5N8C

Crystal structure of Pseudomonas aeruginosa LpxC complexed with inhibitor


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.203 
  • R-Value Work: 0.149 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Structure-based discovery of LpxC inhibitors.

Zhang, J.Chan, A.Lippa, B.Cross, J.B.Liu, C.Yin, N.Romero, J.A.Lawrence, J.Heney, R.Herradura, P.Goss, J.Clark, C.Abel, C.Zhang, Y.Poutsiaka, K.M.Epie, F.Conrad, M.Mahamoon, A.Nguyen, K.Chavan, A.Clark, E.Li, T.C.Cheng, R.K.Wood, M.Andersen, O.A.Brooks, M.Kwong, J.Barker, J.Parr, I.B.Gu, Y.Ryan, M.D.Coleman, S.Metcalf, C.A.

(2017) Bioorg. Med. Chem. Lett. 27: 1670-1680

  • DOI: 10.1016/j.bmcl.2017.03.006

  • PubMed Abstract: 
  • The emergence and spread of multidrug-resistant (MDR) Gram negative bacteria presents a serious threat for public health. Novel antimicrobials that could overcome the resistance problems are urgently needed. UDP-3-O-(R-3-hydroxymyristol)-N-acetylgluc ...

    The emergence and spread of multidrug-resistant (MDR) Gram negative bacteria presents a serious threat for public health. Novel antimicrobials that could overcome the resistance problems are urgently needed. UDP-3-O-(R-3-hydroxymyristol)-N-acetylglucosamine deacetylase (LpxC) is a cytosolic zinc-based deacetylase that catalyzes the first committed step in the biosynthesis of lipid A, which is essential for the survival of Gram-negative bacteria. Our efforts toward the discovery of novel LpxC inhibitors are presented herein.


    Organizational Affiliation

    Cubist Pharmaceuticals Inc., 65 Hayden Avenue, Lexington, MA 02421, USA. Electronic address: jackzhang49@yahoo.com.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
UDP-3-O-acyl-N-acetylglucosamine deacetylase
A, B
304Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1)Mutation(s): 1 
Gene Names: lpxC (envA)
EC: 3.5.1.108
Find proteins for P47205 (Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1))
Go to UniProtKB:  P47205
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

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

Download SDF File 
Download CCD File 
A, B
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
8Q8
Query on 8Q8

Download SDF File 
Download CCD File 
A, B
(2~{S})-3-azanyl-2-[[(1~{R})-5-[2-[4-[[2-(hydroxymethyl)imidazol-1-yl]methyl]phenyl]ethynyl]-2,3-dihydro-1~{H}-inden-1-yl]amino]-3-methyl-~{N}-oxidanyl-butanamide
C27 H31 N5 O3
HMFUASPGNDZNJF-ILBGXUMGSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.203 
  • R-Value Work: 0.149 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 35.440α = 90.00
b = 95.310β = 96.34
c = 89.720γ = 90.00
Software Package:
Software NamePurpose
PDB_EXTRACTdata extraction
PHASERphasing
SCALAdata scaling
MOSFLMdata reduction
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2017-03-29
    Type: Initial release
  • Version 1.1: 2017-04-12
    Type: Database references