6JN4 | pdb_00006jn4

Serine Beta-Lactamase KPC-2 in Complex with Dual MBL/SBL Inhibitor WL-001


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 
    0.221 (Depositor), 0.230 (DCC) 
  • R-Value Work: 
    0.180 (Depositor), 0.190 (DCC) 
  • R-Value Observed: 
    0.181 (Depositor) 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 

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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 of 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.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Serine Beta-Lactamase KPC-2
A, B, C, D
265Klebsiella 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
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
BX9
Query on BX9

Download Ideal Coordinates CCD File 
E [auth A],
K [auth B],
R [auth C],
W [auth D]
[(R)-(4-fluorophenyl)-[[(2S)-2-methyl-3-sulfanyl-propanoyl]amino]methyl]boronic acid
C11 H15 B F N O3 S
CDDJMEDWZMPIRW-XCBNKYQSSA-N
PEG
Query on PEG

Download Ideal Coordinates CCD File 
I [auth A]
J [auth A]
N [auth B]
O [auth B]
P [auth B]
DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
ACY
Query on ACY

Download Ideal Coordinates CCD File 
G [auth A],
H [auth A],
M [auth B],
T [auth C],
Y [auth D]
ACETIC ACID
C2 H4 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-N
ACT
Query on ACT

Download Ideal Coordinates CCD File 
F [auth A],
L [auth B],
S [auth C],
X [auth D]
ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free:  0.221 (Depositor), 0.230 (DCC) 
  • R-Value Work:  0.180 (Depositor), 0.190 (DCC) 
  • R-Value Observed: 0.181 (Depositor) 
Space Group: P 3 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 164.785α = 90
b = 164.785β = 90
c = 94.683γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
SCALEPACKdata scaling
PHASERphasing
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted BX9Click on this verticalbar to view details

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: 2024-11-06
    Changes: Structure summary