6J8Q | pdb_00006j8q

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.79 Å
  • R-Value Free: 
    0.205 (Depositor), 0.210 (DCC) 
  • R-Value Work: 
    0.170 (Depositor), 0.180 (DCC) 
  • R-Value Observed: 
    0.171 (Depositor) 

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Validation slider image for 6J8Q

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: 115.28 kDa 
  • Atom Count: 8,838 
  • Modeled Residue Count: 1,052 
  • Deposited Residue Count: 1,060 
  • 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
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
BHU

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
HXSZVYICUWXMQS-SCSAIBSYSA-N
PEG

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]
DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
SO4

Query on SO4



Download:Ideal Coordinates CCD File
DA [auth D],
Y [auth C]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
ACY

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]
ACETIC ACID
C2 H4 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.79 Å
  • R-Value Free:  0.205 (Depositor), 0.210 (DCC) 
  • R-Value Work:  0.170 (Depositor), 0.180 (DCC) 
  • R-Value Observed: 0.171 (Depositor) 
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
PHASERphasing
PHENIXrefinement
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 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
  • Version 1.3: 2024-11-20
    Changes: Structure summary