6V1J | pdb_00006v1j

Structure of KPC-2 bound to QPX7728 at 1.30 A


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.30 Å
  • R-Value Free: 
    0.180 (Depositor), 0.179 (DCC) 
  • R-Value Work: 
    0.144 (Depositor), 0.146 (DCC) 
  • R-Value Observed: 
    0.146 (Depositor) 

Starting Model: experimental
View more details

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.3 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.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Carbapenem-hydrolyzing beta-lactamase KPC290Klebsiella pneumoniaeMutation(s): 0 
Gene Names: blakpckpc1
EC: 3.5.2.6
UniProt
Find proteins for Q9F663 (Klebsiella pneumoniae)
Explore Q9F663 
Go to UniProtKB:  Q9F663
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9F663
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
QNA (Subject of Investigation/LOI)
Query on QNA

Download Ideal Coordinates CCD File 
C [auth A](1~{a}~{R},7~{b}~{S})-5-fluoranyl-2,2-bis(oxidanyl)-1~{a},7~{b}-dihydro-1~{H}-cyclopropa[c][1,2]benzoxaborinine-4-carboxylic acid
C10 H9 B F O5
RYSXSDTTWIWNFW-PHDIDXHHSA-N
RM9 (Subject of Investigation/LOI)
Query on RM9

Download Ideal Coordinates CCD File 
B [auth A](1aR,7bS)-5-fluoro-2-hydroxy-1,1a,2,7b-tetrahydrocyclopropa[c][1,2]benzoxaborinine-4-carboxylic acid
C10 H8 B F O4
KOHUFVUIYUCFNG-PHDIDXHHSA-N
SO4
Query on SO4

Download Ideal Coordinates CCD File 
E [auth A],
F [auth A]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
GOL
Query on GOL

Download Ideal Coordinates CCD File 
D [auth A]GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
Binding Affinity Annotations 
IDSourceBinding Affinity
RM9 BindingDB:  6V1J Ki: 1.9 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.30 Å
  • R-Value Free:  0.180 (Depositor), 0.179 (DCC) 
  • R-Value Work:  0.144 (Depositor), 0.146 (DCC) 
  • R-Value Observed: 0.146 (Depositor) 
Space Group: P 2 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 55.66α = 90
b = 59.99β = 90
c = 78.16γ = 90
Software Package:
Software NamePurpose
Aimlessdata scaling
PHASERphasing
PHENIXrefinement
PDB_EXTRACTdata extraction
iMOSFLMdata reduction

Structure Validation

View Full Validation Report



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
  • Version 1.3: 2024-11-06
    Changes: Structure summary