4CQF

Crystal structure of Schistosoma mansoni HDAC8 complexed with a mercaptoacetamide inhibitor


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.232 
  • R-Value Work: 0.190 
  • R-Value Observed: 0.192 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

Molecular Basis for the Anti-Parasitic Activity of a Mercaptoacetamide Derivative that Inhibits Histone Deacetylase 8 (Hdac8) from the Human Pathogen Schistosoma Mansoni

Stolfa, D.A.Marek, M.Lancelot, J.Hauser, A.T.Walter, A.Leproult, E.Melesina, J.Rumpf, T.Wurtz, J.M.Cavarelli, J.Sippl, W.Pierce, R.J.Romier, C.Jung, M.

(2014) J Mol Biol 426: 3442

  • DOI: https://doi.org/10.1016/j.jmb.2014.03.007
  • Primary Citation of Related Structures:  
    4CQF

  • PubMed Abstract: 

    Schistosomiasis, caused by the parasitic flatworm Schistosoma mansoni and related species, is a tropical disease that affects over 200 million people worldwide. A new approach for targeting eukaryotic parasites is to tackle their dynamic epigenetic machinery that is necessary for the extensive phenotypic changes during the life cycle of the parasite. Recently, we identified S. mansoni histone deacetylase 8 (smHDAC8) as a potential target for antiparasitic therapy. Here, we present results on the investigations of a focused set of HDAC (histone deacetylase) inhibitors on smHDAC8. Besides several active hydroxamates, we identified a thiol-based inhibitor that inhibited smHDAC8 activity in the micromolar range with unexpected selectivity over the human isotype, which has not been observed so far. The crystal structure of smHDAC8 complexed with the thiol derivative revealed that the inhibitor is accommodated in the catalytic pocket, where it interacts with both the catalytic zinc ion and the essential catalytic tyrosine (Y341) residue via its mercaptoacetamide warhead. To our knowledge, this is the first complex crystal structure of any HDAC inhibited by a mercaptoacetamide inhibitor, and therefore, this finding offers a rationale for further improvement. Finally, an ester prodrug of the thiol HDAC inhibitor exhibited antiparasitic activity on cultured schistosomes in a dose-dependent manner.


  • Organizational Affiliation

    Institute of Pharmaceutical Sciences, Albert-Ludwigs-Universität Freiburg, Albertstraße 25, 79104 Freiburg, Germany.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
HISTONE DEACETYLASE 8
A, B, C, D
446Schistosoma mansoniMutation(s): 0 
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
Expand
  • Reference Sequence
Small Molecules
Ligands 5 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
9Z8
Query on 9Z8

Download Ideal Coordinates CCD File 
H [auth A],
HA [auth D],
N [auth B],
W [auth C]
6-(2-Mercaptoacetylamino)-N-phenylhexanamide
C14 H20 N2 O2 S
ICMLRCZXRBTKLJ-UHFFFAOYSA-N
GOL
Query on GOL

Download Ideal Coordinates CCD File 
BA [auth C]
CA [auth C]
DA [auth C]
KA [auth D]
LA [auth D]
BA [auth C],
CA [auth C],
DA [auth C],
KA [auth D],
LA [auth D],
R [auth B],
S [auth B]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
DMF
Query on DMF

Download Ideal Coordinates CCD File 
AA [auth C]
I [auth A]
IA [auth D]
J [auth A]
JA [auth D]
AA [auth C],
I [auth A],
IA [auth D],
J [auth A],
JA [auth D],
O [auth B],
P [auth B],
Q [auth B],
X [auth C],
Y [auth C],
Z [auth C]
DIMETHYLFORMAMIDE
C3 H7 N O
ZMXDDKWLCZADIW-UHFFFAOYSA-N
ZN
Query on ZN

Download Ideal Coordinates CCD File 
E [auth A],
EA [auth D],
K [auth B],
T [auth C]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
K
Query on K

Download Ideal Coordinates CCD File 
F [auth A]
FA [auth D]
G [auth A]
GA [auth D]
L [auth B]
F [auth A],
FA [auth D],
G [auth A],
GA [auth D],
L [auth B],
M [auth B],
U [auth C],
V [auth C]
POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N
Binding Affinity Annotations 
IDSourceBinding Affinity
9Z8 BindingDB:  4CQF IC50: 5.01e+4 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.232 
  • R-Value Work: 0.190 
  • R-Value Observed: 0.192 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 70.778α = 77.79
b = 70.815β = 75.45
c = 98.024γ = 85.4
Software Package:
Software NamePurpose
BUSTERrefinement
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2014-04-02
    Type: Initial release
  • Version 1.1: 2014-10-08
    Changes: Database references
  • Version 1.2: 2023-12-20
    Changes: Data collection, Database references, Derived calculations, Other, Refinement description