6S1I

Crystal Structure of DYRK1A with small molecule inhibitor


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.38 Å
  • R-Value Free: 0.228 
  • R-Value Work: 0.201 
  • R-Value Observed: 0.202 

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Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

Mining Public Domain Data to Develop Selective DYRK1A Inhibitors.

Henderson, S.H.Sorrell, F.Bennett, J.Hanley, M.T.Robinson, S.Hopkins Navratilova, I.Elkins, J.M.Ward, S.E.

(2020) ACS Med Chem Lett 11: 1620-1626

  • DOI: 10.1021/acsmedchemlett.0c00279
  • Primary Citation of Related Structures:  
    6S1I

  • PubMed Abstract: 
  • Kinases represent one of the most intensively pursued groups of targets in modern-day drug discovery. Often it is desirable to achieve selective inhibition of the kinase of interest over the remaining ∼500 kinases in the human kinome. This is especially true when inhibitors are intended to be used to study the biology of the target of interest ...

    Kinases represent one of the most intensively pursued groups of targets in modern-day drug discovery. Often it is desirable to achieve selective inhibition of the kinase of interest over the remaining ∼500 kinases in the human kinome. This is especially true when inhibitors are intended to be used to study the biology of the target of interest. We present a pipeline of open-source software that analyzes public domain data to repurpose compounds that have been used in previous kinase inhibitor development projects. We define the dual-specificity tyrosine-regulated kinase 1A (DYRK1A) as the kinase of interest, and by addition of a single methyl group to the chosen starting point we remove glycogen synthase kinase β (GSK3β) and cyclin-dependent kinase (CDK) inhibition. Thus, in an efficient manner we repurpose a GSK3β/CDK chemotype to deliver 8b , a highly selective DYRK1A inhibitor.


    Organizational Affiliation

    Medicines Discovery Institute, Cardiff University, Cardiff CF10 3AT, U.K.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Dual specificity tyrosine-phosphorylation-regulated kinase 1AA, B, C, D361Homo 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
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ13627
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
KR8 (Subject of Investigation/LOI)
Query on KR8

Download Ideal Coordinates CCD File 
G [auth A],
L [auth B],
Q [auth C],
T [auth D]
~{N}-methyl-~{N}-phenyl-4-pyrazolo[1,5-b]pyridazin-3-yl-pyrimidin-2-amine
C17 H14 N6
XYEFJKRTJUALOK-UHFFFAOYSA-N
 Ligand Interaction
PG4
Query on PG4

Download Ideal Coordinates CCD File 
F [auth A],
J [auth B],
K [auth B],
O [auth C],
P [auth C]
TETRAETHYLENE GLYCOL
C8 H18 O5
UWHCKJMYHZGTIT-UHFFFAOYSA-N
 Ligand Interaction
SO4
Query on SO4

Download Ideal Coordinates CCD File 
E [auth A],
H [auth B],
I [auth B],
M [auth C],
N [auth C],
E [auth A],
H [auth B],
I [auth B],
M [auth C],
N [auth C],
R [auth D],
S [auth D]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D 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: 2.38 Å
  • R-Value Free: 0.228 
  • R-Value Work: 0.201 
  • R-Value Observed: 0.202 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 244.317α = 90
b = 64.504β = 115.74
c = 147.586γ = 90
Software Package:
Software NamePurpose
Aimlessdata scaling
PHASERphasing
PHENIXrefinement
PDB_EXTRACTdata extraction
DIALSdata reduction

Structure Validation

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Ligand Structure Quality Assessment 



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2019-06-26
    Type: Initial release
  • Version 1.1: 2019-08-21
    Changes: Data collection
  • Version 1.2: 2021-08-11
    Changes: Advisory, Database references, Refinement description