6V7A | pdb_00006v7a

Crystal structure of Danio rerio histone deacetylase 6 catalytic domain 2 (CD2) complexed with NF2657

• PDB DOI: https://doi.org/10.2210/pdb6V7A/pdb

• Classification: HYDROLASE
• Organism(s): Danio rerio
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2019-12-08 Released: 2020-12-02 
• Deposition Author(s): Osko, J.D., Christianson, D.W.
• Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.09 Å
• R-Value Free: 
  0.239 (Depositor), 0.249 (DCC) 
• R-Value Work: 
  0.193 (Depositor), 0.201 (DCC) 
• R-Value Observed: 
  0.196 (Depositor) 

Starting Model: experimental

Literature

Spiroindoline-Capped Selective HDAC6 Inhibitors: Design, Synthesis, Structural Analysis, and Biological Evaluation.

Saraswati, A.P., Relitti, N., Brindisi, M., Osko, J.D., Chemi, G., Federico, S., Grillo, A., Brogi, S., McCabe, N.H., Turkington, R.C., Ibrahim, O., O'Sullivan, J., Lamponi, S., Ghanim, M., Kelly, V.P., Zisterer, D., Amet, R., Hannon Barroeta, P., Vanni, F., Ulivieri, C., Herp, D., Sarno, F., Di Costanzo, A., Saccoccia, F., Ruberti, G., Jung, M., Altucci, L., Gemma, S., Butini, S., Christianson, D.W., Campiani, G.

(2020) ACS Med Chem Lett 11: 2268-2276

• PubMed: 33214839 
• DOI: https://doi.org/10.1021/acsmedchemlett.0c00395
• Primary Citation Related Structures: 
  6V7A


• PubMed Abstract: 
  

  Histone deacetylase inhibitors (HDACi) have emerged as promising therapeutics for the treatment of neurodegeneration, cancer, and rare disorders. Herein, we report the development of a series of spiroindoline-based HDAC6 isoform-selective inhibitors based on the X-ray crystal studies of the hit 6a . We identified compound 6j as the most potent and selective h HDAC6 inhibitor of the series. Biological investigation of compounds 6b , 6h , and 6j demonstrated their antiproliferative activity against several cancer cell lines. Western blotting studies indicated that they were able to increase tubulin acetylation, without significant variation in histone acetylation state, and induced PARP cleavage indicating their apoptotic potential at the molecular level. 6j induced HDAC6-dependent pSTAT3 inhibition.

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Organizational Affiliation: 
• Department of Biotechnology, Chemistry and Pharmacy, DoE Department of Excellence 2018-2022, University of Siena, via Aldo Moro 2, I-53100 Siena, Italy.
Roy and Diana Vagelos Laboratories, Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania 19104-6323, United States.
Department of Pharmacy, University of Pisa, via Bonanno 6, 56126, Pisa, Italy.
Centre for Cancer Research and Cell Biology, Queens University Belfast, Belfast, U.K.
School of Dental Science, Trinity College Dublin, Lincoln Place, Dublin 2, Ireland.
School of Biochemistry and Immunology, Trinity Biomedical Science Institute, Trinity College, 152-160, Pearse Street, Dublin 2, Ireland.
Department of Life Sciences, University of Siena, via Aldo Moro 2, I-53100 Siena, Italy.
Institute of Pharmaceutical Sciences, Albert-Ludwigs-Universität Freiburg, Albertstraße 25, 79104, Freiburg, Germany.
Department of Precision Medicine, University of Campania "Luigi Vanvitelli″, 80138 Naples, Italy.
Institute of Biochemistry and Cell Biology (IBBC), National Research Council (CNR), via E. Ramarini 32, 00015 Monterotondo, Rome, Italy.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 40.78 kDa 
• Atom Count: 2,930 
• Modeled Residue Count: 357 
• Deposited Residue Count: 364 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Hdac6 protein	A	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 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
QQG (Subject of Investigation/LOI)	E [auth A]	N-hydroxy-4-[(1-methyl-1,2-dihydro-1'H-spiro[indole-3,4'-piperidin]-1'-yl)methyl]benzamide C21 H25 N3 O2 KRAFQDJIYXJLQM-UHFFFAOYSA-N
ZN	B [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
K	C [auth A], D [auth A]	POTASSIUM ION K NPYPAHLBTDXSSS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.09 Å
• R-Value Free:  0.239 (Depositor), 0.249 (DCC) 
• R-Value Work:  0.193 (Depositor), 0.201 (DCC) 
• R-Value Observed: 0.196 (Depositor) 

Space Group: P 2 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 45.461	α = 90
b = 64.871	β = 90
c = 142.393	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: 2020-12-02 
Deposition Author(s): Osko, J.D., Christianson, D.W.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	GM49758

Revision History  

• Version 1.0: 2020-12-02
  Type: Initial release
  
• Version 1.1: 2023-10-11
  Changes: Data collection, Database references, Refinement description