6SP6 | pdb_00006sp6

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: 1.10 Å
  • R-Value Free: 
    0.121 (Depositor), 0.132 (DCC) 
  • R-Value Work: 
    0.102 (Depositor), 0.116 (DCC) 
  • R-Value Observed: 
    0.103 (Depositor) 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.3 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: 29.15 kDa 
  • Atom Count: 2,377 
  • Modeled Residue Count: 262 
  • Deposited Residue Count: 262 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Beta-lactamase262Escherichia coliMutation(s): 0 
Gene Names: blactx-m-15
EC: 3.5.2.6
UniProt
Find proteins for A0A223A5J4 (Escherichia coli)
Explore A0A223A5J4 
Go to UniProtKB:  A0A223A5J4
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A223A5J4
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
KJK
(Subject of Investigation/LOI)

Query on KJK



Download:Ideal Coordinates CCD File
G [auth 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
PGE

Query on PGE



Download:Ideal Coordinates CCD File
J [auth A]TRIETHYLENE GLYCOL
C6 H14 O4
ZIBGPFATKBEMQZ-UHFFFAOYSA-N
SO4

Query on SO4



Download:Ideal Coordinates CCD File
B [auth A],
C [auth A],
D [auth A],
E [auth A],
F [auth A]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
EDO

Query on EDO



Download:Ideal Coordinates CCD File
H [auth A],
I [auth A]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.10 Å
  • R-Value Free:  0.121 (Depositor), 0.132 (DCC) 
  • R-Value Work:  0.102 (Depositor), 0.116 (DCC) 
  • R-Value Observed: 0.103 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 44.558α = 90
b = 45.719β = 90
c = 117.219γ = 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, Refinement description
  • Version 1.3: 2024-10-16
    Changes: Structure summary