5KH3

Crystal structure of fragment (3-(5-Chloro-1,3-benzothiazol-2-yl)propanoic acid) bound in the ubiquitin binding pocket of the HDAC6 zinc-finger domain

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.60 Å
  • R-Value Free: 0.191 
  • R-Value Work: 0.157 
  • R-Value Observed: 0.159 

Starting Model: experimental
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This is version 1.3 of the entry. See complete history. 


Literature

Small Molecule Antagonists of the Interaction between the Histone Deacetylase 6 Zinc-Finger Domain and Ubiquitin.

Harding, R.J., Ferreira de Freitas, R., Collins, P., Franzoni, I., Ravichandran, M., Ouyang, H., Juarez-Ornelas, K.A., Lautens, M., Schapira, M., von Delft, F., Santhakumar, V., Arrowsmith, C.H.

(2017) J Med Chem 60: 9090-9096

  • DOI: https://doi.org/10.1021/acs.jmedchem.7b00933
  • Primary Citation of Related Structures:  
    5B8D, 5KH3, 5KH7, 5KH9, 5WPB

  • PubMed Abstract: 

    Inhibitors of HDAC6 have attractive potential in numerous cancers. HDAC6 inhibitors to date target the catalytic domains, but targeting the unique zinc-finger ubiquitin-binding domain (Zf-UBD) of HDAC6 may be an attractive alternative strategy. We developed X-ray crystallography and biophysical assays to identify and characterize small molecules capable of binding to the Zf-UBD and competing with ubiquitin binding. Our results revealed two adjacent ligand-able pockets of HDAC6 Zf-UBD and the first functional ligands for this domain.

    • Organizational Affiliation: 

    Structural Genomics Consortium, University of Toronto , MaRS South Tower, Suite 700, 101 College Street, Toronto, Ontario M5G 1L7, Canada.


Macromolecules
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(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Histone deacetylase 6107Homo sapiensMutation(s): 0 
Gene Names: HDAC6, KIAA0901, JM21
EC: 3.5.1.98 (PDB Primary Data), 3.5.1 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for Q9UBN7 (Homo sapiens)
Explore Q9UBN7 
Go to UniProtKB:  Q9UBN7
PHAROS:  Q9UBN7
GTEx:  ENSG00000094631 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9UBN7
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
6U6
Query on 6U6
Download Ideal Coordinates CCD File 
R [auth A]3-(5-chloranyl-1,3-benzothiazol-2-yl)propanoic acid
C10 H8 Cl N O2 S
UMBLVHSXXWQLDL-UHFFFAOYSA-N
ZN
Query on ZN
Download Ideal Coordinates CCD File 
B [auth A],
C [auth A],
D [auth A]		ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
UNX
Query on UNX
Download Ideal Coordinates CCD File 
E [auth A]
F [auth A]
G [auth A]
H [auth A]
I [auth A]
E [auth A],
F [auth A],
G [auth A],
H [auth A],
I [auth A],
J [auth A],
K [auth A],
L [auth A],
M [auth A],
N [auth A],
O [auth A],
P [auth A],
Q [auth A]
UNKNOWN ATOM OR ION
X
Binding Affinity Annotations 
IDSourceBinding Affinity
6U6 BindingDB:  5KH3 Kd: min: 4.00e+4, max: 6.00e+4 (nM) from 2 assay(s)
IC50: 5.50e+4 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

Unit Cell:
Length ( Å )Angle ( ˚ )
a = 40.7α = 90
b = 44.027β = 90
c = 55.895γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
Aimlessdata scaling
PDB_EXTRACTdata extraction
XDSdata reduction

Structure Validation

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Ligand Structure Quality Assessment 


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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2016-07-27
    Type: Initial release
  • Version 1.1: 2018-03-21
    Changes: Database references, Derived calculations
  • Version 1.2: 2019-02-27
    Changes: Data collection, Database references
  • Version 1.3: 2023-09-27
    Changes: Data collection, Database references, Refinement description