6P86

E.coli LpxD in complex with compound 4.1


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.192 
  • R-Value Work: 0.167 
  • R-Value Observed: 0.168 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


Literature

Structural and Biological Basis of Small Molecule Inhibition ofEscherichia coliLpxD Acyltransferase Essential for Lipopolysaccharide Biosynthesis.

Ma, X.Prathapam, R.Wartchow, C.Chie-Leon, B.Ho, C.M.De Vicente, J.Han, W.Li, M.Lu, Y.Ramurthy, S.Shia, S.Steffek, M.Uehara, T.

(2020) ACS Infect Dis 6: 1480-1489

  • DOI: 10.1021/acsinfecdis.9b00127
  • Primary Citation of Related Structures:  
    6P83, 6P84, 6P85, 6P86, 6P87, 6P88, 6P89, 6P8A, 6P8B

  • PubMed Abstract: 
  • LpxD, acyl-ACP-dependent N -acyltransferase, is the third enzyme of lipid A biosynthesis in Gram-negative bacteria. A recent probe-based screen identified several compounds, including 6359-0284 (compound 1 ), that inhibit the enzymatic activity of Escherichia coli ( E ...

    LpxD, acyl-ACP-dependent N -acyltransferase, is the third enzyme of lipid A biosynthesis in Gram-negative bacteria. A recent probe-based screen identified several compounds, including 6359-0284 (compound 1 ), that inhibit the enzymatic activity of Escherichia coli ( E. coli ) LpxD. Here, we use these inhibitors to chemically validate LpxD as an attractive antibacterial target. We first found that compound 1 was oxidized in solution to the more stable aromatized tetrahydro-pyrazolo-quinolinone compound 1o . From the Escherichia coli strain deficient in efflux, we isolated a mutant that was less susceptible to compound 1o and had an lpxD missense mutation (Gly268Cys), supporting the cellular on-target activity. Using surface plasma resonance, we showed direct binding to E. coli LpxD for compound 1o and other reported LpxD inhibitors in vitro . Furthermore, we determined eight cocrystal structures of E. coli LpxD/inhibitor complexes. These costructures pinpointed the 4'-phosphopantetheine binding site as the common ligand binding hotspot, where hydrogen bonds to Gly269 and/or Gly287 were important for inhibitor binding. In addition, the LpxD/compound 1o costructure rationalized the reduced activity of compound 1o in the LpxD Gly268Cys mutant. Moreover, we obtained the LpxD structure in complex with a previously reported LpxA/LpxD dual targeting peptide inhibitor, RJPXD33, providing structural rationale for the unique dual targeting properties of this peptide. Given that the active site residues of LpxD are conserved in multidrug resistant Enterobacteriaceae, this work paves the way for future LpxD drug discovery efforts combating these Gram-negative pathogens.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
UDP-3-O-(3-hydroxymyristoyl)glucosamine N-acyltransferaseA, B, C343Escherichia coliMutation(s): 0 
Gene Names: 
lpxDlpxD_1lpxD_2A8C65_17800A9R57_04450AC789_1c01770ACN002_0184ACN77_17005ACN81_28485ACU57_18525ACU90_26495AM270_18210AML07_22885AML35_22825APZ14_11060AUQ13_07450AUS26_23195AW059_09890AW106_08805B1K96_12940B7C53_01310BANRA_00558BANRA_00653BANRA_02262BANRA_03350BET08_19125BHF46_07835BHS81_00700BHS87_00855BIZ41_19025BJJ90_21310BK292_13720BK400_03560BMT53_09465BN17_46021BTQ06_06540BUE81_01655BVL39_02135BW690_02415BZL31_14885C2U48_09555C4J69_03380C5N07_08630C5P01_08975C5P43_07335C6669_04195C6986_01145C7235_20180C7B06_05915C7B07_04225CA593_02815CG691_14440CG692_09445CG705_12975CG706_12690COD30_14715COD46_06685CR538_20590CR539_04985CRM83_15040CXB56_23080D0X26_09365D2184_08545D2185_20180D2F89_01460D3821_06260D3O91_03240D3Y67_16455D9D20_18680D9D55_03030D9D69_06830D9E22_13300D9E35_14480D9G42_07535D9H66_18155D9H68_13825D9I18_15010D9I87_01590D9I97_03755D9J11_16875D9J44_14030DIV22_06320DL545_20340DMZ31_06810DNQ41_04690DNQ45_10065DQF57_05615DQO13_06200DS732_05825DTL43_05870EAI42_08350EAI46_03595EAI52_11055EC1094V2_3672EC3234A_2c01610EC3426_00931EC382_03005ECTO6_03883ED287_04550ED600_04595EEP23_00115EFV01_09910EFV02_20465EFV04_15215EFV08_17150EFV11_08135EFV12_18845EFV15_17225EFV17_09875EIA13_13600EL75_3585EL79_3695EL80_3642ERS085374_03841ERS150873_01122ERS150876_00054FORC28_5013HW43_04650JD73_13090NCTC10429_04183NCTC10865_05054NCTC11022_04906NCTC11126_03647NCTC13462_02218NCTC8500_04533NCTC8960_01551NCTC9037_04178NCTC9045_04699NCTC9055_00956NCTC9058_02808NCTC9062_04225NCTC9706_01326NCTC9969_04255PU06_22990RG28_03860RK56_027945RX35_04913SAMEA3472043_02537SAMEA3472044_04146SAMEA3472047_02509SAMEA3472070_02384SAMEA3472080_03763SAMEA3472114_03609SAMEA3484427_01386SAMEA3484429_01095SAMEA3752553_02884SAMEA3752557_00885SAMEA3752559_03701SAMEA3753064_03381SAMEA3753097_03916SAMEA3753290_00404SAMEA3753300_01852SK85_00179WQ89_09605WR15_02380

EC: 2.3.1.191
UniProt
Find proteins for P21645 (Escherichia coli (strain K12))
Explore P21645 
Go to UniProtKB:  P21645
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
O4S (Subject of Investigation/LOI)
Query on O4S

Download Ideal Coordinates CCD File 
F [auth A]N-[(4-ethylphenyl)methyl]-2-[(6aR)-6-oxo-3-(pyrrolidine-1-carbonyl)-6,6a,7,8,9,10-hexahydro-5H-pyrido[1,2-a]quinoxalin-5-yl]acetamide
C28 H34 N4 O3
HPKMORZWWWMLAR-XMMPIXPASA-N
 Ligand Interaction
O3V (Subject of Investigation/LOI)
Query on O3V

Download Ideal Coordinates CCD File 
G [auth B], H [auth C]3-hydroxy-7,7-dimethyl-2-phenyl-4-(thiophen-2-yl)-2,6,7,8-tetrahydro-5H-pyrazolo[3,4-b]quinolin-5-one
C22 H19 N3 O2 S
UAVKPYTVCWRHPL-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

Download Ideal Coordinates CCD File 
D [auth A], E [auth A]MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.192 
  • R-Value Work: 0.167 
  • R-Value Observed: 0.168 
  • Space Group: P 32 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 97.617α = 90
b = 97.617β = 90
c = 216.638γ = 120
Software Package:
Software NamePurpose
SCALAdata scaling
PHENIXrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
PHASERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment  



Entry History 

Deposition Data

  • Deposited Date: 2019-06-06 
  • Released Date: 2019-08-28 
  • Deposition Author(s): Ma, X., Shia, S.

Revision History  (Full details and data files)

  • Version 1.0: 2019-08-28
    Type: Initial release
  • Version 1.1: 2020-06-24
    Changes: Database references