7E9A | pdb_00007e9a

Crystal structure of KPC-2 in complex with (S)-2-(1-hydroxy-1,3-dihydrobenzo[c][1,2]oxaborol-3-yl)acrylic acid (4a-(S))

• PDB DOI: https://doi.org/10.2210/pdb7E9A/pdb

• Classification: HYDROLASE
• Organism(s): Klebsiella pneumoniae
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2021-03-03 Released: 2021-08-04 
• Deposition Author(s): Li, G.-B., Yan, Y.-H.
• Funding Organization(s): National Natural Science Foundation of China (NSFC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.25 Å
• R-Value Free: 
  0.221 (Depositor), 0.229 (DCC) 
• R-Value Work: 
  0.180 (Depositor), 0.189 (DCC) 
• R-Value Observed: 
  0.182 (Depositor) 

Starting Model: experimental

Literature

Design and enantioselective synthesis of 3-( alpha-acrylic acid) benzoxaboroles to combat carbapenemase resistance.

Xiao, Y.C., Chen, X.P., Deng, J., Yan, Y.H., Zhu, K.R., Li, G., Yu, J.L., Brem, J., Chen, F., Schofield, C.J., Li, G.B.

(2021) Chem Commun (Camb) 57: 7709-7712

• PubMed: 34259249 
• DOI: https://doi.org/10.1039/d1cc03026d
• Primary Citation Related Structures: 
  7E9A


• PubMed Abstract: 
  

  Chiral 3-substituted benzoxaboroles were designed as carbapenemase inhibitors and efficiently synthesised via asymmetric Morita-Baylis-Hillman reaction. Some of the benzoxaboroles were potent inhibitors of clinically relevant carbapenemases and restored the activity of meropenem in bacteria harbouring these enzymes. Crystallographic analyses validate the proposed mechanism of binding to carbapenemases, i.e. in a manner relating to their antibiotic substrates. The results illustrate how combining a structure-based design approach with asymmetric catalysis can efficiently lead to potent β-lactamase inhibitors and provide a starting point to develop drugs combatting carbapenemases.

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Organizational Affiliation: 
• Key Laboratory of Drug-Targeting and Drug Delivery System of the Ministry of Education and Sichuan Research Center for Drug Precision Industrial Technology, West China School of Pharmacy, Sichuan University, Chengdu 610041, China. [e-mail].
Department of Chemistry and the Ineos Oxford Institute for Antimicrobial Research, University of Oxford, 12 Mansfield Road, Oxford, OX1 3TA, UK. [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)

Biological Assembly 3  

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

Biological assembly 3 assigned by authors and generated by PISA (software)

Biological Assembly 4  

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

Biological assembly 4 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 114.93 kDa 
• Atom Count: 8,391 
• Modeled Residue Count: 1,055 
• Deposited Residue Count: 1,060 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Beta-lactamase	A, B, C, D	265	Klebsiella pneumoniae	Mutation(s): 0  Gene Names: blaKPC2 EC: 3.5.2.6
UniProt
Find proteins for Q9F663 (Klebsiella pneumoniae) Explore Q9F663  Go to UniProtKB:  Q9F663

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
J00 (Subject of Investigation/LOI)	E [auth A], K [auth B], Q [auth C], X [auth D]	2-[(3S)-1-oxidanyl-3H-2,1-benzoxaborol-3-yl]prop-2-enoic acid C10 H9 B O4 BRBGRVSFRVLGNY-SECBINFHSA-N
PEG	AA [auth D], G [auth A], L [auth B], M [auth B], N [auth B], O [auth B], S [auth C], T [auth C], U [auth C], V [auth C]	DI(HYDROXYETHYL)ETHER C4 H10 O3 MTHSVFCYNBDYFN-UHFFFAOYSA-N
GOL	H [auth A], I [auth A], J [auth A], P [auth B], W [auth C], Z [auth D]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
ACY	F [auth A], R [auth C], Y [auth D]	ACETIC ACID C2 H4 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.25 Å
• R-Value Free:  0.221 (Depositor), 0.229 (DCC) 
• R-Value Work:  0.180 (Depositor), 0.189 (DCC) 
• R-Value Observed: 0.182 (Depositor) 

Space Group: P 3 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 165.421	α = 90
b = 165.421	β = 90
c = 94.86	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data reduction
SCALEPACK	data scaling
PHASER	phasing
PDB_EXTRACT	data extraction

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2021-08-04 
Deposition Author(s): Li, G.-B., Yan, Y.-H.

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Funding Organization	Location	Grant Number
National Natural Science Foundation of China (NSFC)	China	81874291
National Natural Science Foundation of China (NSFC)	China	81502989
National Natural Science Foundation of China (NSFC)	China	82073698

Revision History  

• Version 1.0: 2021-08-04
  Type: Initial release
  
• Version 1.1: 2021-08-11
  Changes: Database references
• Version 1.2: 2021-08-18
  Changes: Database references
• Version 1.3: 2023-11-29
  Changes: Data collection, Refinement description
• Version 1.4: 2024-10-23
  Changes: Structure summary