4XUX

Structure of ampC bound to RPX-7009 at 1.75 A


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.75 Å
  • R-Value Free: 0.186 
  • R-Value Work: 0.154 
  • R-Value Observed: 0.156 

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Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


Literature

Discovery of a Cyclic Boronic Acid beta-Lactamase Inhibitor (RPX7009) with Utility vs Class A Serine Carbapenemases.

Hecker, S.J.Reddy, K.R.Totrov, M.Hirst, G.C.Lomovskaya, O.Griffith, D.C.King, P.Tsivkovski, R.Sun, D.Sabet, M.Tarazi, Z.Clifton, M.C.Atkins, K.Raymond, A.Potts, K.T.Abendroth, J.Boyer, S.H.Loutit, J.S.Morgan, E.E.Durso, S.Dudley, M.N.

(2015) J Med Chem 58: 3682-3692

  • DOI: 10.1021/acs.jmedchem.5b00127
  • Primary Citation of Related Structures:  
    4XUZ, 4XUX

  • PubMed Abstract: 
  • The increasing dissemination of carbapenemases in Gram-negative bacteria has threatened the clinical usefulness of the β-lactam class of antimicrobials. A program was initiated to discover a new series of serine β-lactamase inhibitors containing a boronic acid pharmacophore, with the goal of finding a potent inhibitor of serine carbapenemase enzymes that are currently compromising the utility of the carbapenem class of antibacterials ...

    The increasing dissemination of carbapenemases in Gram-negative bacteria has threatened the clinical usefulness of the β-lactam class of antimicrobials. A program was initiated to discover a new series of serine β-lactamase inhibitors containing a boronic acid pharmacophore, with the goal of finding a potent inhibitor of serine carbapenemase enzymes that are currently compromising the utility of the carbapenem class of antibacterials. Potential lead structures were screened in silico by modeling into the active sites of key serine β-lactamases. Promising candidate molecules were synthesized and evaluated in biochemical and whole-cell assays. Inhibitors were identified with potent inhibition of serine carbapenemases, particularly the Klebsiella pneumoniae carbapenemase (KPC), with no inhibition of mammalian serine proteases. Studies in vitro and in vivo show that RPX7009 (9f) is a broad-spectrum inhibitor, notably restoring the activity of carbapenems against KPC-producing strains. Combined with a carbapenem, 9f is a promising product for the treatment of multidrug resistant Gram-negative bacteria.


    Organizational Affiliation

    †Rempex Pharmaceuticals, Inc., A Subsidiary of The Medicines Company, 3033 Science Park Rd., Suite 200, San Diego, California 92121, United States.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Beta-lactamaseA363Enterobacter cloacaeMutation(s): 0 
Gene Names: ampC
EC: 3.5.2.6
UniProt
Find proteins for P05364 (Enterobacter cloacae)
Explore P05364 
Go to UniProtKB:  P05364
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
4D6 (Subject of Investigation/LOI)
Query on 4D6

Download Ideal Coordinates CCD File 
B [auth A]Vaborbactam
C12 H16 B N O5 S
IOOWNWLVCOUUEX-WPRPVWTQSA-N
 Ligand Interaction
PG0
Query on PG0

Download Ideal Coordinates CCD File 
E [auth A]2-(2-METHOXYETHOXY)ETHANOL
C5 H12 O3
SBASXUCJHJRPEV-UHFFFAOYSA-N
 Ligand Interaction
EDO
Query on EDO

Download Ideal Coordinates CCD File 
C [auth A], D [auth A]1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.75 Å
  • R-Value Free: 0.186 
  • R-Value Work: 0.154 
  • R-Value Observed: 0.156 
  • Space Group: P 2 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 62.56α = 90
b = 69.6β = 90
c = 76.33γ = 90
Software Package:
Software NamePurpose
XDSdata reduction
PHASERphasing
REFMACrefinement
PDB_EXTRACTdata extraction
XSCALEdata scaling
Cootmodel building

Structure Validation

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Ligand Structure Quality Assessment  



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2015-04-01
    Type: Initial release
  • Version 1.1: 2015-05-27
    Changes: Database references