6GJK

A degradation product of PD 404182 (P2742) bound to Histone Deacetylase-like Amidohydrolase


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.47 Å
  • R-Value Free: 0.174 
  • R-Value Work: 0.144 
  • R-Value Observed: 0.146 

Starting Model: experimental
View more details

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

Covalent inhibition of histone deacetylase 8 by 3,4-dihydro-2H-pyrimido[1,2-c][1,3]benzothiazin-6-imine.

Muth, M.Jansch, N.Kopranovic, A.Kramer, A.Wossner, N.Jung, M.Kirschhofer, F.Meyer-Almes, F.J.

(2019) Biochim Biophys Acta Gen Subj 1863: 577-585

  • DOI: https://doi.org/10.1016/j.bbagen.2019.01.001
  • Primary Citation of Related Structures:  
    6GJK

  • PubMed Abstract: 

    HDAC8 is an established target for T-cell lymphoma and childhood neuroblastoma. Benzothiazine-imines are promising HDAC8 inhibitors with unknown binding mechanism lacking a usual zinc binding group. In this study high-resolution and quantitative HPLC-coupled ESI-MS/MS techniques are combined with crystal structure determination and a variety of biochemical and computational methods to elucidate the reaction mechanism between benzothiazine-imine 1 and HDAC8. 1) 1 is a covalent inhibitor of HDAC8; 2) inhibition is reversible in the presence of reducing agents; 3) C153 in the active site and C102 are involved in the inhibition mechanism; 4) 1 modifies various cysteines in HDAC8 forming either thiocyanates or mixed disulfides with 3; 5) 1 and 5 dock in close proximity to C153 within the active site. This is supposed to accelerate covalent inactivation particularly in HDAC8 and suggested as major determinant for the observed nanomolar potency and selectivity of 1. 1 and its analogs are interesting model compounds but unsuitable for therapeutic treatment due to their high unselective reactivity towards thiol groups. However, the postulated preceding non-covalent binding mode of 1 opens a door to optimized next generation compounds that combine potent and selective non-covalent recognition with low reactivity towards C153 at the active site of HDAC8. 1 represents a completely new class of inhibitors for HDAC8. Initial non-covalent interaction at the bottom of the active site is suggested to be the key for its selectivity. Further optimization of non-covalent interaction and thiol-reactivity provides opportunities to develop therapeutic useful covalent HDAC8 inhibitors.


  • Organizational Affiliation

    Department of Chemical Engineering and Biotechnology, University of Applied Sciences Darmstadt, Germany; Bioengineering and Biosystems, Institute of Functional Interfaces, Karlsruhe Institute of Technology, Germany.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Histone deacetylase-like amidohydrolase
A, B
375Alcaligenaceae bacterium FB188Mutation(s): 1 
Gene Names: hdaHhdaH1
EC: 3.5.1
UniProt
Find proteins for Q70I53 (Alcaligenes sp. (strain DSM 11172))
Explore Q70I53 
Go to UniProtKB:  Q70I53
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ70I53
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 7 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
1PE
Query on 1PE

Download Ideal Coordinates CCD File 
F [auth A],
P [auth B]
PENTAETHYLENE GLYCOL
C10 H22 O6
JLFNLZLINWHATN-UHFFFAOYSA-N
F0Z (Subject of Investigation/LOI)
Query on F0Z

Download Ideal Coordinates CCD File 
I [auth A],
J [auth A],
U [auth B],
V [auth B]
2-(1,4,5,6-tetrahydropyrimidin-2-yl)benzenethiol
C10 H12 N2 S
DUHDUYRXLGSMLQ-UHFFFAOYSA-N
MLT
Query on MLT

Download Ideal Coordinates CCD File 
L [auth A]D-MALATE
C4 H6 O5
BJEPYKJPYRNKOW-UWTATZPHSA-N
PEG
Query on PEG

Download Ideal Coordinates CCD File 
G [auth A]
H [auth A]
Q [auth B]
R [auth B]
S [auth B]
G [auth A],
H [auth A],
Q [auth B],
R [auth B],
S [auth B],
T [auth B]
DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
ZN
Query on ZN

Download Ideal Coordinates CCD File 
C [auth A],
M [auth B]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
ACT
Query on ACT

Download Ideal Coordinates CCD File 
K [auth A],
W [auth B]
ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
K
Query on K

Download Ideal Coordinates CCD File 
D [auth A],
E [auth A],
N [auth B],
O [auth B]
POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.47 Å
  • R-Value Free: 0.174 
  • R-Value Work: 0.144 
  • R-Value Observed: 0.146 
  • Space Group: P 42 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 100.68α = 90
b = 100.68β = 90
c = 175.53γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
Aimlessdata 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: 2019-01-16
    Type: Initial release
  • Version 1.1: 2019-01-23
    Changes: Data collection, Database references
  • Version 1.2: 2024-01-17
    Changes: Data collection, Database references, Derived calculations, Refinement description