6CE6

Structure of HDAC6 zinc-finger ubiquitin binding domain soaked with 3,3'-(benzo[1,2-d:5,4-d']bis(thiazole)-2,6-diyl)dipropionic acid


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.60 Å
  • R-Value Free: 0.196 
  • R-Value Work: 0.172 
  • R-Value Observed: 0.173 

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:  
    6CE6, 6CEA, 6CEC, 6CEE, 6CED, 6CEF, 6CE8

  • 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-finger ubiquitin-binding domain (ZnF-UBD) of HDAC6 is an underexplored alternative to catalytic inhibition ...

    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.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Histone deacetylase 6A107Homo sapiensMutation(s): 0 
Gene Names: HDAC6KIAA0901JM21
EC: 3.5.1.98 (PDB Primary Data), 3.5.1 (UniProt)
Find proteins for Q9UBN7 (Homo sapiens)
Explore Q9UBN7 
Go to UniProtKB:  Q9UBN7
NIH Common Fund Data Resources
PHAROS:  Q9UBN7
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
EYP
Query on EYP

Download Ideal Coordinates CCD File 
H [auth A]3,3'-(benzo[1,2-d:5,4-d']bis[1,3]thiazole-2,6-diyl)dipropanoic acid
C14 H12 N2 O4 S2
RNLHVOCFLIRTNO-UHFFFAOYSA-N
 Ligand Interaction
ZN
Query on ZN

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

Download Ideal Coordinates CCD File 
E [auth A], F [auth A], G [auth A]UNKNOWN ATOM OR ION
X
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
EYPIC50:  5100   nM  Binding MOAD
Experimental Data & Validation

Experimental Data

Unit Cell:
Length ( Å )Angle ( ˚ )
a = 40.6α = 90
b = 45.32β = 90
c = 55.82γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
Aimlessdata scaling
PDB_EXTRACTdata extraction
xia2data reduction

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

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