTdata extraction
MOSFLMdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Innovative Medicines InitiativeUnited KingdomENABLE

Revision History  (Full details and data files)

  • Version 1.0: 2021-10-06
    Type: Initial release
  • Version 1.1: 2021-12-22
    Changes: Data collection, Database references
  • Version 1.2: 2022-01-26
    Changes: Database references
  • Version 1.3: 2024-01-31
    Changes: Data collection, Refinement description