7TI2 | pdb_00007ti2

Structure of KPC-2 bound to RPX-7063 at 1.75A

• PDB DOI: https://doi.org/10.2210/pdb7TI2/pdb

• Classification: HYDROLASE
• Organism(s): Klebsiella pneumoniae
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2022-01-12 Released: 2022-10-12 
• Deposition Author(s): Clifton, M.C., Fairman, J.W., Edwards, T.E., Hecker, S.J.
• Funding Organization(s): Other private

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.75 Å
• R-Value Free: 
  0.179 (Depositor), 0.161 (DCC) 
• R-Value Work: 
  0.157 (Depositor) 
• R-Value Observed: 
  0.158 (Depositor) 

Starting Model: experimental

Literature

Broad-spectrum cyclic boronate beta-lactamase inhibitors featuring an intramolecular prodrug for oral bioavailability.

Raja Reddy, K., Totrov, M., Lomovskaya, O., Griffith, D.C., Tarazi, Z., Clifton, M.C., Hecker, S.J.

(2022) Bioorg Med Chem 62: 116722-116722

• PubMed: 35358864 
• DOI: https://doi.org/10.1016/j.bmc.2022.116722
• Primary Citation Related Structures: 
  7TI0, 7TI1, 7TI2


• PubMed Abstract: 
  

  Early efforts to broaden the spectrum and potency of cyclic boronic acid β-lactamase inhibitor vaborbactam included a series of 7-membered ring boronates. Exploration of stereoisomers and incorporation of heteroatoms allowed identification of the all-carbon cyclic boronate with substituents trans as the preferred core structure, showing inhibition of Class A and C enzymes. Crystal structures of one analog bound to important β-lactamase enzymes were obtained. When isolated under acidic conditions, these compounds spontaneously formed a neutral cyclic anhydride (intramolecular prodrug) which was shown to have much-improved oral bioavailability (52-69%) compared to the ring-opened carboxylate salt (9%).

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Organizational Affiliation: 
• Qpex Biopharma, Inc, 6275 Nancy Ridge Dr., Suite 100, San Diego, CA 92121, United States.
Molsoft L.L.C, 11199 Sorrento Valley Road, San Diego, CA 92121, United States.
Beryllium Discovery, 3 Preston Court, Bedford, MA 01730, United States.
Qpex Biopharma, Inc, 6275 Nancy Ridge Dr., Suite 100, San Diego, CA 92121, United States. Electronic address: [e-mail].

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 30 kDa 
• Atom Count: 2,290 
• Modeled Residue Count: 262 
• Deposited Residue Count: 277 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Carbapenem-hydrolyzing beta-lactamase KPC	A	277	Klebsiella pneumoniae	Mutation(s): 0  Gene Names: bla, kpc, kpc1 EC: 3.5.2.6
UniProt
Find proteins for Q9F663 (Klebsiella pneumoniae) Explore Q9F663  Go to UniProtKB:  Q9F663

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ZXQ (Subject of Investigation/LOI)	B [auth A]	{(3R,7S)-2-hydroxy-3-[2-(thiophen-2-yl)acetamido]-2,3,4,7-tetrahydro-1,2-oxaborepin-7-yl}acetic acid C13 H16 B N O5 S JQVILEFLUQMOSI-KOLCDFICSA-N
EDO	C [auth A], D [auth A]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.75 Å
• R-Value Free:  0.179 (Depositor), 0.161 (DCC) 
• R-Value Work:  0.157 (Depositor) 
• R-Value Observed: 0.158 (Depositor) 

Space Group: P 4₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 80.1	α = 90
b = 80.1	β = 90
c = 44.76	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
PDB_EXTRACT	data extraction
XSCALE	data scaling
PHASER	phasing
XDS	data reduction

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2022-10-12 
Deposition Author(s): Clifton, M.C., Fairman, J.W., Edwards, T.E., Hecker, S.J.

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Funding Organization	Location	Grant Number
Other private		--

Revision History  

• Version 1.0: 2022-10-12
  Type: Initial release
  
• Version 1.1: 2023-10-18
  Changes: Data collection, Refinement description
• Version 1.2: 2024-10-30
  Changes: Structure summary