5A4T

DYRK1A IN COMPLEX WITH NITRILE BENZOTHIAZOLE FRAGMENT


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.15 Å
  • R-Value Free: 0.234 
  • R-Value Work: 0.204 

wwPDB Validation 3D Report Full Report


This is version 1.5 of the entry. See complete history

Literature

Probing the ATP-Binding Pocket of Protein Kinase Dyrk1A with Benzothiazole Fragment Molecules

Rothweiler, U.Stensen, W.Brandsdal, B.O.Isaksson, J.Leeson, F.A.Eugh, R.A.Mjoen Svendsen, J.S.

(2016) J.Med.Chem. 59: 9814

  • DOI: 10.1021/acs.jmedchem.6b01086
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • DYRK1A has emerged as a potential target for therapies of Alzheimer's disease using small molecules. On the basis of the observation of selective DYRK1A inhibition by firefly d-luciferin, we have explored static and dynamic structural properties of f ...

    DYRK1A has emerged as a potential target for therapies of Alzheimer's disease using small molecules. On the basis of the observation of selective DYRK1A inhibition by firefly d-luciferin, we have explored static and dynamic structural properties of fragment sized variants of the benzothiazole scaffold with respect to DYRK1A using X-ray crystallography and NMR techniques. The compounds have excellent ligand efficiencies and show a remarkable diversity of binding modes in dynamic equilibrium. Binding geometries are determined in part by interactions often considered "weak", including "orthogonal multipolar" types represented by, for example, F-CO, sulfur-aromatic, and halogen-aromatic interactions, together with hydrogen bonds that are modulated by variation of electron withdrawing groups. These studies show how the benzothiazole scaffold is highly promising for the development of therapeutic DYRK1A inhibitors. In addition, the subtleties of the binding interactions, including dynamics, show how full structural studies are required to fully interpret the essential physical determinants of binding.


    Organizational Affiliation

    The Centre of Theoretical and Computational Chemistry, Department of Chemistry, UiT The Arctic University of Norway , N-9037 Tromsø, Norway.,The Norwegian Structural Biology Centre, Department of Chemistry, UiT The Arctic University of Norway , N-9037 Tromsø, Norway.,Department of Chemistry, UiT The Arctic University of Norway , N-9037 Tromsø, Norway.,Pharmasum Therapeutics AS , Smørblomstvn. 36, N-9102 Kvaløysletta, Norway.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
DUAL SPECIFICITY TYROSINE-PHOSPHORYLATION- REGULATED KINASE 1A
A, B, C, D
368Homo sapiensMutation(s): 0 
Gene Names: DYRK1A (DYRK, MNB, MNBH)
EC: 2.7.12.1
Find proteins for Q13627 (Homo sapiens)
Go to Gene View: DYRK1A
Go to UniProtKB:  Q13627
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
AJG
Query on AJG

Download SDF File 
Download CCD File 
A, B, C, D
N-(6-CYANO-3H-1,3-BENZOTHIAZOL-2-YLIDENE)ETHANAMIDE
C10 H7 N3 O S
JGSLDMQYARUFDJ-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
PTR
Query on PTR
A, B, C, D
L-PEPTIDE LINKINGC9 H12 N O6 PTYR
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
AJGIC50: 1300 nM BINDINGMOAD
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.15 Å
  • R-Value Free: 0.234 
  • R-Value Work: 0.204 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 87.753α = 90.00
b = 87.702β = 90.00
c = 229.611γ = 90.00
Software Package:
Software NamePurpose
XDSdata reduction
XDSdata scaling
REFMACrefinement
PHASERphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2015-06-15 
  • Released Date: 2016-06-29 
  • Deposition Author(s): Rothweiler, U.

Revision History 

  • Version 1.0: 2016-06-29
    Type: Initial release
  • Version 1.1: 2016-11-23
    Type: Database references
  • Version 1.2: 2016-12-14
    Type: Database references
  • Version 1.3: 2016-12-28
    Type: Database references
  • Version 1.4: 2019-01-30
    Type: Data collection, Experimental preparation, Other
  • Version 1.5: 2019-02-06
    Type: Data collection, Experimental preparation