8B1W | pdb_00008b1w

NDM-1 metallo-beta-lactamase in complex with triazole-based inhibitor CP35


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free: 
    0.222 (Depositor), 0.222 (DCC) 
  • R-Value Work: 
    0.192 (Depositor), 0.192 (DCC) 
  • R-Value Observed: 
    0.193 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history

Literature

Structure-Based Optimization of 1,2,4-Triazole-3-Thione Derivatives: Improving Inhibition of NDM-/VIM-Type Metallo-beta-Lactamases and Synergistic Activity on Resistant Bacteria.

Bersani, M.Failla, M.Vascon, F.Gianquinto, E.Bertarini, L.Baroni, M.Cruciani, G.Verdirosa, F.Sannio, F.Docquier, J.D.Cendron, L.Spyrakis, F.Lazzarato, L.Tondi, D.

(2023) Pharmaceuticals (Basel) 16

  • DOI: https://doi.org/10.3390/ph16121682
  • Primary Citation Related Structures: 
    8B1W, 8B1Z, 8B20

  • PubMed Abstract: 

    The worldwide emergence and dissemination of Gram-negative bacteria expressing metallo-β-lactamases (MBLs) menace the efficacy of all β-lactam antibiotics, including carbapenems, a last-line treatment usually restricted to severe pneumonia and urinary tract infections. Nonetheless, no MBL inhibitor is yet available in therapy. We previously identified a series of 1,2,4-triazole-3-thione derivatives acting as micromolar inhibitors of MBLs in vitro, but devoid of synergistic activity in microbiological assays. Here, via a multidisciplinary approach, including molecular modelling, synthesis, enzymology, microbiology, and X-ray crystallography, we optimized this series of compounds and identified low micromolar inhibitors active against clinically relevant MBLs (NDM-1- and VIM-type). The best inhibitors increased, to a certain extent, the susceptibility of NDM-1- and VIM-4-producing clinical isolates to meropenem. X-ray structures of three selected inhibitors in complex with NDM-1 elucidated molecular recognition at the base of potency improvement, confirmed in silico predicted orientation, and will guide further development steps.


  • Organizational Affiliation
    • Department of Drug Science and Technology, University of Turin, Via Pietro Giuria 9, 10125 Turin, Italy.

Macromolecule Content 

  • Total Structure Weight: 52.81 kDa 
  • Atom Count: 3,668 
  • Modeled Residue Count: 462 
  • Deposited Residue Count: 484 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Beta-lactamase NDM-1
A, B
242Pseudomonas aeruginosaMutation(s): 0 
Gene Names: blaNDM-1blaNDM1E5D53_33975
EC: 3.5.2.6
UniProt
Find proteins for F6IAY7 (Pseudomonas aeruginosa)
Explore F6IAY7 
Go to UniProtKB:  F6IAY7
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupF6IAY7
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 5 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
OQU
(Subject of Investigation/LOI)

Query on OQU



Download:Ideal Coordinates CCD File
G [auth A],
M [auth B]
4-[(~{E})-(3-bromophenyl)methylideneamino]-5-(trifluoromethyl)-1,2,4-triazole-3-thiol
C10 H6 Br F3 N4 S
VLJIPDZUVTZJIE-PJQLUOCWSA-N
EPE

Query on EPE



Download:Ideal Coordinates CCD File
N [auth B]4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID
C8 H18 N2 O4 S
JKMHFZQWWAIEOD-UHFFFAOYSA-N
ZN

Query on ZN



Download:Ideal Coordinates CCD File
C [auth A],
D [auth A],
I [auth B],
J [auth B]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
EDO

Query on EDO



Download:Ideal Coordinates CCD File
H [auth A],
O [auth B],
P [auth B]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
CA

Query on CA



Download:Ideal Coordinates CCD File
E [auth A],
F [auth A],
K [auth B],
L [auth B]
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free:  0.222 (Depositor), 0.222 (DCC) 
  • R-Value Work:  0.192 (Depositor), 0.192 (DCC) 
  • R-Value Observed: 0.193 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 70.19α = 90
b = 73.699β = 90
c = 77.28γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
Aimlessdata scaling
MOLREPphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Italian Ministry of EducationItaly--

Revision History  (Full details and data files)

  • Version 1.0: 2023-12-27
    Type: Initial release
  • Version 1.1: 2024-03-20
    Changes: Database references
  • Version 1.2: 2026-03-04
    Changes: Refinement description, Structure summary