6B1J

Crystal structure KPC-2 beta-lactamase complexed with WCK 5107 by soaking


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.60 Å
  • R-Value Free: 0.187 
  • R-Value Work: 0.150 
  • R-Value Observed: 0.152 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


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Literature

Strategic Approaches to Overcome Resistance against Gram-Negative Pathogens Using beta-Lactamase Inhibitors and beta-Lactam Enhancers: Activity of Three Novel Diazabicyclooctanes WCK 5153, Zidebactam (WCK 5107), and WCK 4234.

Papp-Wallace, K.M.Nguyen, N.Q.Jacobs, M.R.Bethel, C.R.Barnes, M.D.Kumar, V.Bajaksouzian, S.Rudin, S.D.Rather, P.N.Bhavsar, S.Ravikumar, T.Deshpande, P.K.Patil, V.Yeole, R.Bhagwat, S.S.Patel, M.V.van den Akker, F.Bonomo, R.A.

(2018) J Med Chem 61: 4067-4086

  • DOI: https://doi.org/10.1021/acs.jmedchem.8b00091
  • Primary Citation of Related Structures:  
    6B1F, 6B1H, 6B1J, 6B1W, 6B1X, 6B1Y, 6B22

  • PubMed Abstract: 

    Limited treatment options exist to combat infections caused by multidrug-resistant (MDR) Gram-negative bacteria possessing broad-spectrum β-lactamases. The design of novel β-lactamase inhibitors is of paramount importance. Here, three novel diazabicyclooctanes (DBOs), WCK 5153, zidebactam (WCK 5107), and WCK 4234 (compounds 1-3, respectively), were synthesized and biochemically characterized against clinically important bacteria. Compound 3 inhibited class A, C, and D β-lactamases with unprecedented k 2 / K values against OXA carbapenemases. Compounds 1 and 2 acylated class A and C β-lactamses rapidly but not the tested OXAs. Compounds 1-3 formed highly stable acyl-complexes as demonstrated by mass spectrometry. Crystallography revealed that 1-3 complexed with KPC-2 adopted a "chair conformation" with the sulfate occupying the carboxylate binding region. The cefepime-2 and meropenem-3 combinations were effective in murine peritonitis and neutropenic lung infection models caused by MDR Acinetobacter baumannii. Compounds 1-3 are novel β-lactamase inhibitors that demonstate potent cross-class inhibition, and clinical studies targeting MDR infections are warranted.


  • Organizational Affiliation

    Research Service , Louis Stokes Cleveland Department of Veterans Affairs Medical Center , 10701 East Boulevard , Cleveland , Ohio 44106 , United States.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Carbapenem-hydrolyzing beta-lactamase KPC
A, B
268Klebsiella pneumoniaeMutation(s): 0 
Gene Names: blakpckpc1
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 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
C8V (Subject of Investigation/LOI)
Query on C8V

Download Ideal Coordinates CCD File 
C [auth A],
M [auth B]
(2S,5R)-1-formyl-N'-[(3R)-piperidine-3-carbonyl]-5-[(sulfooxy)amino]piperidine-2-carbohydrazide
C13 H23 N5 O7 S
KMYLRFCWFBWPGR-MXWKQRLJSA-N
CIT
Query on CIT

Download Ideal Coordinates CCD File 
D [auth A],
E [auth A],
F [auth A]
CITRIC ACID
C6 H8 O7
KRKNYBCHXYNGOX-UHFFFAOYSA-N
EDO
Query on EDO

Download Ideal Coordinates CCD File 
G [auth A]
H [auth A]
I [auth A]
J [auth A]
K [auth A]
G [auth A],
H [auth A],
I [auth A],
J [auth A],
K [auth A],
L [auth A],
N [auth B],
O [auth B],
P [auth B],
Q [auth B]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.60 Å
  • R-Value Free: 0.187 
  • R-Value Work: 0.150 
  • R-Value Observed: 0.152 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 34.44α = 92.31
b = 37.416β = 90.04
c = 82.128γ = 95.26
Software Package:
Software NamePurpose
Aimlessdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
XDSdata reduction

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
WockhardtUnited States--

Revision History  (Full details and data files)

  • Version 1.0: 2018-08-01
    Type: Initial release