6I46 | pdb_00006i46

Structure of P. aeruginosa LpxC with compound 8: (2RS)-4-(5-(2-Fluoro-4-methoxyphenyl)-2-oxooxazol-3(2H)-yl)-N-hydroxy-2-methyl-2-(methylsulfonyl)butanamide


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.75 Å
  • R-Value Free: 
    0.223 (Depositor) 
  • R-Value Work: 
    0.178 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history

Literature

Discovery of Novel Inhibitors of LpxC Displaying Potent in Vitro Activity against Gram-Negative Bacteria.

Surivet, J.P.Panchaud, P.Specklin, J.L.Diethelm, S.Blumstein, A.C.Gauvin, J.C.Jacob, L.Masse, F.Mathieu, G.Mirre, A.Schmitt, C.Lange, R.Tidten-Luksch, N.Gnerre, C.Seeland, S.Herrmann, C.Seiler, P.Enderlin-Paput, M.Mac Sweeney, A.Wicki, M.Hubschwerlen, C.Ritz, D.Rueedi, G.

(2020) J Med Chem 63: 66-87

  • DOI: https://doi.org/10.1021/acs.jmedchem.9b01604
  • Primary Citation Related Structures: 
    6I46, 6I47, 6I48, 6I49, 6I4A

  • PubMed Abstract: 

    UDP-3- O -(( R )-3-hydroxymyristoyl)- N -glucosamine deacetylase (LpxC) is as an attractive target for the discovery and development of novel antibacterial drugs to address the critical medical need created by multidrug resistant Gram-negative bacteria. By using a scaffold hopping approach on a known family of methylsulfone hydroxamate LpxC inhibitors, several hit series eliciting potent antibacterial activities against Enterobacteriaceae and Pseudomonas aeruginosa were identified. Subsequent hit-to-lead optimization, using cocrystal structures of inhibitors bound to Pseudomonas aeruginosa LpxC as guides, resulted in the discovery of multiple chemical series based on (i) isoindolin-1-ones, (ii) 4,5-dihydro-6 H -thieno[2,3- c ]pyrrol-6-ones, and (iii) 1,2-dihydro-3 H -pyrrolo[1,2- c ]imidazole-3-ones. Synthetic methods, antibacterial activities and relative binding affinities, as well as physicochemical properties that allowed compound prioritization are presented. Finally, in vivo properties of lead molecules which belong to the most promising pyrrolo-imidazolone series, such as 18d , are discussed.


  • Organizational Affiliation
    • Idorsia Pharmaceuticals Ltd. , Hegenheimermattweg 91 , CH-4123 Allschwil , Switzerland.

Macromolecule Content 

  • Total Structure Weight: 33.71 kDa 
  • Atom Count: 2,468 
  • Modeled Residue Count: 299 
  • Deposited Residue Count: 299 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
UDP-3-O-acyl-N-acetylglucosamine deacetylaseA [auth AAA]299Pseudomonas aeruginosa LESB58Mutation(s): 1 
Gene Names: lpxCPLES_47851
EC: 3.5.1.108
UniProt
Find proteins for B7UZI4 (Pseudomonas aeruginosa (strain LESB58))
Explore B7UZI4 
Go to UniProtKB:  B7UZI4
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupB7UZI4
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
H2N

Query on H2N



Download:Ideal Coordinates CCD File
C [auth AAA](2~{R})-4-[5-(2-fluoranyl-4-methoxy-phenyl)-2-oxidanylidene-1,3-oxazol-3-yl]-2-methyl-2-methylsulfonyl-~{N}-oxidanyl-butanamide
C16 H19 F N2 O7 S
ARJXRYFNKZIMJA-MRXNPFEDSA-N
GOL

Query on GOL



Download:Ideal Coordinates CCD File
D [auth AAA]GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
ZN

Query on ZN



Download:Ideal Coordinates CCD File
B [auth AAA]ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.75 Å
  • R-Value Free:  0.223 (Depositor) 
  • R-Value Work:  0.178 (Depositor) 
Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 35.754α = 90
b = 66.614β = 90.415
c = 62.926γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Revision History  (Full details and data files)

  • Version 1.0: 2019-12-18
    Type: Initial release
  • Version 1.1: 2020-01-22
    Changes: Database references
  • Version 1.2: 2024-01-24
    Changes: Data collection, Database references, Refinement description