7P2V

Crystal structure of Schistosoma mansoni HDAC8 in complex with a 4-chlorophenyl-spiroindoline capped hydroxamate-based inhibitor, bound to a novel site


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.25 Å
  • R-Value Free: 0.252 
  • R-Value Work: 0.212 
  • R-Value Observed: 0.214 

Starting Model: experimental
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This is version 1.3 of the entry. See complete history


Literature

Crystal structures of Schistosoma mansoni histone deacetylase 8 reveal a novel binding site for allosteric inhibitors.

Saccoccia, F.Pozzetti, L.Gimmelli, R.Butini, S.Guidi, A.Papoff, G.Giannaccari, M.Brogi, S.Scognamiglio, V.Gemma, S.Ruberti, G.Campiani, G.

(2022) J Biol Chem 298: 102375-102375

  • DOI: https://doi.org/10.1016/j.jbc.2022.102375
  • Primary Citation of Related Structures:  
    7P2S, 7P2T, 7P2U, 7P2V, 7POZ

  • PubMed Abstract: 

    Parasitic diseases cause significant global morbidity and mortality particularly in the poorest regions of the world. Schistosomiasis, one of the most widespread neglected tropical diseases, affects more than 200 million people worldwide. Histone deacetylase (HDAC) inhibitors are prominent epigenetic drugs that are being investigated in the treatment of several diseases, including cancers and parasitic diseases. Schistosoma mansoni HDAC8 (SmHDAC8) is highly expressed in all life cycle stages of the parasite, and selective inhibition is required in order to avoid undesirable off-target effects in the host. Herein, by X-ray crystal structures of SmHDAC8-inhibitor complexes, biochemical and phenotypic studies, we found two schistosomicidal spiroindoline derivatives binding a novel site, next to Trp198, on the enzyme surface. We determined that by acting on this site, either by mutation of the Trp198 or by compound binding, a decrease in the activity of the enzyme is achieved. Remarkably, this allosteric site differs from the human counterpart; rather, it is conserved in all Schistosoma species, as well as Rhabidoptera and Trematoda classes, thus paving the way for the design of HDAC8-selective allosteric inhibitors with improved properties.


  • Organizational Affiliation

    Institute of Biochemistry and Cell Biology, Italian National Research Council (IBBC-CNR), Adriano Buzzati-Traverso Campus, Monterotondo Scalo, Rome, Italy. Electronic address: fulvio.saccoccia@cnr.it.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Histone deacetylase 8440Schistosoma mansoniMutation(s): 0 
Gene Names: HDAC8
EC: 3.5.1.98
UniProt
Find proteins for A5H660 (Schistosoma mansoni)
Explore A5H660 
Go to UniProtKB:  A5H660
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA5H660
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 5 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
4XI (Subject of Investigation/LOI)
Query on 4XI

Download Ideal Coordinates CCD File 
F [auth A]5-[[(2S)-2-(4-chlorophenyl)-1'-methyl-spiro[2H-indole-3,4'-piperidine]-1-yl]methyl]-N-oxidanyl-thiophene-2-carboxamide
C25 H26 Cl N3 O2 S
DLQYRYFSBDRUBH-QHCPKHFHSA-N
TLA
Query on TLA

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E [auth A]L(+)-TARTARIC ACID
C4 H6 O6
FEWJPZIEWOKRBE-JCYAYHJZSA-N
PEG
Query on PEG

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G [auth A]DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
ZN
Query on ZN

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B [auth A]ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
K
Query on K

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C [auth A],
D [auth A]
POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.25 Å
  • R-Value Free: 0.252 
  • R-Value Work: 0.212 
  • R-Value Observed: 0.214 
  • Space Group: P 41 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 71.14α = 90
b = 71.14β = 90
c = 186.911γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
Aimlessdata scaling
PDB_EXTRACTdata extraction
XDSdata reduction
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2022-07-20
    Type: Initial release
  • Version 1.1: 2022-08-31
    Changes: Database references
  • Version 1.2: 2022-09-28
    Changes: Database references
  • Version 1.3: 2024-01-31
    Changes: Data collection, Refinement description