5KH9

Crystal structure of a low occupancy fragment candidate (5-[(4-Isopropylphenyl)amino]-6-methyl-1,2,4-triazin-3(2H)-one) bound in the ubiquitin binding pocket of the HDAC6 zinc-finger domain


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.07 Å
  • R-Value Free: 0.150 
  • R-Value Work: 0.136 

wwPDB Validation 3D Report Full Report


This is version 1.1 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: 10.1021/acs.jmedchem.7b00933
  • Primary Citation of Related Structures:  

  • 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 de ...

    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

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 5 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

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A
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
NA
Query on NA

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A
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
FMT
Query on FMT

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A
FORMIC ACID
C H2 O2
BDAGIHXWWSANSR-UHFFFAOYSA-N
 Ligand Interaction
UNX
Query on UNX

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A
UNKNOWN ATOM OR ION
X
*
 Ligand Interaction
6T5
Query on 6T5

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Download CCD File 
A
6-methyl-5-[(4-propan-2-ylphenyl)amino]-2~{H}-1,2,4-triazin-3-one
C13 H16 N4 O
SRUWPAISQUBIOQ-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

Unit Cell:
Length (Å)Angle (°)
a = 41.434α = 90.00
b = 44.157β = 90.00
c = 56.549γ = 90.00
Software Package:
Software NamePurpose
XDSdata reduction
PDB_EXTRACTdata extraction
REFMACrefinement
Aimlessdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Revision History 

  • Version 1.0: 2016-07-27
    Type: Initial release
  • Version 1.1: 2018-03-21
    Type: Data collection, Database references, Derived calculations