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

Experimental Data Snapshot

  • Resolution: 1.79 Å
  • R-Value Free: 0.205 
  • R-Value Work: 0.170 
  • R-Value Observed: 0.171 

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Ligand Structure Quality Assessment 

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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.

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: blaKPC2
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
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on BHU

Download Ideal Coordinates CCD File 
AA [auth D],
E [auth A],
O [auth B],
V [auth C]
[[(2S)-2-methyl-3-sulfanyl-propanoyl]amino]methylboronic acid
C5 H12 B N O3 S
Query on PEG

Download Ideal Coordinates CCD File 
BA [auth D]
CA [auth D]
F [auth A]
FA [auth D]
G [auth A]
BA [auth D],
CA [auth D],
F [auth A],
FA [auth D],
G [auth A],
H [auth A],
I [auth A],
J [auth A],
K [auth A],
L [auth A],
P [auth B],
Q [auth B],
R [auth B],
S [auth B],
W [auth C],
X [auth C]
C4 H10 O3
Query on SO4

Download Ideal Coordinates CCD File 
DA [auth D],
Y [auth C]
O4 S
Query on ACY

Download Ideal Coordinates CCD File 
EA [auth D]
M [auth A]
N [auth A]
T [auth B]
U [auth B]
EA [auth D],
M [auth A],
N [auth A],
T [auth B],
U [auth B],
Z [auth C]
C2 H4 O2
Experimental Data & Validation

Experimental Data

  • Resolution: 1.79 Å
  • R-Value Free: 0.205 
  • R-Value Work: 0.170 
  • R-Value Observed: 0.171 
  • Space Group: P 3 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 165.159α = 90
b = 165.159β = 90
c = 94.895γ = 120
Software Package:
Software NamePurpose
HKL-2000data reduction
SCALEPACKdata scaling
PDB_EXTRACTdata extraction

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; 81502989

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