8HLT

The co-crystal structure of DYRK2 with YK-2-99B


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.267 
  • R-Value Work: 0.209 
  • R-Value Observed: 0.213 

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Ligand Structure Quality Assessment 


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Literature

Discovery of Potent DYRK2 Inhibitors with High Selectivity, Great Solubility, and Excellent Safety Properties for the Treatment of Prostate Cancer.

Yuan, K.Shen, H.Zheng, M.Xia, F.Li, Q.Chen, W.Ji, M.Yang, H.Zhuang, X.Cai, Z.Min, W.Wang, X.Xiao, Y.Yang, P.

(2023) J Med Chem 66: 4215-4230

  • DOI: https://doi.org/10.1021/acs.jmedchem.3c00106
  • Primary Citation of Related Structures:  
    8HLT

  • PubMed Abstract: 

    Prostate cancer (PCa) is a common male cancer with high incidence and mortality, and hormonal therapy as the major treatment for PCa patients is troubled by the inevitable resistance that makes us identify novel targets for PCa. Dual-specificity tyrosine phosphorylation-regulated kinase 2 (DYRK2) was found to be an effective target for the treatment of PCa, but the research on its inhibitors is rather little. In this work, a potent DYRK2 inhibitor 43 (IC 50 = 0.6 nM) was acquired through virtual screening and structural optimization, which displayed high selectivity among 205 kinases; meanwhile, detailed interactions of 43 with DYRK2 were illustrated by the cocrystal. Furthermore, 43 possessed great water solubility (29.5 mg/mL), favorable safety properties (LD 50 > 10,000 mg/kg), and potent anti-PCa activities, which could be used as a potential candidate in further preclinical studies.


  • Organizational Affiliation

    State Key Laboratory of Natural Medicines and Jiangsu Key Laboratory of Drug Design and Optimization, China Pharmaceutical University, Nanjing 210009, China.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Dual specificity tyrosine-phosphorylation-regulated kinase 2
A, B
393Homo sapiensMutation(s): 0 
Gene Names: DYRK2
EC: 2.7.12.1
UniProt & NIH Common Fund Data Resources
Find proteins for Q92630 (Homo sapiens)
Explore Q92630 
Go to UniProtKB:  Q92630
PHAROS:  Q92630
GTEx:  ENSG00000127334 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ92630
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
XSE
Query on XSE

Download Ideal Coordinates CCD File 
C [auth A],
D [auth B]
(6-{[(4P)-4-(1,3-benzothiazol-5-yl)-5-fluoropyrimidin-2-yl]amino}pyridin-3-yl)(piperazin-1-yl)methanone
C21 H18 F N7 O S
FXOGSEZDYASZGS-UHFFFAOYSA-N
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
PTR
Query on PTR
A, B
L-PEPTIDE LINKINGC9 H12 N O6 PTYR
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.267 
  • R-Value Work: 0.209 
  • R-Value Observed: 0.213 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 129.82α = 90
b = 60.67β = 113.08
c = 155.34γ = 90
Software Package:
Software NamePurpose
XDSdata scaling
PHENIXrefinement
HKL-2000data reduction
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Science Foundation (NSF, China)China31970547

Revision History  (Full details and data files)

  • Version 1.0: 2023-12-13
    Type: Initial release