5B8D

Crystal structure of a low occupancy fragment candidate (N-(4-Methyl-1,3-thiazol-2-yl)propanamide) bound adjacent to the ubiquitin binding pocket of the HDAC6 zinc-finger domain

• PDB DOI: https://doi.org/10.2210/pdb5B8D/pdb

• Classification: HYDROLASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2016-06-14 Released: 2016-07-27 
• Deposition Author(s): Harding, R.J., Tempel, W., Collins, P., Pearce, N., Brandao-Neto, J., Douangamath, A., Ravichandran, M., Schapira, M., Bountra, C., Edwards, A.M., von Delft, F., Santhakumar, V., Arrowsmith, C.M., Structural Genomics Consortium (SGC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.05 Å
• R-Value Free: 0.146 
• R-Value Work: 0.128 
• R-Value Observed: 0.129 

Starting Model: experimental

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

• PubMed: 29019676 
• 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.

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Organizational Affiliation: 

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

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 12.4 kDa 
• Atom Count: 999 
• Modelled Residue Count: 100 
• Deposited Residue Count: 107 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Histone deacetylase 6	A	107	Homo sapiens	Mutation(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

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
6T4	G [auth A]	~{N}-(4-methyl-1,3-thiazol-2-yl)ethanamide C6 H8 N2 O S DPDJXTANWGNJOE-UHFFFAOYSA-N
ZN	B [auth A], C [auth A], D [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
FMT	E [auth A], F [auth A]	FORMIC ACID C H2 O2 BDAGIHXWWSANSR-UHFFFAOYSA-N
NA	RA [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N
UNX	AA [auth A], BA [auth A], CA [auth A], DA [auth A], EA [auth A], FA [auth A], GA [auth A], H [auth A], HA [auth A], I [auth A], IA [auth A], J [auth A], JA [auth A], K [auth A], KA [auth A], L [auth A], LA [auth A], M [auth A], MA [auth A], N [auth A], NA [auth A], O [auth A], OA [auth A], P [auth A], PA [auth A], Q [auth A], QA [auth A], R [auth A], S [auth A], T [auth A], U [auth A], V [auth A], W [auth A], X [auth A], Y [auth A], Z [auth A]	UNKNOWN ATOM OR ION X

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.05 Å
• R-Value Free: 0.146 
• R-Value Work: 0.128 
• R-Value Observed: 0.129 
• Space Group: P 2₁ 2₁ 2₁
• Diffraction Data: https://doi.org/10.18430/M35B8D

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 41.434	α = 90
b = 44.157	β = 90
c = 56.549	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
Aimless	data scaling
PDB_EXTRACT	data extraction
XDS	data reduction

Structure Validation

Entry History 

Deposition Data

• Released Date: 2016-07-27 
Deposition Author(s): Harding, R.J., Tempel, W., Collins, P., Pearce, N., Brandao-Neto, J., Douangamath, A., Ravichandran, M., Schapira, M., Bountra, C., Edwards, A.M., von Delft, F., Santhakumar, V., Arrowsmith, C.M., Structural Genomics Consortium (SGC)

Revision History  

• Version 1.0: 2016-07-27
  Type: Initial release
  
• Version 1.1: 2018-03-21
  Changes: Data collection, Database references, Derived calculations
• Version 1.2: 2019-02-27
  Changes: Data collection, Database references
• Version 1.3: 2022-10-12
  Changes: Data collection, Database references, Other
• Version 1.4: 2023-10-18
  Changes: Data collection, Refinement description