6JN5 | pdb_00006jn5

Serine Beta-Lactamase KPC-2 in Complex with Dual MBL/SBL Inhibitor MS23


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.97 Å
  • R-Value Free: 
    0.316 (Depositor), 0.322 (DCC) 
  • R-Value Work: 
    0.275 (Depositor), 0.282 (DCC) 
  • R-Value Observed: 
    0.275 (Depositor) 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history

Literature

Structure-Based Development of (1-(3'-Mercaptopropanamido)methyl)boronic Acid Derived Broad-Spectrum, Dual-Action Inhibitors of Metallo- and Serine-beta-lactamases.

Wang, Y.L.Liu, S.Yu, Z.J.Lei, Y.Huang, M.Y.Yan, Y.H.Ma, Q.Zheng, Y.Deng, H.Sun, Y.Wu, C.Yu, Y.Chen, Q.Wang, Z.Wu, Y.Li, G.B.

(2019) J Med Chem 62: 7160-7184

  • DOI: https://doi.org/10.1021/acs.jmedchem.9b00735
  • Primary Citation Related Structures: 
    6J8Q, 6J8R, 6JN3, 6JN4, 6JN5, 6JN6

  • PubMed Abstract: 

    The emergence and spread of bacterial pathogens acquired metallo-β-lactamase (MBL) and serine-β-lactamase (SBL) medicated β-lactam resistance gives rise to an urgent need for the development of new dual-action MBL/SBL inhibitors. Application of a pharmacophore fusion strategy led to the identification of (2' S )-(1-(3'-mercapto-2'-methylpropanamido)methyl)boronic acid ( MS01 ) as a new dual-action inhibitor, which manifests broad-spectrum inhibition to representative MBL/SBL enzymes, including the widespread VIM-2 and KPC-2. Guided by the VIM-2: MS01 and KPC-2: MS01 complex structures, further structural optimization yielded new, more potent dual-action inhibitors. Selectivity studies indicated that the inhibitors had no apparent inhibition to human angiotensin-converting enzyme-2 and showed selectivity across serine hydrolyases in E. coli and human HEK293T cells labeled by the activity-based probe TAMRA-FP. Moreover, the inhibitors displayed potentiation of meropenem efficacy against MBL- or SBL-positive clinical isolates without apparent cytotoxicity. This work will aid efforts to develop new types of clinically useful dual-action inhibitors targeting MBL/SBL enzymes.


  • Organizational Affiliation
    • Key Laboratory of Drug-Targeting and Drug Delivery System of the Education Ministry, Sichuan Engineering Laboratory for Plant-Sourced Drug and Sichuan Research Center for Drug Precision Industrial Technology, West China School of Pharmacy , Sichuan University , Sichuan 610041 , China.

Macromolecule Content 

  • Total Structure Weight: 113.05 kDa 
  • Atom Count: 8,101 
  • Modeled Residue Count: 1,049 
  • Deposited Residue Count: 1,056 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Serine Beta-Lactamase KPC-2
A, B, C, D
264Klebsiella pneumoniaeMutation(s): 0 
Gene Names: KPC-2
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
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.97 Å
  • R-Value Free:  0.316 (Depositor), 0.322 (DCC) 
  • R-Value Work:  0.275 (Depositor), 0.282 (DCC) 
  • R-Value Observed: 0.275 (Depositor) 
Space Group: P 3 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 164.757α = 90
b = 164.757β = 90
c = 94.499γ = 120
Software Package:
Software NamePurpose
SCALEPACKdata scaling
PHASERphasing
PHENIXrefinement
PDB_EXTRACTdata extraction
HKL-3000data reduction

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Natural Science Foundation of ChinaChina81874291
National Natural Science Foundation of ChinaChina81502989

Revision History  (Full details and data files)

  • Version 1.0: 2019-07-17
    Type: Initial release
  • Version 1.1: 2019-08-21
    Changes: Data collection, Database references
  • Version 1.2: 2023-11-22
    Changes: Data collection, Database references, Refinement description
  • Version 1.3: 2024-11-13
    Changes: Structure summary