7OK2

Crystal structure of Pseudomonas aeruginosa LpxA in complex with compound 3


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.89 Å
  • R-Value Free: 0.231 
  • R-Value Work: 0.192 
  • R-Value Observed: 0.194 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


Literature

Discovery of Novel UDP- N -Acetylglucosamine Acyltransferase (LpxA) Inhibitors with Activity against Pseudomonas aeruginosa .

Ryan, M.D.Parkes, A.L.Corbett, D.Dickie, A.P.Southey, M.Andersen, O.A.Stein, D.B.Barbeau, O.R.Sanzone, A.Thommes, P.Barker, J.Cain, R.Compper, C.Dejob, M.Dorali, A.Etheridge, D.Evans, S.Faulkner, A.Gadouleau, E.Gorman, T.Haase, D.Holbrow-Wilshaw, M.Krulle, T.Li, X.Lumley, C.Mertins, B.Napier, S.Odedra, R.Papadopoulos, K.Roumpelakis, V.Spear, K.Trimby, E.Williams, J.Zahn, M.Keefe, A.D.Zhang, Y.Soutter, H.T.Centrella, P.A.Clark, M.A.Cuozzo, J.W.Dumelin, C.E.Deng, B.Hunt, A.Sigel, E.A.Troast, D.M.DeJonge, B.L.M.

(2021) J Med Chem 64: 14377-14425

  • DOI: 10.1021/acs.jmedchem.1c00888
  • Primary Citation of Related Structures:  
    7OJ6, 7OJP, 7OJQ, 7OJW, 7OJY, 7OK1, 7OK2, 7OKA, 7OKB, 7OKC

  • PubMed Abstract: 
  • This study describes a novel series of UDP- N -acetylglucosamine acyltransferase (LpxA) inhibitors that was identified through affinity-mediated selection from a DNA-encoded compound library. The original hit was a selective inhibitor of Pseudomonas aeruginosa LpxA with no activity against Escherichia coli LpxA ...

    This study describes a novel series of UDP- N -acetylglucosamine acyltransferase (LpxA) inhibitors that was identified through affinity-mediated selection from a DNA-encoded compound library. The original hit was a selective inhibitor of Pseudomonas aeruginosa LpxA with no activity against Escherichia coli LpxA. The biochemical potency of the series was optimized through an X-ray crystallography-supported medicinal chemistry program, resulting in compounds with nanomolar activity against P. aeruginosa LpxA (best half-maximal inhibitory concentration (IC 50 ) <5 nM) and cellular activity against P. aeruginosa (best minimal inhibitory concentration (MIC) of 4 μg/mL). Lack of activity against E. coli was maintained (IC 50 > 20 μM and MIC > 128 μg/mL). The mode of action of analogues was confirmed through genetic analyses. As expected, compounds were active against multidrug-resistant isolates. Further optimization of pharmacokinetics is needed before efficacy studies in mouse infection models can be attempted. To our knowledge, this is the first reported LpxA inhibitor series with selective activity against P. aeruginosa .


    Organizational Affiliation

    X-Biotix Therapeutics, 465 Waverly Oaks Road, Waltham, Massachusetts 02452, United States.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Acyl-[acyl-carrier-protein]-UDP-N-acetylglucosamine O-acyltransferase261Pseudomonas 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
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
VFN (Subject of Investigation/LOI)
Query on VFN

Download Ideal Coordinates CCD File 
AB [auth G] , BC [auth T] , CB [auth H] , DB [auth H] , EA [auth 1] , EC [auth V] , FA [auth 1] , GB [auth J] , 
AB [auth G], BC [auth T], CB [auth H], DB [auth H], EA [auth 1], EC [auth V], FA [auth 1], GB [auth J], GC [auth W], HA [auth 2], HC [auth W], IB [auth K], JA [auth 3], KA [auth 3], KB [auth L], LC [auth Z], NA [auth A], NB [auth N], OA [auth A], PB [auth O], QA [auth B], QB [auth O], SB [auth P], TB [auth P], UA [auth D], VA [auth D], WB [auth R], YA [auth F], YB [auth S], ZB [auth S]
~{N}-[(5-azanyl-1,3,4-oxadiazol-2-yl)methyl]-2-(2-chlorophenyl)sulfanyl-~{N}-[(4-cyanophenyl)methyl]ethanamide
C19 H16 Cl N5 O2 S
DDHNQWBEECYOFY-UHFFFAOYSA-N
 Ligand Interaction
SO4
Query on SO4

Download Ideal Coordinates CCD File 
AC [auth S] , BB [auth G] , CC [auth T] , DC [auth U] , EB [auth H] , FB [auth I] , FC [auth V] , GA [auth 1] , 
AC [auth S], BB [auth G], CC [auth T], DC [auth U], EB [auth H], FB [auth I], FC [auth V], GA [auth 1], HB [auth J], IA [auth 2], IC [auth W], JB [auth K], JC [auth X], KC [auth Y], LA [auth 3], LB [auth L], MA [auth 4], MB [auth M], MC [auth Z], OB [auth N], PA [auth A], RA [auth B], RB [auth O], SA [auth C], TA [auth C], UB [auth P], VB [auth Q], WA [auth D], XA [auth E], XB [auth R], ZA [auth F]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.89 Å
  • R-Value Free: 0.231 
  • R-Value Work: 0.192 
  • R-Value Observed: 0.194 
  • Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 247.292α = 90
b = 367.65β = 90
c = 372.076γ = 90
Software Package:
Software NamePurpose
BUSTERrefinement
PDB_EXTRACTdata extraction
xia2data reduction
Aimlessdata scaling
MOLREPphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment  



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2021-10-13
    Type: Initial release
  • Version 1.1: 2021-10-27
    Changes: Data collection, Database references