7DEM | pdb_00007dem

Crystal structure of P.aeruginosa LpxC in complex with inhibitor

• PDB DOI: https://doi.org/10.2210/pdb7DEM/pdb

• Classification: HYDROLASE
• Organism(s): Pseudomonas aeruginosa PAO1
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2020-11-04 Released: 2021-01-13 
• Deposition Author(s): Mima, M., Ushiyama, F., Matsuda, Y.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 
  0.238 (Depositor), 0.240 (DCC) 
• R-Value Work: 
  0.194 (Depositor), 0.200 (DCC) 
• R-Value Observed: 
  0.196 (Depositor) 

Starting Model: experimental

Literature

Lead optimization of 2-hydroxymethyl imidazoles as non-hydroxamate LpxC inhibitors: Discovery of TP0586532.

Ushiyama, F., Takashima, H., Matsuda, Y., Ogata, Y., Sasamoto, N., Kurimoto-Tsuruta, R., Ueki, K., Tanaka-Yamamoto, N., Endo, M., Mima, M., Fujita, K., Takata, I., Tsuji, S., Yamashita, H., Okumura, H., Otake, K., Sugiyama, H.

(2020) Bioorg Med Chem 30: 115964-115964

• PubMed: 33385955 
• DOI: https://doi.org/10.1016/j.bmc.2020.115964
• Primary Citation of Related Structures:  
  7DEL, 7DEM, 7DEN


• PubMed Abstract: 
  

  Infectious diseases caused by resistant Gram-negative bacteria have become a serious problem, and the development of therapeutic drugs with a novel mechanism of action and that do not exhibit cross-resistance with existing drugs has been earnestly desired. UDP-3-O-acyl-N-acetylglucosamine deacetylase (LpxC) is a drug target that has been studied for a long time. However, no LpxC inhibitors are available on the market at present. In this study, we sought to create a new antibacterial agent without a hydroxamate moiety, which is a common component of the major LpxC inhibitors that have been reported to date and that may cause toxicity. As a result, a development candidate, TP0586532, was created that is effective against carbapenem-resistant Klebsiella pneumoniae and does not pose a cardiovascular risk.

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Organizational Affiliation: 

Taisho Pharmaceutical Co., Ltd, 1-403 Yoshino-Cho, Kita-Ku, Saitama 331-9530, Japan. Electronic address: [e-mail].

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 33.56 kDa 
• Atom Count: 2,575 
• Modelled Residue Count: 295 
• Deposited Residue Count: 299 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
UDP-3-O-acyl-N-acetylglucosamine deacetylase	A	299	Pseudomonas aeruginosa PAO1	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 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
H4O (Subject of Investigation/LOI)	C [auth A]	5-[4-[3-[[2-[(1~{S})-1-oxidanylethyl]imidazol-1-yl]methyl]-1,2-oxazol-5-yl]phenyl]pent-4-yn-1-ol C20 H21 N3 O3 LYWGLMYUHVPQCZ-HNNXBMFYSA-N
ZN (Subject of Investigation/LOI)	B [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free:  0.238 (Depositor), 0.240 (DCC) 
• R-Value Work:  0.194 (Depositor), 0.200 (DCC) 
• R-Value Observed: 0.196 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 35.854	α = 90
b = 66.306	β = 90.63
c = 63.542	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
CrysalisPro	data reduction
CrysalisPro	data scaling
MOLREP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2021-01-13 
Deposition Author(s): Mima, M., Ushiyama, F., Matsuda, Y.

Revision History  

• Version 1.0: 2021-01-13
  Type: Initial release
  
• Version 1.1: 2023-11-29
  Changes: Data collection, Database references, Refinement description