6FJ1 | pdb_00006fj1

Structure of the Ldtfm-avibactam carbamoyl enzyme


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.69 Å
  • R-Value Free: 
    0.228 (Depositor), 0.232 (DCC) 
  • R-Value Work: 
    0.197 (Depositor), 0.205 (DCC) 
  • R-Value Observed: 
    0.199 (Depositor) 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history

Literature

Synthesis of Avibactam Derivatives and Activity on beta-Lactamases and Peptidoglycan Biosynthesis Enzymes of Mycobacteria.

Edoo, Z.Iannazzo, L.Compain, F.Li de la Sierra Gallay, I.van Tilbeurgh, H.Fonvielle, M.Bouchet, F.Le Run, E.Mainardi, J.L.Arthur, M.Etheve-Quelquejeu, M.Hugonnet, J.E.

(2018) Chemistry 24: 8081-8086

  • DOI: https://doi.org/10.1002/chem.201800923
  • Primary Citation Related Structures: 
    6FJ1

  • PubMed Abstract: 

    There is a renewed interest for β-lactams for treating infections due to Mycobacterium tuberculosis and M. abscessus because their β-lactamases are inhibited by classical (clavulanate) or new generation (avibactam) inhibitors, respectively. Here, access to an azido derivative of the diazabicyclooctane (DBO) scaffold of avibactam for functionalization by the Huisgen-Sharpless cycloaddition reaction is reported. The amoxicillin-DBO combinations were active, indicating that the triazole ring is compatible with drug penetration (minimal inhibitory concentration of 16 μg mL -1 for both species). Mechanistically, β-lactamase inhibition was not sufficient to account for the potentiation of amoxicillin by DBOs. Thus, the latter compounds were investigated as inhibitors of l,d-transpeptidases (Ldts), which are the main peptidoglycan polymerases in mycobacteria. The DBOs acted as slow-binding inhibitors of Ldts by S-carbamoylation indicating that optimization of DBOs for Ldt inhibition is an attractive strategy to obtain drugs selectively active on mycobacteria.


  • Organizational Affiliation
    • Sorbonne Université, Sorbonne Paris Cité, Université Paris Descartes, Université Paris Diderot, INSERM, Centre de Recherche des Cordeliers, CRC, 75006, Paris, France.

Macromolecule Content 

  • Total Structure Weight: 88.75 kDa 
  • Atom Count: 6,192 
  • Modeled Residue Count: 759 
  • Deposited Residue Count: 774 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
L,D-TRANSPEPTIDASE
A, B, C
258Enterococcus faeciumMutation(s): 0 
Gene Names: CQR42_01530

Small Molecules

Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
NXL

Query on NXL



Download:Ideal Coordinates CCD File
E [auth A],
I [auth B],
O [auth C]
(2S,5R)-1-formyl-5-[(sulfooxy)amino]piperidine-2-carboxamide
C7 H13 N3 O6 S
WJDGWXPPFHLLNL-RITPCOANSA-N
P3G

Query on P3G



Download:Ideal Coordinates CCD File
D [auth A],
J [auth B],
P [auth C]
3,6,9,12,15-PENTAOXAHEPTADECANE
C12 H26 O5
HYDWALOBQJFOMS-UHFFFAOYSA-N
GOL

Query on GOL



Download:Ideal Coordinates CCD File
F [auth A]
G [auth A]
K [auth B]
L [auth B]
M [auth B]
F [auth A],
G [auth A],
K [auth B],
L [auth B],
M [auth B],
N [auth B],
Q [auth C],
R [auth C]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
CL

Query on CL



Download:Ideal Coordinates CCD File
H [auth A]CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.69 Å
  • R-Value Free:  0.228 (Depositor), 0.232 (DCC) 
  • R-Value Work:  0.197 (Depositor), 0.205 (DCC) 
  • R-Value Observed: 0.199 (Depositor) 
Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 208.54α = 90
b = 131.97β = 90.14
c = 70.09γ = 90
Software Package:
Software NamePurpose
XDSdata reduction
REFMACrefinement
PDB_EXTRACTdata extraction
XDSdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Fondation pour la recherche medicaleFranceECO20160736080
French National Research AgencyFranceANR-17-CE18-0010-03

Revision History  (Full details and data files)

  • Version 1.0: 2019-01-30
    Type: Initial release
  • Version 1.1: 2023-06-21
    Changes: Database references, Structure summary
  • Version 1.2: 2024-02-07
    Changes: Data collection, Refinement description
  • Version 1.3: 2024-10-23
    Changes: Structure summary