6V1M | pdb_00006v1m

Structure of NDM-1 bound to QPX7728 at 1.05 A


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.05 Å
  • R-Value Free: 
    0.158 (Depositor), 0.155 (DCC) 
  • R-Value Work: 
    0.141 (Depositor), 0.141 (DCC) 
  • R-Value Observed: 
    0.142 (Depositor) 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history

Literature

Discovery of Cyclic Boronic Acid QPX7728, an Ultrabroad-Spectrum Inhibitor of Serine and Metallo-beta-lactamases.

Hecker, S.J.Reddy, K.R.Lomovskaya, O.Griffith, D.C.Rubio-Aparicio, D.Nelson, K.Tsivkovski, R.Sun, D.Sabet, M.Tarazi, Z.Parkinson, J.Totrov, M.Boyer, S.H.Glinka, T.W.Pemberton, O.A.Chen, Y.Dudley, M.N.

(2020) J Med Chem 63: 7491-7507

  • DOI: https://doi.org/10.1021/acs.jmedchem.9b01976
  • Primary Citation Related Structures: 
    6V1J, 6V1M, 6V1O, 6V1P

  • PubMed Abstract: 

    Despite major advances in the β-lactamase inhibitor field, certain enzymes remain refractory to inhibition by agents recently introduced. Most important among these are the class B (metallo) enzyme NDM-1 of Enterobacteriaceae and the class D (OXA) enzymes of Acinetobacter baumannii . Continuing the boronic acid program that led to vaborbactam, efforts were directed toward expanding the spectrum to allow treatment of a wider range of organisms. Through key structural modifications of a bicyclic lead, stepwise gains in spectrum of inhibition were achieved, ultimately resulting in QPX7728 ( 35 ). This compound displays a remarkably broad spectrum of inhibition, including class B and class D enzymes, and is little affected by porin modifications and efflux. Compound 35 is a promising agent for use in combination with a β-lactam antibiotic for the treatment of a wide range of multidrug resistant Gram-negative bacterial infections, by both intravenous and oral administration.


  • Organizational Affiliation
    • Qpex Biopharma, Inc., 6275 Nancy Ridge Drive, Suite 100, San Diego, California 92121, United States.

Macromolecule Content 

  • Total Structure Weight: 24.97 kDa 
  • Atom Count: 2,114 
  • Modeled Residue Count: 229 
  • Deposited Residue Count: 233 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Metallo-beta-lactamase type 2233Klebsiella 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

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.05 Å
  • R-Value Free:  0.158 (Depositor), 0.155 (DCC) 
  • R-Value Work:  0.141 (Depositor), 0.141 (DCC) 
  • R-Value Observed: 0.142 (Depositor) 
Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 41.4α = 90
b = 60.24β = 98.46
c = 42.06γ = 90
Software Package:
Software NamePurpose
Aimlessdata scaling
PHASERphasing
PHENIXrefinement
PDB_EXTRACTdata extraction
iMOSFLMdata reduction

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Department of Health & Human Services (HHS)United StatesHHSO100201600026C

Revision History  (Full details and data files)

  • Version 1.0: 2020-03-25
    Type: Initial release
  • Version 1.1: 2020-08-05
    Changes: Database references
  • Version 1.2: 2023-10-11
    Changes: Data collection, Database references, Refinement description