5FUE

Crystal structure of Schistosoma mansoni HDAC8 complexed with 3- benzamido-benzohydroxamate


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.196 
  • R-Value Work: 0.148 
  • R-Value Observed: 0.150 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history


Literature

Structure-Based Design and Synthesis of Novel Inhibitors Targeting Hdac8 from Schistosoma Mansoni for the Treatment of Schistosomiasis.

Heimburg, T.Chakrabarti, A.Lancelot, J.Marek, M.Melesina, J.Hauser, A.T.Shaik, T.B.Duclaud, S.Robaa, D.Erdmann, F.Schmidt, M.Romier, C.Pierce, R.J.Jung, M.Sippl, W.

(2016) J Med Chem 59: 2423

  • DOI: https://doi.org/10.1021/acs.jmedchem.5b01478
  • Primary Citation of Related Structures:  
    5FUE

  • PubMed Abstract: 

    Schistosomiasis is a major neglected parasitic disease that affects more than 265 million people worldwide and for which the control strategy consists of mass treatment with the only available drug, praziquantel. In this study, a series of new benzohydroxamates were prepared as potent inhibitors of Schistosoma mansoni histone deacetylase 8 (smHDAC8). Crystallographic analysis provided insights into the inhibition mode of smHDAC8 activity by these 3-amidobenzohydroxamates. The newly designed inhibitors were evaluated in screens for enzyme inhibitory activity against schistosome and human HDACs. Twenty-seven compounds were found to be active in the nanomolar range, and some of them showed selectivity toward smHDAC8 over the major human HDACs (1 and 6). The active benzohydroxamates were additionally screened for lethality against the schistosome larval stage using a fluorescence-based assay. Four of these showed significant dose-dependent killing of the schistosome larvae and markedly impaired egg laying of adult worm pairs maintained in culture.


  • Organizational Affiliation

    Institute of Pharmacy, Martin-Luther University of Halle-Wittenberg , 06120 Halle/Saale, 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 
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
Expand
  • Reference Sequence
Small Molecules
Ligands 5 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
UV4
Query on UV4

Download Ideal Coordinates CCD File 
DA [auth D],
H [auth A],
N [auth B],
U [auth C]
3-(benzoylamino)-N-oxobenzamide
C14 H10 N2 O3
BZGLPPUMZXGKFN-UHFFFAOYSA-N
GOL
Query on GOL

Download Ideal Coordinates CCD File 
EA [auth D]
FA [auth D]
GA [auth D]
I [auth A]
J [auth A]
EA [auth D],
FA [auth D],
GA [auth D],
I [auth A],
J [auth A],
O [auth B],
V [auth C],
W [auth C],
X [auth C]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
DMF
Query on DMF

Download Ideal Coordinates CCD File 
HA [auth D],
P [auth B],
Q [auth B],
Y [auth C],
Z [auth C]
DIMETHYLFORMAMIDE
C3 H7 N O
ZMXDDKWLCZADIW-UHFFFAOYSA-N
ZN
Query on ZN

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

Download Ideal Coordinates CCD File 
BA [auth D]
CA [auth D]
F [auth A]
G [auth A]
L [auth B]
BA [auth D],
CA [auth D],
F [auth A],
G [auth A],
L [auth B],
M [auth B],
S [auth C],
T [auth C]
POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.196 
  • R-Value Work: 0.148 
  • R-Value Observed: 0.150 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 70.955α = 77.99
b = 70.669β = 75.41
c = 98.656γ = 85.4
Software Package:
Software NamePurpose
PHENIXrefinement
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2016-03-09
    Type: Initial release
  • Version 1.1: 2016-03-16
    Changes: Database references
  • Version 1.2: 2016-04-06
    Changes: Database references
  • Version 1.3: 2024-05-08
    Changes: Data collection, Database references, Derived calculations, Other