5LI3 | pdb_00005li3

Crystal structure of HDAC-like protein from P. aeruginosa in complex with a photo-switchable inhibitor.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 
    0.270 (Depositor), 0.276 (DCC) 
  • R-Value Work: 
    0.225 (Depositor) 
  • R-Value Observed: 
    0.227 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 5LI3

Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history

Literature

Toward Photopharmacological Antimicrobial Chemotherapy Using Photoswitchable Amidohydrolase Inhibitors.

Weston, C.E.Kramer, A.Colin, F.Yildiz, O.Baud, M.G.Meyer-Almes, F.J.Fuchter, M.J.

(2017) ACS Infect Dis 3: 152-161

  • DOI: https://doi.org/10.1021/acsinfecdis.6b00148
  • Primary Citation Related Structures: 
    5G1C, 5G3W, 5LI3

  • PubMed Abstract: 

    Photopharmacological agents exhibit light-dependent biological activity and may have potential in the development of new antimicrobial agents/modalities. Amidohydrolase enzymes homologous to the well-known human histone deacetylases (HDACs) are present in bacteria, including resistant organisms responsible for a significant number of hospital-acquired infections and deaths. We report photopharmacological inhibitors of these enzymes, using two classes of photoswitches embedded in the inhibitor pharmacophore: azobenzenes and arylazopyrazoles. Although both classes of inhibitor show excellent inhibitory activity (nM IC 50 values) of the target enzymes and promising differential activity of the switchable E- and Z-isomeric forms, the arylazopyrazoles exhibit better intrinsic photoswitch performance (more complete switching, longer thermal lifetime of the Z-isomer). We also report protein-ligand crystal structures of the E-isomers of both an azobenzene and an arylazopyrazole inhibitor, bound to bacterial histone deacetylase-like amidohydrolases (HDAHs). These structures not only uncover interactions important for inhibitor binding but also reveal conformational differences between the two photoswitch inhibitor classes. As such, our data may pave the way for the design of improved photopharmacological agents targeting the HDAC superfamily.


  • Organizational Affiliation
    • Department of Chemistry, Imperial College London , London SW7 2AZ, United Kingdom.

Macromolecule Content 

  • Total Structure Weight: 83.08 kDa 
  • Atom Count: 5,857 
  • Modeled Residue Count: 742 
  • Deposited Residue Count: 760 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Acetoin utilization protein
A, B
380Pseudomonas aeruginosaMutation(s): 0 
Gene Names: AO946_14160
EC: 3.5.1
UniProt
Find proteins for Q9HXM1 (Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1))
Explore Q9HXM1 
Go to UniProtKB:  Q9HXM1
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9HXM1
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
9RB

Query on 9RB



Download:Ideal Coordinates CCD File
F [auth A],
J [auth B]
(2E)-N-hydroxy-3-{4-[(E)-(1,3,5-trimethyl-1H-pyrazol-4-yl)diazenyl]phenyl}prop-2-enamide
C15 H17 N5 O2
GGZOJTXQALEQJU-OUWLFTCQSA-N
ZN

Query on ZN



Download:Ideal Coordinates CCD File
C [auth A],
G [auth B]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
K

Query on K



Download:Ideal Coordinates CCD File
D [auth A],
E [auth A],
H [auth B],
I [auth B]
POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free:  0.270 (Depositor), 0.276 (DCC) 
  • R-Value Work:  0.225 (Depositor) 
  • R-Value Observed: 0.227 (Depositor) 
Space Group: P 41 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 82.19α = 90
b = 82.19β = 90
c = 217.03γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
Aimlessdata scaling
MOLREPphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
German Research FoundationGermanyME 3122/2-1

Revision History  (Full details and data files)

  • Version 1.0: 2016-11-23
    Type: Initial release
  • Version 1.1: 2017-02-22
    Changes: Database references
  • Version 1.2: 2017-09-06
    Changes: Author supporting evidence
  • Version 1.3: 2024-01-10
    Changes: Data collection, Database references, Derived calculations, Refinement description