3ANR

human DYRK1A/harmine complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free: 0.264 
  • R-Value Work: 0.232 
  • R-Value Observed: 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:  
    3ANQ, 3ANR

  • 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 potent ...

    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:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Dual specificity tyrosine-phosphorylation-regulated kinase 1A ABCD368Homo sapiensMutation(s): 0 
Gene Names: DYRK1ADYRKMNBMNBH
EC: 2.7.12.1
Find proteins for Q13627 (Homo sapiens)
Explore Q13627 
Go to UniProtKB:  Q13627
NIH Common Fund Data Resources
PHAROS:  Q13627
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
HRM
Query on HRM

Download Ideal Coordinates CCD File 
A, B, C, D
7-METHOXY-1-METHYL-9H-BETA-CARBOLINE
C13 H12 N2 O
BXNJHAXVSOCGBA-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
PTR
Query on PTR
A,B,C,DL-PEPTIDE LINKINGC9 H12 N O6 PTYR
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
HRMIC50:  85   nM  BindingDB
HRMKi:  33   nM  BindingDB
HRMIC50:  80   nM  BindingDB
HRMIC50:  56   nM  BindingDB
HRMIC50:  30   nM  BindingDB
HRMIC50:  29   nM  BindingDB
HRMIC50:  400   nM  BindingDB
HRMIC50:  700   nM  BindingDB
HRMIC50:  8.800000190734863   nM  BindingDB
HRMIC50:  41   nM  BindingDB
HRMIC50:  33   nM  BindingDB
HRMIC50:  130   nM  BindingDB
HRMIC50:  29   nM  BindingDB
HRMIC50:  60   nM  BindingDB
HRMIC50:  56   nM  BindingDB
HRMIC50 :  350   nM  PDBBind
HRMIC50:  34   nM  BindingDB
HRMIC50:  48   nM  BindingDB
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free: 0.264 
  • R-Value Work: 0.232 
  • R-Value Observed: 0.232 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 87.578α = 90
b = 88.142β = 90
c = 227.139γ = 90
Software Package:
Software NamePurpose
HKL-2000data collection
CNSrefinement
HKL-2000data reduction
HKL-2000data scaling
CNSphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

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