7E9A

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))


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.25 Å
  • R-Value Free: 0.221 
  • R-Value Work: 0.180 
  • R-Value Observed: 0.182 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history


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

  • DOI: https://doi.org/10.1039/d1cc03026d
  • Primary Citation of 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.


  • 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. liguobo@scu.edu.cn.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Beta-lactamase
A, B, C, D
265Klebsiella pneumoniaeMutation(s): 0 
Gene Names: blaKPC2
EC: 3.5.2.6
UniProt
Find proteins for Q9F663 (Klebsiella pneumoniae)
Explore Q9F663 
Go to UniProtKB:  Q9F663
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9F663
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
J00 (Subject of Investigation/LOI)
Query on J00

Download Ideal Coordinates CCD File 
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
Query on PEG

Download Ideal Coordinates CCD File 
AA [auth D]
G [auth A]
L [auth B]
M [auth B]
N [auth B]
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
Query on GOL

Download Ideal Coordinates CCD File 
H [auth A]
I [auth A]
J [auth A]
P [auth B]
W [auth C]
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
Query on ACY

Download Ideal Coordinates CCD File 
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 
  • R-Value Work: 0.180 
  • R-Value Observed: 0.182 
  • Space Group: P 3 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 165.421α = 90
b = 165.421β = 90
c = 94.86γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data reduction
SCALEPACKdata scaling
PHASERphasing
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Natural Science Foundation of China (NSFC)China81874291
National Natural Science Foundation of China (NSFC)China81502989
National Natural Science Foundation of China (NSFC)China82073698

Revision History  (Full details and data files)

  • 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