6T6A

Crystal structure of DYRK1A complexed with KuFal319 (compound 11)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.242 
  • R-Value Work: 0.205 
  • R-Value Observed: 0.207 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

[ b ]-Annulated Halogen-Substituted Indoles as Potential DYRK1A Inhibitors.

Lechner, C.Flasshoff, M.Falke, H.Preu, L.Loaec, N.Meijer, L.Knapp, S.Chaikuad, A.Kunick, C.

(2019) Molecules 24

  • DOI: https://doi.org/10.3390/molecules24224090
  • Primary Citation of Related Structures:  
    6T6A

  • PubMed Abstract: 

    Since hyperactivity of the protein kinase DYRK1A is linked to several neurodegenerative disorders, DYRK1A inhibitors have been suggested as potential therapeutics for Down syndrome and Alzheimer's disease. Most published inhibitors to date suffer from low selectivity against related kinases or from unfavorable physicochemical properties. In order to identify DYRK1A inhibitors with improved properties, a series of new chemicals based on [ b ]-annulated halogenated indoles were designed, synthesized, and evaluated for biological activity. Analysis of crystal structures revealed a typical type-I binding mode of the new inhibitor 4-chlorocyclohepta[ b ]indol-10(5 H )-one in DYRK1A, exploiting mainly shape complementarity for tight binding. Conversion of the DYRK1A inhibitor 8-chloro-1,2,3,9-tetrahydro-4 H -carbazol-4-one into a corresponding Mannich base hydrochloride improved the aqueous solubility but abrogated kinase inhibitory activity.


  • Organizational Affiliation

    Institut für Medizinische und Pharmazeutische Chemie, Technische Universität Braunschweig, Beethovenstraße 55, 38106 Braunschweig, Germany.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Dual specificity tyrosine-phosphorylation-regulated kinase 1A
A, B, C, D
361Homo sapiensMutation(s): 0 
Gene Names: DYRK1ADYRKMNBMNBH
EC: 2.7.12.1
UniProt & NIH Common Fund Data Resources
Find proteins for Q13627 (Homo sapiens)
Explore Q13627 
Go to UniProtKB:  Q13627
PHAROS:  Q13627
GTEx:  ENSG00000157540 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ13627
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
MLW (Subject of Investigation/LOI)
Query on MLW

Download Ideal Coordinates CCD File 
K [auth A],
Q [auth B],
W [auth C]
4-chloranyl-5~{H}-cyclohepta[b]indol-10-one
C13 H8 Cl N O
BBOUTVQTMMUARP-UHFFFAOYSA-N
PG4
Query on PG4

Download Ideal Coordinates CCD File 
E [auth A],
F [auth A],
G [auth A],
L [auth B],
R [auth C]
TETRAETHYLENE GLYCOL
C8 H18 O5
UWHCKJMYHZGTIT-UHFFFAOYSA-N
SO4
Query on SO4

Download Ideal Coordinates CCD File 
H [auth A]
I [auth A]
J [auth A]
M [auth B]
N [auth B]
H [auth A],
I [auth A],
J [auth A],
M [auth B],
N [auth B],
O [auth B],
P [auth B],
S [auth C],
T [auth C],
U [auth C],
V [auth C],
X [auth D],
Y [auth D]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
PTR
Query on PTR
A, B, C, D
L-PEPTIDE LINKINGC9 H12 N O6 PTYR
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.242 
  • R-Value Work: 0.205 
  • R-Value Observed: 0.207 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 244.882α = 90
b = 65.395β = 115.18
c = 148.055γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
SCALAdata scaling
PDB_EXTRACTdata extraction
xia2data reduction
PHASERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2019-12-04
    Type: Initial release
  • Version 1.1: 2020-09-30
    Changes: Database references
  • Version 1.2: 2024-01-24
    Changes: Data collection, Database references, Refinement description