6WAA

K. pneumoniae Topoisomerase IV (ParE-ParC) in complex with DNA and compound 34 (7-[(1S,5R)-1-amino-3-azabicyclo[3.1.0]hexan-3-yl]-4-(aminomethyl)-1-cyclopropyl-3,6-difluoro-8-methylquinolin-2(1H)-one)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.20 Å
  • R-Value Free: 0.301 
  • R-Value Work: 0.274 
  • R-Value Observed: 0.275 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history


Literature

Topoisomerase Inhibitors Addressing Fluoroquinolone Resistance in Gram-Negative Bacteria.

Skepper, C.K.Armstrong, D.Balibar, C.J.Bauer, D.Bellamacina, C.Benton, B.M.Bussiere, D.De Pascale, G.De Vicente, J.Dean, C.R.Dhumale, B.Fisher, L.M.Fuller, J.Fulsunder, M.Holder, L.M.Hu, C.Kantariya, B.Lapointe, G.Leeds, J.A.Li, X.Lu, P.Lvov, A.Ma, S.Madhavan, S.Malekar, S.McKenney, D.Mergo, W.Metzger, L.Moser, H.E.Mutnick, D.Noeske, J.Osborne, C.Patel, A.Patel, D.Patel, T.Prajapati, K.Prosen, K.R.Reck, F.Richie, D.L.Rico, A.Sanderson, M.R.Satasia, S.Sawyer, W.S.Selvarajah, J.Shah, N.Shanghavi, K.Shu, W.Thompson, K.V.Traebert, M.Vala, A.Vala, L.Veselkov, D.A.Vo, J.Wang, M.Widya, M.Williams, S.L.Xu, Y.Yue, Q.Zang, R.Zhou, B.Rivkin, A.

(2020) J Med Chem 63: 7773-7816

  • DOI: https://doi.org/10.1021/acs.jmedchem.0c00347
  • Primary Citation of Related Structures:  
    6WAA

  • PubMed Abstract: 

    Since their discovery over 5 decades ago, quinolone antibiotics have found enormous success as broad spectrum agents that exert their activity through dual inhibition of bacterial DNA gyrase and topoisomerase IV. Increasing rates of resistance, driven largely by target-based mutations in the GyrA/ParC quinolone resistance determining region, have eroded the utility and threaten the future use of this vital class of antibiotics. Herein we describe the discovery and optimization of a series of 4-(aminomethyl)quinolin-2(1 H )-ones, exemplified by 34 , that inhibit bacterial DNA gyrase and topoisomerase IV and display potent activity against ciprofloxacin-resistant Gram-negative pathogens. X-ray crystallography reveals that 34 occupies the classical quinolone binding site in the topoisomerase IV-DNA cleavage complex but does not form significant contacts with residues in the quinolone resistance determining region.


  • Organizational Affiliation

    Novartis Institutes for BioMedical Research, Emeryville, California 94608, United States.


Macromolecules

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
DNA topoisomerase 4 subunit B,DNA topoisomerase (ATP-hydrolyzing) chimeraA [auth B],
B [auth D],
C [auth F],
D [auth H]
743Klebsiella pneumoniae 342Mutation(s): 1 
Gene Names: parENCTC5052_03997parC_1NCTC5047_02751
EC: 5.6.2.2
UniProt
Find proteins for B5XU60 (Klebsiella pneumoniae (strain 342))
Explore B5XU60 
Go to UniProtKB:  B5XU60
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupB5XU60
Sequence Annotations
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  • Reference Sequence

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Entity ID: 2
MoleculeChains LengthOrganismImage
DNA (5'-D(*TP*TP*AP*CP*GP*TP*TP*GP*TP*AP*T)-3')E [auth I],
H [auth L],
I [auth M],
L [auth P]
11Klebsiella pneumoniae 342
Sequence Annotations
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  • Reference Sequence

Find similar nucleic acids by:  Sequence   |   3D Structure  

Entity ID: 3
MoleculeChains LengthOrganismImage
DNA (5'-D(*GP*AP*TP*CP*AP*TP*AP*CP*AP*AP*CP*GP*TP*AP*A)-3')F [auth J],
G [auth K],
J [auth N],
K [auth O]
15Klebsiella pneumoniae 342
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
TNJ
Query on TNJ

Download Ideal Coordinates CCD File 
CA [auth J],
DA [auth J],
GA [auth N],
HA [auth N]
7-[(1S,5R)-1-amino-3-azabicyclo[3.1.0]hexan-3-yl]-4-(aminomethyl)-1-cyclopropyl-3,6-difluoro-8-methylquinolin-2(1H)-one
C19 H22 F2 N4 O
LZLLPIGCIXMSRM-GIGQVBGESA-N
MPD
Query on MPD

Download Ideal Coordinates CCD File 
M [auth B]
N [auth B]
R [auth D]
T [auth F]
X [auth H]
M [auth B],
N [auth B],
R [auth D],
T [auth F],
X [auth H],
Y [auth H]
(4S)-2-METHYL-2,4-PENTANEDIOL
C6 H14 O2
SVTBMSDMJJWYQN-YFKPBYRVSA-N
CL
Query on CL

Download Ideal Coordinates CCD File 
AA [auth H],
Q [auth B]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
MG
Query on MG

Download Ideal Coordinates CCD File 
BA [auth I]
EA [auth L]
FA [auth M]
IA [auth O]
O [auth B]
BA [auth I],
EA [auth L],
FA [auth M],
IA [auth O],
O [auth B],
P [auth B],
S [auth D],
U [auth F],
V [auth F],
W [auth F],
Z [auth H]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
PTR
Query on PTR
A [auth B],
B [auth D],
C [auth F],
D [auth H]
L-PEPTIDE LINKINGC9 H12 N O6 PTYR
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.20 Å
  • R-Value Free: 0.301 
  • R-Value Work: 0.274 
  • R-Value Observed: 0.275 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 94.59α = 90
b = 157.481β = 94.93
c = 144.06γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
SCALAdata scaling
PDB_EXTRACTdata extraction
XDSdata reduction
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2020-07-15
    Type: Initial release
  • Version 1.1: 2020-08-05
    Changes: Database references, Derived calculations
  • Version 1.2: 2023-10-18
    Changes: Data collection, Database references, Refinement description
  • Version 1.3: 2023-11-15
    Changes: Data collection