3ANR

human DYRK1A/harmine complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.6 Å
  • R-Value Free: 0.264 
  • R-Value Work: 0.232 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Development of a novel selective inhibitor of the Down syndrome-related kinase Dyrk1A

Ogawa, Y.Nonaka, Y.Goto, T.Ohnishi, E.Hiramatsu, T.Kii, I.Yoshida, M.Ikura, T.Onogi, H.Shibuya, H.Hosoya, T.Ito, N.Hagiwara, M.

(2010) Nat Commun 1: 1-9

  • DOI: 10.1038/ncomms1090
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Dyrk1A (dual-specificity tyrosine-(Y)-phosphorylation-regulated kinase 1A) is a serine/threonine kinase essential for brain development and function, and its excessive activity is considered a pathogenic factor in Down syndrome. The development of po ...

    Dyrk1A (dual-specificity tyrosine-(Y)-phosphorylation-regulated kinase 1A) is a serine/threonine kinase essential for brain development and function, and its excessive activity is considered a pathogenic factor in Down syndrome. The development of potent, selective inhibitors of Dyrk1A would help to elucidate the molecular mechanisms of normal and diseased brains, and may provide a new lead compound for molecular-targeted drug discovery. Here, we report a novel Dyrk1A inhibitor, INDY, a benzothiazole derivative showing a potent ATP-competitive inhibitory effect with IC(50) and K(i) values of 0.24 and 0.18 μM, respectively. X-ray crystallography of the Dyrk1A/INDY complex revealed the binding of INDY in the ATP pocket of the enzyme. INDY effectively reversed the aberrant tau-phosphorylation and rescued the repressed NFAT (nuclear factor of activated T cell) signalling induced by Dyrk1A overexpression. Importantly, proINDY, a prodrug of INDY, effectively recovered Xenopus embryos from head malformation induced by Dyrk1A overexpression, resulting in normally developed embryos and demonstrating the utility of proINDY in vivo.


    Organizational Affiliation

    Laboratory of Gene Expression, Graduate School of Biomedical Science, Tokyo Medical and Dental University, 1-5-45, Yushima, Bunkyo-ku, Tokyo 113-8510, Japan.




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
HRM
Query on HRM

Download SDF File 
Download CCD File 
A, B, C, D
7-METHOXY-1-METHYL-9H-BETA-CARBOLINE
7-METHOXY-1-METHYL-9H-PYRIDO[3,4-B]INDOL, HARMINE
C13 H12 N2 O
BXNJHAXVSOCGBA-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 %)
HRMIC50: 29 - 400 nM (100) BINDINGDB
HRMKi: 33 nM (100) BINDINGDB
HRMIC50: 350 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.6 Å
  • R-Value Free: 0.264 
  • R-Value Work: 0.232 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 87.578α = 90.00
b = 88.142β = 90.00
c = 227.139γ = 90.00
Software Package:
Software NamePurpose
HKL-2000data reduction
CNSrefinement
HKL-2000data collection
HKL-2000data scaling
CNSphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2010-11-10
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance