8R5T | pdb_00008r5t

Crystal structure of NDM-1 in complex with benzobisheterocycle compound 14.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.58 Å
  • R-Value Free: 
    0.213 (Depositor), 0.213 (DCC) 
  • R-Value Work: 
    0.169 (Depositor), 0.169 (DCC) 
  • R-Value Observed: 
    0.171 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 8R5T

Ligand Structure Quality Assessment 


This is version 1.0 of the entry. See complete history

Literature

Rational Design of Benzobisheterocycle Metallo-beta-Lactamase Inhibitors: A Tricyclic Scaffold Enhances Potency against Target Enzymes.

Villamil, V.Rossi, M.A.Mojica, M.F.Hinchliffe, P.Martinez, V.Castillo, V.Saiz, C.Banchio, C.Macias, M.A.Spencer, J.Bonomo, R.A.Vila, A.Moreno, D.M.Mahler, G.

(2024) J Med Chem 67: 3795-3812

  • DOI: https://doi.org/10.1021/acs.jmedchem.3c02209
  • Primary Citation Related Structures: 
    8R5T, 8R5U

  • PubMed Abstract: 

    Antimicrobial resistance is a global public health threat. Metallo-β-lactamases (MBLs) inactivate β-lactam antibiotics, including carbapenems, are disseminating among Gram-negative bacteria, and lack clinically useful inhibitors. The evolving bisthiazolidine (BTZ) scaffold inhibits all three MBL subclasses (B1-B3). We report design, synthesis, and evaluation of BTZ analogues. Structure-activity relationships identified the BTZ thiol as essential, while carboxylate is replaceable, with its removal enhancing potency by facilitating hydrophobic interactions within the MBL active site. While the introduction of a flexible aromatic ring is neutral or detrimental for inhibition, a rigid (fused) ring generated nM benzobisheterocycle (BBH) inhibitors that potentiated carbapenems against MBL-producing strains. Crystallography of BBH:MBL complexes identified hydrophobic interactions as the basis of potency toward B1 MBLs. These data underscore BTZs as versatile, potent broad-spectrum MBL inhibitors (with activity extending to enzymes refractory to other inhibitors) and provide a rational approach to further improve the tricyclic BBH scaffold.


  • Organizational Affiliation
    • Laboratorio de Química Farmacéutica, Departamento de Química Orgánica, Facultad de Química, Universidad de la República (UdelaR), Avda. General Flores, 2124 Montevideo, Uruguay.

Macromolecule Content 

  • Total Structure Weight: 52.23 kDa 
  • Atom Count: 3,786 
  • Modeled Residue Count: 451 
  • Deposited Residue Count: 488 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Metallo-beta-lactamase type 2
A, B
244Klebsiella pneumoniaeMutation(s): 0 
Gene Names: blaNDM-1
EC: 3.5.2.6
UniProt
Find proteins for C7C422 (Klebsiella pneumoniae)
Explore C7C422 
Go to UniProtKB:  C7C422
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupC7C422
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Y4E
(Subject of Investigation/LOI)

Query on Y4E



Download:Ideal Coordinates CCD File
C [auth A][(1~{R},3~{a}~{R})-1,3,3~{a},4-tetrahydro-[1,3]thiazolo[3,4-a]benzimidazol-1-yl]methanethiol
C10 H12 N2 S2
PBXWHODMWKJRIF-NXEZZACHSA-N
SO4

Query on SO4



Download:Ideal Coordinates CCD File
F [auth A],
G [auth A]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
ZN

Query on ZN



Download:Ideal Coordinates CCD File
D [auth A],
E [auth A],
H [auth B],
I [auth B]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
Binding Affinity Annotations 
IDSourceBinding Affinity
Y4E BindingDB:  8R5T IC50: 770 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.58 Å
  • R-Value Free:  0.213 (Depositor), 0.213 (DCC) 
  • R-Value Work:  0.169 (Depositor), 0.169 (DCC) 
  • R-Value Observed: 0.171 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 70.1α = 90
b = 73.768β = 90
c = 77.647γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
PDB_EXTRACTdata extraction
xia2data reduction
Aimlessdata scaling

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)United StatesR01AI100560

Revision History  (Full details and data files)

  • Version 1.0: 2024-04-10
    Type: Initial release