5G1C | pdb_00005g1c

Structure of HDAC like protein from Bordetella Alcaligenes bound the photoswitchable pyrazole Inhibitor CEW395


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.81 Å
  • R-Value Free: 
    0.219 (Depositor), 0.218 (DCC) 
  • R-Value Work: 
    0.171 (Depositor) 
  • R-Value Observed: 
    0.173 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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Ligand Structure Quality Assessment 


This is version 2.0 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: 81.24 kDa 
  • Atom Count: 6,742 
  • Modeled Residue Count: 740 
  • Deposited Residue Count: 740 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
HISTONE DEACETYLASE-LIKE AMIDOHYDROLASE
A, B
370AlcaligenesMutation(s): 0 
EC: 3.5.1.4 (PDB Primary Data), 3.5.1 (UniProt)
UniProt
Find proteins for Q70I53 (Alcaligenes sp. (strain DSM 11172))
Explore Q70I53 
Go to UniProtKB:  Q70I53
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ70I53
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 5 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
9RB

Query on 9RB



Download:Ideal Coordinates CCD File
F [auth A],
O [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
1PE

Query on 1PE



Download:Ideal Coordinates CCD File
G [auth A],
P [auth B]
PENTAETHYLENE GLYCOL
C10 H22 O6
JLFNLZLINWHATN-UHFFFAOYSA-N
PEG

Query on PEG



Download:Ideal Coordinates CCD File
H [auth A]
I [auth A]
J [auth A]
K [auth A]
Q [auth B]
H [auth A],
I [auth A],
J [auth A],
K [auth A],
Q [auth B],
R [auth B],
S [auth B]
DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
ZN

Query on ZN



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

Query on K



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

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.81 Å
  • R-Value Free:  0.219 (Depositor), 0.218 (DCC) 
  • R-Value Work:  0.171 (Depositor) 
  • R-Value Observed: 0.173 (Depositor) 
Space Group: P 42 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 101.099α = 90
b = 101.099β = 90
c = 175.057γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
Aimlessdata scaling
MOLREPphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2016-11-23
    Type: Initial release
  • Version 1.1: 2016-12-28
    Changes: Atomic model, Derived calculations, Non-polymer description, Other
  • Version 1.2: 2017-03-15
    Changes: Database references
  • Version 2.0: 2024-01-10
    Changes: Atomic model, Data collection, Database references, Derived calculations, Other, Refinement description