6HU3

Crystal structure of Schistosoma mansoni HDAC8 complexed with a triazole hydroxamate inhibitor


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.655 Å
  • R-Value Free: 0.194 
  • R-Value Work: 0.162 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Characterization of Histone Deacetylase 8 (HDAC8) Selective Inhibition Reveals Specific Active Site Structural and Functional Determinants.

Marek, M.Shaik, T.B.Heimburg, T.Chakrabarti, A.Lancelot, J.Ramos-Morales, E.Da Veiga, C.Kalinin, D.Melesina, J.Robaa, D.Schmidtkunz, K.Suzuki, T.Holl, R.Ennifar, E.Pierce, R.J.Jung, M.Sippl, W.Romier, C.

(2018) J. Med. Chem. 61: 10000-10016

  • DOI: 10.1021/acs.jmedchem.8b01087
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Metal-dependent histone deacetylases (HDACs) are key epigenetic regulators that represent promising therapeutic targets for the treatment of numerous human diseases. Yet the currently FDA-approved HDAC inhibitors nonspecifically target at least sever ...

    Metal-dependent histone deacetylases (HDACs) are key epigenetic regulators that represent promising therapeutic targets for the treatment of numerous human diseases. Yet the currently FDA-approved HDAC inhibitors nonspecifically target at least several of the 11 structurally similar but functionally different HDAC isozymes, which hampers their broad usage in clinical settings. Selective inhibitors targeting single HDAC isozymes are being developed, but precise understanding in molecular terms of their selectivity remains sparse. Here, we show that HDAC8-selective inhibitors adopt a L-shaped conformation required for their binding to a HDAC8-specific pocket formed by HDAC8 catalytic tyrosine and HDAC8 L1 and L6 loops. In other HDAC isozymes, a L1-L6 lock sterically prevents L-shaped inhibitor binding. Shielding of the HDAC8-specific pocket by protein engineering decreases potency of HDAC8-selective inhibitors and affects catalytic activity. Collectively, our results unravel key HDAC8 active site structural and functional determinants important for the design of next-generation chemical probes and epigenetic drugs.


    Organizational Affiliation

    Institute of Pharmaceutical and Medicinal Chemistry , University of Münster , Corrensstraße 48 , 48149 Münster , Germany.,Architecture et Réactivité de l'ARN, Institut de Biologie Moléculaire et Cellulaire (IBMC), UPR 9004 du CNRS , Université de Strasbourg , 15 Rue René Descartes , 67084 Strasbourg Cedex , France.,Institute of Pharmaceutical Sciences , Albert-Ludwigs-Universität Freiburg , Albertstraße 25 , 79104 Freiburg , Germany.,Institut de Génétique et Biologie Moléculaire et Cellulaire (IGBMC), Département de Biologie Structurale Intégrative , Université de Strasbourg, Centre National de la Recherche Scientifique (CNRS UMR7104), Institut National de la Santé et de la Recherche Médicale (INSERM U1258) , 1 rue Laurent Fries , 67404 Illkirch Cedex , France.,CNRS, Inserm, CHU Lille, Institut Pasteur de Lille, U1019-UMR 8204-CIIL-Centre d'Infection et d'Immunité de Lille , Université de Lille , F-59000 Lille , France.,Department of Chemistry, Institute of Organic Chemistry , University of Hamburg , Martin-Luther-King-Platz 6 , 20146 Hamburg , Germany.,Institute of Pharmacy , Martin-Luther-Universität Halle-Wittenberg , Wolfgang-Langenbeck-Straße 4 , 06120 Halle/Saale , Germany.,Graduate School of Medical Science , Kyoto Prefectural University of Medicine , 1-5 Shimogamohangi-Cho, Sakyo-Ku , 606-0823 Kyoto , Japan.,CREST , Japan Science and Technology Agency (JST) , 4-1-8 Honcho Kawaguchi , 332-0012 Saitama , Japan.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Histone deacetylase
A, B, C, D
447Schistosoma mansoniMutation(s): 0 
Gene Names: HDAC8
Find proteins for A5H660 (Schistosoma mansoni)
Go to Gene View: HDAC8
Go to UniProtKB:  A5H660
Small Molecules
Ligands 5 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
K
Query on K

Download SDF File 
Download CCD File 
A, B, C, D
POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N
 Ligand Interaction
ZN
Query on ZN

Download SDF File 
Download CCD File 
A, B, C, D
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
GOL
Query on GOL

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Download CCD File 
A, B, C, D
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
DMF
Query on DMF

Download SDF File 
Download CCD File 
A, B, C, D
DIMETHYLFORMAMIDE
C3 H7 N O
ZMXDDKWLCZADIW-UHFFFAOYSA-N
 Ligand Interaction
GRZ
Query on GRZ

Download SDF File 
Download CCD File 
A, B, C, D
1-[5-chloranyl-2-(4-fluoranylphenoxy)phenyl]-~{N}-oxidanyl-1,2,3-triazole-4-carboxamide
C15 H10 Cl F N4 O3
NXLUFTCWMNFMML-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.655 Å
  • R-Value Free: 0.194 
  • R-Value Work: 0.162 
  • Space Group: P 1
Unit Cell:
Length (Å)Angle (°)
a = 70.640α = 75.48
b = 70.430β = 78.20
c = 97.920γ = 86.17
Software Package:
Software NamePurpose
PHENIXphasing
XDSdata reduction
XDSdata scaling
PHENIXrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
European CommissionFrance241865
European CommissionFrance602080

Revision History 

  • Version 1.0: 2018-10-31
    Type: Initial release
  • Version 1.1: 2018-11-07
    Type: Data collection, Database references
  • Version 1.2: 2018-11-28
    Type: Data collection, Database references