6CEE

Crystal structure of fragment 3-(1-Methyl-2-oxo-1,2-dihydroquinoxalin-3-yl)propionic acid bound in the ubiquitin binding pocket of the HDAC6 zinc-finger domain


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.55 Å
  • R-Value Free: 0.169 
  • R-Value Work: 0.153 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Identification and Structure-Activity Relationship of HDAC6 Zinc-Finger Ubiquitin Binding Domain Inhibitors.

Ferreira de Freitas, R.Harding, R.J.Franzoni, I.Ravichandran, M.Mann, M.K.Ouyang, H.Lautens, M.Santhakumar, V.Arrowsmith, C.H.Schapira, M.

(2018) J. Med. Chem. 61: 4517-4527

  • DOI: 10.1021/acs.jmedchem.8b00258
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • HDAC6 plays a central role in the recruitment of protein aggregates for lysosomal degradation and is a promising target for combination therapy with proteasome inhibitors in multiple myeloma. Pharmacologically displacing ubiquitin from the zinc-finge ...

    HDAC6 plays a central role in the recruitment of protein aggregates for lysosomal degradation and is a promising target for combination therapy with proteasome inhibitors in multiple myeloma. Pharmacologically displacing ubiquitin from the zinc-finger ubiquitin-binding domain (ZnF-UBD) of HDAC6 is an underexplored alternative to catalytic inhibition. Here, we present the discovery of an HDAC6 ZnF-UBD-focused chemical series and its progression from virtual screening hits to low micromolar inhibitors. A carboxylate mimicking the C-terminal extremity of ubiquitin, and an extended aromatic system stacking with W1182 and R1155, are necessary for activity. One of the compounds induced a conformational remodeling of the binding site where the primary binding pocket opens up onto a ligand-able secondary pocket that may be exploited to increase potency. The preliminary structure-activity relationship accompanied by nine crystal structures should enable further optimization into a chemical probe to investigate the merit of targeting the ZnF-UBD of HDAC6 in multiple myeloma and other diseases.


    Organizational Affiliation

    Department of Pharmacology and Toxicology , University of Toronto , Toronto , Ontario M5S 1A8 , Canada.,Department of Chemistry, Davenport Chemical Laboratories , University of Toronto , 80 St. George Street , Toronto , Ontario M5S 3H6 Canada.,Structural Genomics Consortium , University of Toronto , MaRS South Tower, Suite 700, 101 College Street , Toronto , Ontario M5G 1L7 , Canada.,Princess Margaret Cancer Centre , University Health Network , Toronto , Ontario , Canada.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Histone deacetylase 6
A
107Homo sapiensMutation(s): 0 
Gene Names: HDAC6 (KIAA0901)
EC: 3.5.1.98
Find proteins for Q9UBN7 (Homo sapiens)
Go to Gene View: HDAC6
Go to UniProtKB:  Q9UBN7
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

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

Download SDF File 
Download CCD File 
A
3-(4-methyl-3-oxo-3,4-dihydroquinoxalin-2-yl)propanoic acid
C12 H12 N2 O3
JIXBAXULUJSRDR-UHFFFAOYSA-N
 Ligand Interaction
UNX
Query on UNX

Download SDF File 
Download CCD File 
A
UNKNOWN ATOM OR ION
X
*
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
EYMIC50: 65000 nM BINDINGMOAD
Experimental Data & Validation

Experimental Data

Unit Cell:
Length (Å)Angle (°)
a = 40.720α = 90.00
b = 44.110β = 90.00
c = 55.910γ = 90.00
Software Package:
Software NamePurpose
REFMACrefinement
xia2data reduction
PDB_EXTRACTdata extraction
Aimlessdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Revision History 

  • Version 1.0: 2018-02-28
    Type: Initial release
  • Version 1.1: 2018-05-16
    Type: Data collection, Database references
  • Version 1.2: 2018-05-30
    Type: Data collection, Database references