3UHM

UDP-3-O-[3-hydroxymyristoyl] N-acetylglucosamine deacetylase in complex with inhibitor

• PDB DOI: https://doi.org/10.2210/pdb3UHM/pdb

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


• Deposited: 2011-11-03 Released: 2012-02-01 
• Deposition Author(s): Montgomery, J., Liu, S.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.26 Å
• R-Value Free: 0.201 
• R-Value Work: 0.180 
• R-Value Observed: 0.181 

Starting Model: experimental

Literature

Pyridone methylsulfone hydroxamate LpxC inhibitors for the treatment of serious gram-negative infections.

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

(2012) J Med Chem 55: 1662-1670

• PubMed: 22257165 
• DOI: https://doi.org/10.1021/jm2014875
• Primary Citation of Related Structures:  
  3UHM


• PubMed Abstract: 
  

  The synthesis and biological activity of a new series of LpxC inhibitors represented by pyridone methylsulfone hydroxamate 2a is presented. Members of this series have improved solubility and free fraction when compared to compounds in the previously described biphenyl methylsulfone hydroxamate series, and they maintain superior Gram-negative antibacterial activity to comparator agents.

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Organizational Affiliation: 

Worldwide Medicinal Chemistry, Pfizer Worldwide Research and Development, 445 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 and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 33.7 kDa 
• Atom Count: 2,627 
• Modelled Residue Count: 299 
• Deposited Residue Count: 299 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
UDP-3-O-[3-hydroxymyristoyl] N-acetylglucosamine deacetylase	A	299	Pseudomonas aeruginosa	Mutation(s): 1  Gene Names: lpxC, envA, PA4406 EC: 3.5.1 (PDB Primary Data), 3.5.1.108 (UniProt)
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 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
RFN	C [auth A]	(2R)-N-hydroxy-2-methyl-2-(methylsulfonyl)-4-(2-oxo-4-phenylpyridin-1(2H)-yl)butanamide C17 H20 N2 O5 S NFQOWMXNJNMRTA-QGZVFWFLSA-N
ZN	B [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
EDO	E [auth A]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N
GAI	D [auth A]	GUANIDINE C H5 N3 ZRALSGWEFCBTJO-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
RFN	PDBBind:  3UHM	IC50: 3.6 (nM) from 1 assay(s)
	BindingDB:  3UHM	IC50: 3.6 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.26 Å
• R-Value Free: 0.201 
• R-Value Work: 0.180 
• R-Value Observed: 0.181 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 34.138	α = 90
b = 80.965	β = 95.5
c = 49.779	γ = 90

Software Package:

Software Name	Purpose
BUSTER	refinement

Structure Validation

Entry History 

Deposition Data

• Released Date: 2012-02-01 
Deposition Author(s): Montgomery, J., Liu, S.

Revision History  

• Version 1.0: 2012-02-01
  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