7PKM

LpxC Inhibitors With Fluoroproline As A Novel Zinc-Binding Group Can Serve As A Novel Class of Antibiotic With Activity Against Multidrug-Resistant Gram-Negative Bacteria


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.239 
  • R-Value Work: 0.179 
  • R-Value Observed: 0.182 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


Literature

LpxC Inhibitors With Fluoroproline As A Novel Zinc-Binding Group Can Serve As A Novel Class of Antibiotic With Activity Against Multidrug-Resistant Gram-Negative Bacteria

Ryan, M.D.Pallin, T.D.Mullins, T.Blench, T.Fraser, I.Dallow, J.Ahmed, N.Ellwood, C.Gaines, S.Flores, J.Blackwell, Y.Garcia, C.T.Spence, G.Reeve, A.Panchal, T.Dominguez-Fernandez, B.Leonard, P.M.Lamers, M.B.A.C.Arduin, A.Fotinou, C.Gancia, E.Clark, D.E.Bush, E.Betts, J.Richards, C.Rea-Davies, T.Keefe, A.D.Zhang, Y.Soutter, H.T.Centrella, P.A.Clark, M.A.Cuozzo, J.W.Dumelin, C.E.Habeshian, S.Hunt, A.Sigel, E.A.Troast, D.M.DeJonge, B.L.M.

To be published.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
UDP-3-O-acyl-N-acetylglucosamine deacetylase312Pseudomonas aeruginosa PAO1Mutation(s): 0 
Gene Names: lpxCenvAPA4406
EC: 3.5.1.108
UniProt
Find proteins for P47205 (Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1))
Explore P47205 
Go to UniProtKB:  P47205
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP47205
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
6G8 (Subject of Investigation/LOI)
Query on 6G8

Download Ideal Coordinates CCD File 
C [auth A](2S,4S)-N-[(3R,5R)-1-cyclopropylcarbonyl-5-[[[2-methyl-4-[2-[4-(morpholin-4-ylmethyl)phenyl]ethynyl]phenyl]carbonylamino]methyl]pyrrolidin-3-yl]-4-fluoranyl-pyrrolidine-2-carboxamide
C35 H42 F N5 O4
VANITAVOZBNWHX-TWXNZYBRSA-N
ZN
Query on ZN

Download Ideal Coordinates CCD File 
B [auth A]ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.239 
  • R-Value Work: 0.179 
  • R-Value Observed: 0.182 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 35.531α = 90
b = 66.81β = 90.35
c = 62.691γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
DIALSdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Not funded--

Revision History  (Full details and data files)

  • Version 1.0: 2022-09-07
    Type: Initial release
  • Version 1.1: 2024-01-31
    Changes: Data collection, Refinement description