6V7A

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.09 Å
  • R-Value Free: 0.239 
  • R-Value Work: 0.193 
  • R-Value Observed: 0.196 

wwPDB Validation   3D Report Full Report

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This is version 1.1 of the entry. See complete history


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

  • DOI: https://doi.org/10.1021/acsmedchemlett.0c00395
  • Primary Citation of 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.


  • 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.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Hdac6 protein364Danio rerioMutation(s): 0 
Gene Names: hdac6
UniProt
Find proteins for F8W4B7 (Danio rerio)
Explore F8W4B7 
Go to UniProtKB:  F8W4B7
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupF8W4B7
Sequence Annotations
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  • Reference Sequence
Small Molecules
Binding Affinity Annotations 
IDSourceBinding Affinity
QQG Binding MOAD:  6V7A IC50: 264.4 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.09 Å
  • R-Value Free: 0.239 
  • R-Value Work: 0.193 
  • R-Value Observed: 0.196 
  • Space Group: P 2 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 45.461α = 90
b = 64.871β = 90
c = 142.393γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
iMOSFLMdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesGM49758

Revision History  (Full details and data files)

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