7PHJ | pdb_00007phj

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/pdb7PHJ/pdb

• Classification: HYDROLASE
• Organism(s): Escherichia coli K-12
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2021-08-17 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

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.45 Å
• R-Value Free: 
  0.241 (Depositor), 0.220 (DCC) 
• R-Value Work: 
  0.200 (Depositor) 
• R-Value Observed: 
  0.202 (Depositor) 

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.

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 34.57 kDa 
• Atom Count: 2,351 
• Modeled Residue Count: 299 
• Deposited Residue Count: 305 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
UDP-3-O-acyl-N-acetylglucosamine deacetylase	A	305	Escherichia coli K-12	Mutation(s): 0  Gene Names: lpxC, asmB, envA, b0096, JW0094 EC: 3.5.1.108
UniProt
Find proteins for P0A725 (Escherichia coli (strain K12)) Explore P0A725  Go to UniProtKB:  P0A725

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
7PX (Subject of Investigation/LOI)	C [auth A]	(2~{R},4~{R})-4-[[(2~{S},4~{S})-4-fluoranylpyrrolidin-2-yl]carbonylamino]-1-(2-methylpropanoyl)-~{N}-[[4-(2-phenylethynyl)phenyl]methyl]pyrrolidine-2-carboxamide C29 H33 F N4 O3 VUQQJEHSKZCJDR-ROXDYWFKSA-N
ZN	B [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
7PX	BindingDB:  7PHJ	IC50: 1500 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.45 Å
• R-Value Free:  0.241 (Depositor), 0.220 (DCC) 
• R-Value Work:  0.200 (Depositor) 
• R-Value Observed: 0.202 (Depositor) 

Space Group: P 6₃ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 129.497	α = 90
b = 129.497	β = 90
c = 103.35	γ = 120

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.

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Funding Organization	Location	Grant Number
Not funded		--

Revision History  

• Version 1.0: 2022-09-07
  Type: Initial release
  
• Version 2.0: 2023-05-24
  Changes: Non-polymer description
• Version 2.1: 2024-02-07
  Changes: Data collection, Refinement description