3PS1

Crystal structure of the Escherichia Coli LPXC/LPC-011 complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.85 Å
  • R-Value Free: 0.210 
  • R-Value Work: 0.193 

wwPDB Validation 3D Report Full Report


This is version 1.4 of the entry. See complete history

Literature

Syntheses, structures and antibiotic activities of LpxC inhibitors based on the diacetylene scaffold.

Liang, X.Lee, C.J.Chen, X.Chung, H.S.Zeng, D.Raetz, C.R.Li, Y.Zhou, P.Toone, E.J.

(2011) Bioorg.Med.Chem. 19: 852-860

  • DOI: 10.1016/j.bmc.2010.12.017
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Compounds inhibiting LpxC in the lipid A biosynthetic pathway are promising leads for novel antibiotics against multidrug-resistant Gram-negative pathogens. We report the syntheses and structural and biochemical characterizations of LpxC inhibitors b ...

    Compounds inhibiting LpxC in the lipid A biosynthetic pathway are promising leads for novel antibiotics against multidrug-resistant Gram-negative pathogens. We report the syntheses and structural and biochemical characterizations of LpxC inhibitors based on a diphenyl-diacetylene (1,4-diphenyl-1,3-butadiyne) threonyl-hydroxamate scaffold. These studies provide a molecular interpretation for the differential antibiotic activities of compounds with a substituted distal phenyl ring as well as the absolute stereochemical requirement at the C2, but not C3, position of the threonyl group.


    Organizational Affiliation

    Department of Chemistry, Jilin University, Changchun, PR China.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
UDP-3-O-[3-hydroxymyristoyl] N-acetylglucosamine deacetylase
A
300N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Small Molecules
Ligands 5 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download SDF File 
Download CCD File 
A
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
SO4
Query on SO4

Download SDF File 
Download CCD File 
A
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
ZH2
Query on ZH2

Download SDF File 
Download CCD File 
A
4-[4-(4-aminophenyl)buta-1,3-diyn-1-yl]-N-[(2S,3R)-3-hydroxy-1-(hydroxyamino)-1-oxobutan-2-yl]benzamide
C21 H19 N3 O4
SNVYDNOGPYZQEV-KUHUBIRLSA-N
 Ligand Interaction
DMS
Query on DMS

Download SDF File 
Download CCD File 
A
DIMETHYL SULFOXIDE
C2 H6 O S
IAZDPXIOMUYVGZ-UHFFFAOYSA-N
 Ligand Interaction
UKW
Query on UKW

Download SDF File 
Download CCD File 
A
4-ethynyl-N-[(1S,2R)-2-hydroxy-1-(oxocarbamoyl)propyl]benzamide
C13 H12 N2 O4
JJXZDQZGPLQGCP-KCJUWKMLSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
ZH2Ki: 0.067 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.85 Å
  • R-Value Free: 0.210 
  • R-Value Work: 0.193 
  • Space Group: P 61
Unit Cell:
Length (Å)Angle (°)
a = 107.130α = 90.00
b = 107.130β = 90.00
c = 52.087γ = 120.00
Software Package:
Software NamePurpose
DENZOdata reduction
PHASERphasing
SCALEPACKdata scaling
PHENIXrefinement
HKL-2000data collection
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2010-11-30 
  • Released Date: 2011-01-19 
  • Deposition Author(s): Lee, C.-J., Zhou, P.

Revision History 

  • Version 1.0: 2011-01-19
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance
  • Version 1.2: 2015-09-23
    Type: Non-polymer description
  • Version 1.3: 2017-11-08
    Type: Refinement description
  • Version 1.4: 2018-01-24
    Type: Structure summary