3U1Y

Potent Inhibitors of LpxC for the Treatment of Gram-Negative Infections

• PDB DOI: https://doi.org/10.2210/pdb3U1Y/pdb

• Classification: Hydrolase/Hydrolase inhibitor
• Organism(s): Pseudomonas aeruginosa
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2011-09-30 Released: 2012-01-04 
• Deposition Author(s): Brown, M., Abramite, J., Liu, S.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 0.233 
• R-Value Work: 0.192 
• R-Value Observed: 0.193 

Starting Model: experimental

Literature

Potent inhibitors of LpxC for the treatment of Gram-negative infections.

Brown, M.F., Reilly, U., Abramite, J.A., Arcari, J.T., Oliver, R., Barham, R.A., Che, Y., Chen, J.M., Collantes, E.M., Chung, S.W., Desbonnet, C., Doty, J., Doroski, M., Engtrakul, J.J., Harris, T.M., Huband, M., Knafels, J.D., Leach, K.L., Liu, S., Marfat, A., Marra, A., McElroy, E., Melnick, M., Menard, C.A., Montgomery, J.I., Mullins, L., Noe, M.C., O'Donnell, J., Penzien, J., Plummer, M.S., Price, L.M., Shanmugasundaram, V., Thoma, C., Uccello, D.P., Warmus, J.S., Wishka, D.G.

(2012) J Med Chem 55: 914-923

• PubMed: 22175825 
• DOI: https://doi.org/10.1021/jm2014748
• Primary Citation of Related Structures:  
  3U1Y


• PubMed Abstract: 
  

  In this paper, we present the synthesis and SAR as well as selectivity, pharmacokinetic, and infection model data for representative analogues of a novel series of potent antibacterial LpxC inhibitors represented by hydroxamic acid.

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Organizational Affiliation: 

Worldwide Medicinal Chemistry, Pfizer Global Research and Development, Eastern Point Road, Groton, Connecticut 06340, United States. [e-mail]

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly 2  

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

Biological assembly 2 assigned by authors.

Biological Assembly 3  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 3 generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 67.47 kDa 
• Atom Count: 5,074 
• Modelled Residue Count: 598 
• Deposited Residue Count: 598 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
UDP-3-O-[3-hydroxymyristoyl] N-acetylglucosamine deacetylase	A, B	299	Pseudomonas aeruginosa	Mutation(s): 1  Gene Names: lpxC, envA, PA4406 EC: 3.5.1
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
03I	D [auth A], F [auth B]	(2R)-N-hydroxy-2-methyl-2-(methylsulfonyl)-4-{4'-[3-(morpholin-4-yl)propoxy]biphenyl-4-yl}butanamide C25 H34 N2 O6 S GGIDQMXKOSYOHO-RUZDIDTESA-N
ZN	C [auth A], E [auth B], G [auth B]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
03I	BindingDB:  3U1Y	IC50: 0.17 (nM) from 1 assay(s)
	PDBBind:  3U1Y	IC50: 2.13 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 0.233 
• R-Value Work: 0.192 
• R-Value Observed: 0.193 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 35.995	α = 90
b = 70.396	β = 90
c = 219.617	γ = 90

Software Package:

Software Name	Purpose
BUSTER	refinement

Structure Validation

Entry History 

Deposition Data

• Released Date: 2012-01-04 
Deposition Author(s): Brown, M., Abramite, J., Liu, S.

Revision History  

• Version 1.0: 2012-01-04
  Type: Initial release
  
• Version 1.1: 2013-01-02
  Changes: Database references
• Version 1.2: 2023-09-13
  Changes: Data collection, Database references, Derived calculations, Refinement description