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


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

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

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

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

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

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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