6SP6

Ultra-high Resolution Crystal Structure of the CTX-M-15 Extended-Spectrum beta-Lactamase in Complex with Taniborbactam (VNRX-5133)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.1 Å
  • R-Value Free: 0.121 
  • R-Value Work: 0.102 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

Discovery of Taniborbactam (VNRX-5133): A Broad-Spectrum Serine- and Metallo-beta-lactamase Inhibitor for Carbapenem-Resistant Bacterial Infections.

Liu, B.Trout, R.E.L.Chu, G.H.McGarry, D.Jackson, R.W.Hamrick, J.C.Daigle, D.M.Cusick, S.M.Pozzi, C.De Luca, F.Benvenuti, M.Mangani, S.Docquier, J.D.Weiss, W.J.Pevear, D.C.Xerri, L.Burns, C.J.

(2019) J. Med. Chem. --: --

  • DOI: 10.1021/acs.jmedchem.9b01518
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • A major resistance mechanism in Gram-negative bacteria is the production of β-lactamase enzymes. Originally recognized for their ability to hydrolyze penicillins, emergent β-lactamases can now confer resistance to other β-lactam drugs, including both ...

    A major resistance mechanism in Gram-negative bacteria is the production of β-lactamase enzymes. Originally recognized for their ability to hydrolyze penicillins, emergent β-lactamases can now confer resistance to other β-lactam drugs, including both cephalosporins and carbapenems. The emergence and global spread of β-lactamase-producing multi-drug-resistant "superbugs" has caused increased alarm within the medical community due to the high mortality rate associated with these difficult-to-treat bacterial infections. To address this unmet medical need, we initiated an iterative program combining medicinal chemistry, structural biology, biochemical testing, and microbiological profiling to identify broad-spectrum inhibitors of both serine- and metallo-β-lactamase enzymes. Lead optimization, beginning with narrower-spectrum, weakly active compounds, provided 20 (VNRX-5133, taniborbactam), a boronic-acid-containing pan-spectrum β-lactamase inhibitor. In vitro and in vivo studies demonstrated that 20 restored the activity of β-lactam antibiotics against carbapenem-resistant Pseudomonas aeruginosa and carbapenem-resistant Enterobacteriaceae. Taniborbactam is the first pan-spectrum β-lactamase inhibitor to enter clinical development.


    Related Citations: 
    • VNRX-5133 (Taniborbactam), a broad-spectrum inhibitor of serine- and metallo-beta-lactamases, restores activity of cefepime in Enterobacterales and Pseudomonas aeruginosa.
      Hamrick, J.C.,Docquier, J.D.,Uehara, T.,Myers, C.L.,Six, D.A.,Chatwin, C.L.,John, K.J.,Vernacchio, S.F.,Cusick, S.M.,Trout, R.E.L.,Pozzi, C.,De Luca, F.,Benvenuti, M.,Mangani, S.,Liu, B.,Jackson, R.W.,Moeck, G.,Xerri, L.,Burns, C.J.,Pevear, D.C.,Daigle, D.M.
      (2019) Antimicrob. Agents Chemother. --: --


    Organizational Affiliation

    Department of Biotechnology, Chemistry and Pharmacy , University of Siena , I-53100 Siena , Italy.,Venatorx Pharmaceuticals, Inc. , 30 Spring Mill Drive , Malvern , Pennsylvania 19355 , United States.,Department of Medical Biotechnology , University of Siena , I-53100 Siena , Italy.,UNT System College of Pharmacy , University of North Texas Health Science Center , 3500 Camp Bowie Boulevard , Fort Worth , Texas 76107-2699 , United States.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Beta-lactamase
A
262Escherichia coliMutation(s): 0 
Gene Names: blactx-m-15
EC: 3.5.2.6
Find proteins for A0A223A5J4 (Escherichia coli)
Go to UniProtKB:  A0A223A5J4
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
KJK
Query on KJK

Download SDF File 
Download CCD File 
A
(3~{R})-3-[2-[4-(2-azanylethylamino)cyclohexyl]ethanoylamino]-2-oxidanyl-3,4-dihydro-1,2-benzoxaborinine-8-carboxylic acid
C19 H28 B N3 O5
PFZUWUXKQPRWAL-NOLJZWGESA-N
 Ligand Interaction
SO4
Query on SO4

Download SDF File 
Download CCD File 
A
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
EDO
Query on EDO

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Download CCD File 
A
1,2-ETHANEDIOL
ETHYLENE GLYCOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
PGE
Query on PGE

Download SDF File 
Download CCD File 
A
TRIETHYLENE GLYCOL
C6 H14 O4
ZIBGPFATKBEMQZ-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.1 Å
  • R-Value Free: 0.121 
  • R-Value Work: 0.102 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 44.558α = 90.00
b = 45.719β = 90.00
c = 117.219γ = 90.00
Software Package:
Software NamePurpose
MOLREPphasing
MOSFLMdata reduction
PDB_EXTRACTdata extraction
REFMACrefinement
SCALAdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2020-01-22
    Type: Initial release