5VWM

Crystal structure of UDP-3-O-[3-hydroxymyristoyl] N-acetylglucosamine deacetylase (LpxC) from Pseudomonas aeruginosa in complex with CHIR-090 inhibitor


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.178 
  • R-Value Work: 0.138 
  • R-Value Observed: 0.142 

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Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history


Literature

Crystal structure of UDP-3-O-[3-hydroxymyristoyl] N-acetylglucosamine deacetylase (LpxC) from Pseudomonas aeruginosa in complex with CHIR-090 inhibitor

Delker, S.L.Mayclin, S.J.Phan, J.N.Abendroth, J.Lorimer, D.Edwards, T.E.

To be published.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
UDP-3-O-acyl-N-acetylglucosamine deacetylaseA400Pseudomonas aeruginosa PAO1Mutation(s): 0 
Gene Names: lpxCenvAPA4406
EC: 3.5.1.108
UniProt
Find proteins for P47205 (Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1))
Explore P47205 
Go to UniProtKB:  P47205
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP47205
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 5 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
C90
Query on C90

Download Ideal Coordinates CCD File 
B [auth A]N-{(1S,2R)-2-hydroxy-1-[(hydroxyamino)carbonyl]propyl}-4-{[4-(morpholin-4-ylmethyl)phenyl]ethynyl}benzamide
C24 H27 N3 O5
FQYBTYFKOHPWQT-VGSWGCGISA-N
 Ligand Interaction
ZN
Query on ZN

Download Ideal Coordinates CCD File 
C [auth A]ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
EDO
Query on EDO

Download Ideal Coordinates CCD File 
F [auth A],
G [auth A],
H [auth A]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
CA
Query on CA

Download Ideal Coordinates CCD File 
E [auth A]CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
CL
Query on CL

Download Ideal Coordinates CCD File 
D [auth A]CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
Binding Affinity Annotations 
IDSourceBinding Affinity
C90 BindingDB:  5VWM Kd: 0.48 (nM) from 1 assay(s)
IC50: min: 1, max: 310 (nM) from 3 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.178 
  • R-Value Work: 0.138 
  • R-Value Observed: 0.142 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 35.85α = 111.3
b = 47.59β = 109
c = 48.41γ = 98.39
Software Package:
Software NamePurpose
XSCALEdata scaling
PHENIXrefinement
PDB_EXTRACTdata extraction
XDSdata reduction

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2017-06-07
    Type: Initial release
  • Version 1.1: 2017-09-27
    Changes: Data collection
  • Version 1.2: 2018-03-07
    Changes: Data collection
  • Version 1.3: 2019-02-06
    Changes: Data collection, Other