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

• PDB DOI: https://doi.org/10.2210/pdb7PKM/pdb

• Classification: HYDROLASE
• Organism(s): Pseudomonas aeruginosa PAO1
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2021-08-25 Released: 2022-09-07 
• Deposition Author(s): Ryan, M.D., Pallin, T.D., Lamers, M.B.A.C., Leonard, P.M.
• Funding Organization(s): Not funded

---

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

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.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 35.54 kDa 
• Atom Count: 2,550 
• Modelled Residue Count: 297 
• Deposited Residue Count: 312 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
UDP-3-O-acyl-N-acetylglucosamine deacetylase	A	312	Pseudomonas aeruginosa PAO1	Mutation(s): 0  Gene Names: lpxC, envA, PA4406 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

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
6G8 (Subject of Investigation/LOI)	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	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 = 35.531	α = 90
b = 66.81	β = 90.35
c = 62.691	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
DIALS	data reduction
Aimless	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2022-09-07 
Deposition Author(s): Ryan, M.D., Pallin, T.D., Lamers, M.B.A.C., Leonard, P.M.

---

Funding Organization	Location	Grant Number
Not funded		--

Revision History  

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