6VNR | pdb_00006vnr

Crystal Structure of Danio rerio Histone Deacetylase 6 Catalytic Domain 2 (CD2) Complexed with Bishydroxamic Acid Inhibitor

• PDB DOI: https://doi.org/10.2210/pdb6VNR/pdb

• Classification: Hydrolase/Hydrolase Inhibitor
• Organism(s): Danio rerio
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2020-01-29 Released: 2020-05-13 
• Deposition Author(s): Osko, J.D., Porter, N.J., Christianson, D.W.
• Funding Organization(s): National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI)

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.94 Å
• R-Value Free: 
  0.211 (Depositor), 0.211 (DCC) 
• R-Value Work: 
  0.163 (Depositor), 0.163 (DCC) 
• R-Value Observed: 
  0.165 (Depositor) 

Starting Model: experimental

Literature

Design and Synthesis of Dihydroxamic Acids as HDAC6/8/10 Inhibitors.

Morgen, M., Steimbach, R.R., Geraldy, M., Hellweg, L., Sehr, P., Ridinger, J., Witt, O., Oehme, I., Herbst-Gervasoni, C.J., Osko, J.D., Porter, N.J., Christianson, D.W., Gunkel, N., Miller, A.K.

(2020) ChemMedChem 15: 1163-1174

• PubMed: 32348628 
• DOI: https://doi.org/10.1002/cmdc.202000149
• Primary Citation Related Structures: 
  6VNQ, 6VNR


• PubMed Abstract: 
  

  We report the synthesis and evaluation of a class of selective multitarget agents for the inhibition of HDAC6, HDAC8, and HDAC10. The concept for this study grew out of a structural analysis of the two selective inhibitors Tubastatin A (HDAC6/10) and PCI-34051 (HDAC8), which we recognized share the same N-benzylindole core. Hybridization of the two inhibitor structures resulted in dihydroxamic acids with benzyl-indole and -indazole core motifs. These substances exhibit potent activity against HDAC6, HDAC8, and HDAC10, while retaining selectivity over HDAC1, HDAC2, and HDAC3. The best substance inhibited the viability of the SK-N-BE(2)C neuroblastoma cell line with an IC ₅₀ value similar to a combination treatment with Tubastatin A and PCI-34051. This compound class establishes a proof of concept for such hybrid molecules and could serve as a starting point for the further development of enhanced HDAC6/8/10 inhibitors.

---

Organizational Affiliation: 
• Cancer Drug Development Group, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, 69120, Heidelberg, Germany.
Faculty of Biosciences, University of Heidelberg, 69120, Heidelberg, Germany.
Chemical Biology Core Facility, European Molecular Biology Laboratory (EMBL), 69117, Heidelberg, Germany.
Hopp Children's Cancer Center Heidelberg (KiTZ), 69120, Heidelberg, Germany.
Clinical Cooperation Unit Pediatric Oncology, German Cancer Research Center (DKFZ), 69120, Heidelberg, Germany.
Department of Pediatric Oncology, Hematology and Immunology, University Hospital Heidelberg, 69120, Heidelberg, Germany.
German Cancer Consortium (DKTK), 69120, Heidelberg, Germany.
Roy and Diana Vagelos Laboratories, Department of Chemistry, University of Pennsylvania, Philadelphia, PA 19104-6323, USA.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Biological Assembly 2  

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

Biological assembly 2 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 81.63 kDa 
• Atom Count: 5,990 
• Modeled Residue Count: 708 
• Deposited Residue Count: 728 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Hdac6 protein	A, B	364	Danio rerio	Mutation(s): 0  Gene Names: hdac6
UniProt
Find proteins for F8W4B7 (Danio rerio) Explore F8W4B7  Go to UniProtKB:  F8W4B7

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
R5G (Subject of Investigation/LOI)	F [auth A], L [auth B]	N-hydroxy-1-{[4-(hydroxycarbamoyl)phenyl]methyl}-1H-indole-6-carboxamide C17 H15 N3 O4 IRJZGNPPEWBPKI-UHFFFAOYSA-N
ZN	C [auth A], I [auth B]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
EDO	G [auth A], H [auth A]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N
K	D [auth A], E [auth A], J [auth B], K [auth B]	POTASSIUM ION K NPYPAHLBTDXSSS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.94 Å
• R-Value Free:  0.211 (Depositor), 0.211 (DCC) 
• R-Value Work:  0.163 (Depositor), 0.163 (DCC) 
• R-Value Observed: 0.165 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 48.38	α = 90
b = 107.14	β = 90
c = 74.35	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
iMOSFLM	data reduction
Aimless	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2020-05-13 
Deposition Author(s): Osko, J.D., Porter, N.J., Christianson, D.W.

---

Funding Organization	Location	Grant Number
National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI)	United States	GM49758

Revision History  

• Version 1.0: 2020-05-13
  Type: Initial release
  
• Version 1.1: 2020-07-15
  Changes: Database references
• Version 1.2: 2023-10-11
  Changes: Data collection, Database references, Derived calculations, Refinement description