6UIP

DYRK1A Kinase Domain in Complex with a 6-azaindole Derivative, GNF2133.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.70 Å
  • R-Value Free: 0.290 
  • R-Value Work: 0.271 
  • R-Value Observed: 0.272 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history


Literature

Selective DYRK1A Inhibitor for the Treatment of Type 1 Diabetes: Discovery of 6-Azaindole Derivative GNF2133.

Liu, Y.A.Jin, Q.Zou, Y.Ding, Q.Yan, S.Wang, Z.Hao, X.Nguyen, B.Zhang, X.Pan, J.Mo, T.Jacobsen, K.Lam, T.Wu, T.Y.Petrassi, H.M.Bursulaya, B.DiDonato, M.Gordon, W.P.Liu, B.Baaten, J.Hill, R.Nguyen-Tran, V.Qiu, M.Zhang, Y.Q.Kamireddy, A.Espinola, S.Deaton, L.Ha, S.Harb, G.Jia, Y.Li, J.Shen, W.Schumacher, A.M.Colman, K.Glynne, R.Pan, S.McNamara, P.Laffitte, B.Meeusen, S.Molteni, V.Loren, J.

(2020) J Med Chem 63: 2958-2973

  • DOI: https://doi.org/10.1021/acs.jmedchem.9b01624
  • Primary Citation of Related Structures:  
    6UIP

  • PubMed Abstract: 

    Autoimmune deficiency and destruction in either β-cell mass or function can cause insufficient insulin levels and, as a result, hyperglycemia and diabetes. Thus, promoting β-cell proliferation could be one approach toward diabetes intervention. In this report we describe the discovery of a potent and selective DYRK1A inhibitor GNF2133, which was identified through optimization of a 6-azaindole screening hit. In vitro , GNF2133 is able to proliferate both rodent and human β-cells. In vivo , GNF2133 demonstrated significant dose-dependent glucose disposal capacity and insulin secretion in response to glucose-potentiated arginine-induced insulin secretion (GPAIS) challenge in rat insulin promoter and diphtheria toxin A (RIP-DTA) mice. The work described here provides new avenues to disease altering therapeutic interventions in the treatment of type 1 diabetes (T1D).


  • Organizational Affiliation

    Genomics Institute of the Novartis Research Foundation (GNF), 10675 John Jay Hopkins Drive, San Diego, California 92121, United States.


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
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
GTEx:  ENSG00000157540 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ13627
Sequence Annotations
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  • Reference Sequence
Small Molecules
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
PTR
Query on PTR
A, B, C
L-PEPTIDE LINKINGC9 H12 N O6 PTYR
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.70 Å
  • R-Value Free: 0.290 
  • R-Value Work: 0.271 
  • R-Value Observed: 0.272 
  • Space Group: P 31 1 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 112.884α = 90
b = 112.884β = 90
c = 304.651γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data reduction
SCALEPACKdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2020-03-04
    Type: Initial release
  • Version 1.1: 2020-04-08
    Changes: Database references
  • Version 1.2: 2023-10-11
    Changes: Data collection, Database references, Refinement description
  • Version 1.3: 2023-11-15
    Changes: Data collection