6SP7 | pdb_00006sp7

Crystal Structure of the VIM-2 Acquired Metallo-beta-Lactamase in Complex with Taniborbactam (VNRX-5133)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 
    0.244 (Depositor), 0.252 (DCC) 
  • R-Value Work: 
    0.189 (Depositor), 0.200 (DCC) 
  • R-Value Observed: 
    0.192 (Depositor) 

Starting Model: experimental
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This is version 1.2 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.

(2020) J Med Chem 63: 2789-2801

  • DOI: https://doi.org/10.1021/acs.jmedchem.9b01518
  • Primary Citation Related Structures: 
    6SP6, 6SP7

  • 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 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.


  • Organizational Affiliation
    • Venatorx Pharmaceuticals, Inc., 30 Spring Mill Drive, Malvern, Pennsylvania 19355, United States.

Macromolecule Content 

  • Total Structure Weight: 50.49 kDa 
  • Atom Count: 3,757 
  • Modeled Residue Count: 460 
  • Deposited Residue Count: 460 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Metallo-beta-lactamase VIM-2A,
B [auth E]
230Pseudomonas aeruginosaMutation(s): 0 
EC: 3.5.2.6
Membrane Entity: Yes 
UniProt
Find proteins for Q9K2N0 (Pseudomonas aeruginosa)
Explore Q9K2N0 
Go to UniProtKB:  Q9K2N0
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9K2N0
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
K9B
(Subject of Investigation/LOI)

Query on K9B



Download:Ideal Coordinates CCD File
H [auth A],
N [auth E]
(4~{R})-4-[2-[4-(2-azanylethylamino)cyclohexyl]ethanoylamino]-3,3-bis(oxidanyl)-2-oxa-3-boranuidabicyclo[4.4.0]deca-1(10),6,8-triene-10-carboxylic acid
C19 H29 B N3 O6
BZPCNLIYJBPHQK-NOLJZWGESA-N
ZN

Query on ZN



Download:Ideal Coordinates CCD File
C [auth A]
D [auth A]
E [auth A]
I [auth E]
J [auth E]
C [auth A],
D [auth A],
E [auth A],
I [auth E],
J [auth E],
K [auth E]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
ACT

Query on ACT



Download:Ideal Coordinates CCD File
F [auth A],
G [auth A],
L [auth E],
M [auth E]
ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free:  0.244 (Depositor), 0.252 (DCC) 
  • R-Value Work:  0.189 (Depositor), 0.200 (DCC) 
  • R-Value Observed: 0.192 (Depositor) 
Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 102.91α = 90
b = 79.04β = 130.5
c = 67.49γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing
PDB_EXTRACTdata extraction

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2020-01-22
    Type: Initial release
  • Version 1.1: 2020-04-08
    Changes: Database references
  • Version 1.2: 2024-01-24
    Changes: Data collection, Database references, Derived calculations, Refinement description