6I49

Structure of P. aeruginosa LpxC with compound 17a: (2R)-N-Hydroxy-2-methyl-2-(methylsulfonyl)-4(6((4(morpholinomethyl)phenyl)ethynyl)-3-oxo-1H-pyrrolo[1,2-c]imidazol-2(3H)yl)butanamide


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.94 Å
  • R-Value Free: 0.243 
  • R-Value Work: 0.183 

wwPDB Validation   3D Report Full Report


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 of 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.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
UDP-3-O-acyl-N-acetylglucosamine deacetylaseA [auth AAA],
B [auth BBB]
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
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
H2Z
Query on H2Z

Download Ideal Coordinates CCD File 
D [auth AAA],
F [auth BBB]
(2~{R})-2-methyl-2-methylsulfonyl-4-[6-[2-[4-(morpholin-4-ylmethyl)phenyl]ethynyl]-3-oxidanylidene-1~{H}-pyrrolo[1,2-c]imidazol-2-yl]-~{N}-oxidanyl-butanamide
C25 H30 N4 O6 S
HKFPYIZPYVWIPB-RUZDIDTESA-N
ZN
Query on ZN

Download Ideal Coordinates CCD File 
C [auth AAA],
E [auth BBB]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.94 Å
  • R-Value Free: 0.243 
  • R-Value Work: 0.183 
  • Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 167.313α = 90
b = 89.178β = 90
c = 35.383γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



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, Derived calculations, Refinement description