7T60

P. aeruginosa LpxA in complex with ligand L13


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.218 
  • R-Value Work: 0.192 
  • R-Value Observed: 0.193 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history


Literature

Structure-Based Ligand Design Targeting Pseudomonas aeruginosa LpxA in Lipid A Biosynthesis.

Sacco, M.D.Defrees, K.Zhang, X.Lawless, W.Nwanochie, E.Balsizer, A.Darch, S.E.Renslo, A.R.Chen, Y.

(2022) ACS Infect Dis 8: 1231-1240

  • DOI: https://doi.org/10.1021/acsinfecdis.1c00650
  • Primary Citation of Related Structures:  
    7T5R, 7T5S, 7T5X, 7T5Z, 7T60, 7T61

  • PubMed Abstract: 

    Enzymes involved in lipid A biosynthesis are promising antibacterial drug targets in Gram-negative bacteria. In this study, we use a structure-based design approach to develop a series of novel tetrazole ligands with low μM affinity for LpxA, the first enzyme in the lipid A pathway. Aided by previous structural data, X-ray crystallography, and surface plasmon resonance bioanalysis, we identify 17 hit compounds. Two of these hits were subsequently modified to optimize interactions with three regions of the LpxA active site. This strategy ultimately led to the discovery of ligand L13, which had a K D of 3.0 μM. The results reveal new chemical scaffolds as potential LpxA inhibitors, important binding features for ligand optimization, and protein conformational changes in response to ligand binding. Specifically, they show that a tetrazole ring is well-accommodated in a small cleft formed between Met169, the "hydrophobic-ruler" and His156, both of which demonstrate significant conformational flexibility. Furthermore, we find that the acyl-chain binding pocket is the most tractable region of the active site for realizing affinity gains and, along with a neighboring patch of hydrophobic residues, preferentially binds aliphatic and aromatic groups. The results presented herein provide valuable chemical and structural information for future inhibitor discovery against this important antibacterial drug target.


  • Organizational Affiliation

    Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, Tampa, Florida 33612, United States.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Acyl-[acyl-carrier-protein]--UDP-N-acetylglucosamine O-acyltransferase
A, B, C, D, E
A, B, C, D, E, F
258Pseudomonas aeruginosa PA7Mutation(s): 0 
Gene Names: lpxAPSPA7_1495
EC: 2.3.1.129
UniProt
Find proteins for A6V1E4 (Pseudomonas aeruginosa (strain PA7))
Explore A6V1E4 
Go to UniProtKB:  A6V1E4
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA6V1E4
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
F9H (Subject of Investigation/LOI)
Query on F9H

Download Ideal Coordinates CCD File 
H [auth B]
K [auth C]
L [auth C]
M [auth C]
N [auth D]
H [auth B],
K [auth C],
L [auth C],
M [auth C],
N [auth D],
O [auth E],
P [auth E],
Q [auth F]
(3S)-3-(5,5-dimethyl-2-oxo-1,3-oxazolidin-3-yl)-N-(1H-tetrazol-5-yl)-1-[3-(trifluoromethyl)benzoyl]-2,3-dihydro-1H-indole-3-carboxamide
C23 H20 F3 N7 O4
CIOWYUCMYWZPAD-JOCHJYFZSA-N
TRS
Query on TRS

Download Ideal Coordinates CCD File 
I [auth B]2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
C4 H12 N O3
LENZDBCJOHFCAS-UHFFFAOYSA-O
GOL
Query on GOL

Download Ideal Coordinates CCD File 
G [auth A],
J [auth B]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.218 
  • R-Value Work: 0.192 
  • R-Value Observed: 0.193 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 80.1α = 90
b = 82.22β = 90
c = 222.01γ = 90
Software Package:
Software NamePurpose
Aimlessdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
MOSFLMdata reduction
MOLREPphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Not funded--

Revision History  (Full details and data files)

  • Version 1.0: 2022-07-06
    Type: Initial release
  • Version 1.1: 2022-07-13
    Changes: Database references
  • Version 1.2: 2022-07-20
    Changes: Database references
  • Version 1.3: 2023-10-18
    Changes: Data collection, Refinement description