5N8C

Crystal structure of Pseudomonas aeruginosa LpxC complexed with inhibitor

• PDB DOI: https://doi.org/10.2210/pdb5N8C/pdb

• Classification: HYDROLASE
• Organism(s): Pseudomonas aeruginosa
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2017-02-23 Released: 2017-03-29 
• Deposition Author(s): Cross, J.B., Ryan, M.D., Zhang, J., Cheng, R.K., Wood, M., Andersen, O.A., Brooks, M., Kwong, J., Barker, J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 0.203 
• R-Value Work: 0.149 
• R-Value Observed: 0.152 

Literature

Structure-based discovery of LpxC inhibitors.

Zhang, J., Chan, A., Lippa, B., Cross, J.B., Liu, C., Yin, N., Romero, J.A., Lawrence, J., Heney, R., Herradura, P., Goss, J., Clark, C., Abel, C., Zhang, Y., Poutsiaka, K.M., Epie, F., Conrad, M., Mahamoon, A., Nguyen, K., Chavan, A., Clark, E., Li, T.C., Cheng, R.K., Wood, M., Andersen, O.A., Brooks, M., Kwong, J., Barker, J., Parr, I.B., Gu, Y., Ryan, M.D., Coleman, S., Metcalf, C.A.

(2017) Bioorg Med Chem Lett 27: 1670-1680

• PubMed: 28302397 
• DOI: https://doi.org/10.1016/j.bmcl.2017.03.006
• Primary Citation of Related Structures:  
  5N8C


• PubMed Abstract: 
  

  The emergence and spread of multidrug-resistant (MDR) Gram negative bacteria presents a serious threat for public health. Novel antimicrobials that could overcome the resistance problems are urgently needed. UDP-3-O-(R-3-hydroxymyristol)-N-acetylglucosamine deacetylase (LpxC) is a cytosolic zinc-based deacetylase that catalyzes the first committed step in the biosynthesis of lipid A, which is essential for the survival of Gram-negative bacteria. Our efforts toward the discovery of novel LpxC inhibitors are presented herein.

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Organizational Affiliation: 

Cubist Pharmaceuticals Inc., 65 Hayden Avenue, Lexington, MA 02421, USA. Electronic address: [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.

Macromolecule Content

• Total Structure Weight: 68.37 kDa 
• Atom Count: 5,419 
• Modelled Residue Count: 600 
• Deposited Residue Count: 608 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
UDP-3-O-acyl-N-acetylglucosamine deacetylase	A, B	304	Pseudomonas aeruginosa	Mutation(s): 1  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 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
8Q8	E [auth A], I [auth B]	(2~{S})-3-azanyl-2-[[(1~{R})-5-[2-[4-[[2-(hydroxymethyl)imidazol-1-yl]methyl]phenyl]ethynyl]-2,3-dihydro-1~{H}-inden-1-yl]amino]-3-methyl-~{N}-oxidanyl-butanamide C27 H31 N5 O3 HMFUASPGNDZNJF-ILBGXUMGSA-N
ZN	C [auth A], D [auth A], G [auth B], H [auth B]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
CL	F [auth A], J [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 0.203 
• R-Value Work: 0.149 
• R-Value Observed: 0.152 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 35.44	α = 90
b = 95.31	β = 96.34
c = 89.72	γ = 90

Software Package:

Software Name	Purpose
SCALA	data scaling
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
MOSFLM	data reduction

Structure Validation

Entry History 

Deposition Data

• Released Date: 2017-03-29 
Deposition Author(s): Cross, J.B., Ryan, M.D., Zhang, J., Cheng, R.K., Wood, M., Andersen, O.A., Brooks, M., Kwong, J., Barker, J.

Revision History  

• Version 1.0: 2017-03-29
  Type: Initial release
  
• Version 1.1: 2017-04-12
  Changes: Database references
• Version 1.2: 2024-01-17
  Changes: Data collection, Database references, Derived calculations, Refinement description