4X69

Crystal structure of OP0595 complexed with CTX-M-44

• PDB DOI: https://doi.org/10.2210/pdb4X69/pdb

• Classification: HYDROLASE/HYDROLASE INHIBITOR
• Organism(s): Escherichia coli
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2014-12-07 Released: 2015-07-01 
• Deposition Author(s): Yamada, M., Watanabe, T.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.42 Å
• R-Value Free: 0.208 
• R-Value Work: 0.183 
• R-Value Observed: 0.185 

Literature

OP0595, a new diazabicyclooctane: mode of action as a serine beta-lactamase inhibitor, antibiotic and beta-lactam 'enhancer'

Morinaka, A., Tsutsumi, Y., Yamada, M., Suzuki, K., Watanabe, T., Abe, T., Furuuchi, T., Inamura, S., Sakamaki, Y., Mitsuhashi, N., Ida, T., Livermore, D.M.

(2015) J Antimicrob Chemother 70: 2779-2786

• PubMed: 26089439 
• DOI: https://doi.org/10.1093/jac/dkv166
• Primary Citation of Related Structures:  
  4X68, 4X69


• PubMed Abstract: 
  

  The production of a growing diversity of β-lactamases by Gram-negative bacteria challenges antimicrobial chemotherapy. OP0595, discovered separately by each of Meiji Seika Pharma and Fedora Pharmaceuticals, is a new diazabicyclooctane serine β-lactamase inhibitor that also acts as an antibiotic and as a β-lactamase-independent β-lactam 'enhancer'.

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Organizational Affiliation: 

Meiji Seika Pharma Co., Ltd, Yokohama, Japan [e-mail].

Biological Assembly 1  

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

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly 2  

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

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 57.27 kDa 
• Atom Count: 4,391 
• Modelled Residue Count: 522 
• Deposited Residue Count: 524 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Beta-lactamase Toho-1	A, B	262	Escherichia coli	Mutation(s): 1  Gene Names: bla EC: 3.5.2.6
UniProt
Find proteins for Q47066 (Escherichia coli) Explore Q47066  Go to UniProtKB:  Q47066

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
OP0	C [auth A], E [auth B]	(2S,5R)-N-(2-aminoethoxy)-1-formyl-5-[(sulfooxy)amino]piperidine-2-carboxamide C9 H18 N4 O7 S YTAWXXHGLPATIN-SFYZADRCSA-N
EDO	D [auth A], F [auth B]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.42 Å
• R-Value Free: 0.208 
• R-Value Work: 0.183 
• R-Value Observed: 0.185 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 51.533	α = 90
b = 72.982	β = 109.29
c = 63.052	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data reduction
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-2000	data scaling
MOLREP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2015-07-01 
Deposition Author(s): Yamada, M., Watanabe, T.

Revision History  

• Version 1.0: 2015-07-01
  Type: Initial release
  
• Version 1.1: 2015-07-15
  Changes: Derived calculations
• Version 1.2: 2015-10-14
  Changes: Database references
• Version 1.3: 2020-02-05
  Changes: Data collection, Derived calculations
• Version 1.4: 2023-11-08
  Changes: Data collection, Database references, Refinement description