5G3W

Structure of HDAC like protein from Bordetella Alcaligenes in complex with the photoswitchable inhibitor CEW65


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.60 Å
  • R-Value Free: 0.167 
  • R-Value Work: 0.125 
  • R-Value Observed: 0.127 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.1 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: 10.1021/acsinfecdis.6b00148
  • Primary Citation of 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 ...

    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.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
HISTONE DEACETYLASE-LIKE AMIDOHYDROLASEA, B, C, D374BordetellaMutation(s): 1 
EC: 3.5.1
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
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 5 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
C65
Query on C65

Download Ideal Coordinates CCD File 
DA [auth D],
K [auth A],
S [auth B],
W [auth C]
(2E)-N-hydroxy-3-{4-[(E)-phenyldiazenyl]phenyl}prop-2-enamide
C15 H13 N3 O2
FBLBOLZQIKQUIK-USZUYCLASA-N
 Ligand Interaction
1PE
Query on 1PE

Download Ideal Coordinates CCD File 
P [auth B],
Y [auth C]
PENTAETHYLENE GLYCOL
C10 H22 O6
JLFNLZLINWHATN-UHFFFAOYSA-N
 Ligand Interaction
PEG
Query on PEG

Download Ideal Coordinates CCD File 
EA [auth D],
FA [auth D],
GA [auth D],
H [auth A],
I [auth A],
EA [auth D],
FA [auth D],
GA [auth D],
H [auth A],
I [auth A],
J [auth A],
O [auth B],
Q [auth B],
R [auth B],
X [auth C],
Z [auth C]
DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
 Ligand Interaction
ZN
Query on ZN

Download Ideal Coordinates CCD File 
AA [auth D],
E [auth A],
L [auth B],
T [auth C]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
K
Query on K

Download Ideal Coordinates CCD File 
BA [auth D],
CA [auth D],
F [auth A],
G [auth A],
M [auth B],
BA [auth D],
CA [auth D],
F [auth A],
G [auth A],
M [auth B],
N [auth B],
U [auth C],
V [auth C]
POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.60 Å
  • R-Value Free: 0.167 
  • R-Value Work: 0.125 
  • R-Value Observed: 0.127 
  • Space Group: I 2 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 92.27α = 90
b = 130.14β = 90
c = 251.13γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
Aimlessdata scaling

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: 2017-03-15
    Changes: Database references