8G8X

X-ray co-crystal structure of compound 27 in with complex JAK2


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.97 Å
  • R-Value Free: 
    0.236 (Depositor), 0.240 (DCC) 
  • R-Value Work: 
    0.195 (Depositor), 0.200 (DCC) 
  • R-Value Observed: 
    0.197 (Depositor) 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted YT8Click on this verticalbar to view details

This is version 1.4 of the entry. See complete history


Literature

Eyes on Topical Ocular Disposition: The Considered Design of a Lead Janus Kinase (JAK) Inhibitor That Utilizes a Unique Azetidin-3-Amino Bridging Scaffold to Attenuate Off-Target Kinase Activity, While Driving Potency and Aqueous Solubility.

Gordhan, H.M.Miller, S.T.Clancy, D.C.Ina, M.McDougal, A.V.Cutno, D.K.Brown, R.V.Lichorowic, C.L.Sturdivant, J.M.Vick, K.A.Williams, S.S.deLong, M.A.White, J.C.Kopczynski, C.C.Ellis, D.A.

(2023) J Med Chem 66: 8929-8950

  • DOI: https://doi.org/10.1021/acs.jmedchem.3c00519
  • Primary Citation of Related Structures:  
    8G6Z, 8G8O, 8G8X

  • PubMed Abstract: 

    An unmet medical need remains for patients suffering from dry eye disease (DED). A fast-acting, better-tolerated noncorticosteroid anti-inflammatory eye drop could improve patient outcomes and quality of life. Herein, we describe a small-molecule drug discovery effort to identify novel, potent, and water-soluble JAK inhibitors as immunomodulating agents for topical ocular disposition. A focused library of known 3-(4-(2-(arylamino)pyrimidin-4-yl)-1 H -pyrazol-1-yl)propanenitriles was evaluated as a molecular starting point. Structure-activity relationships (SARs) revealed a ligand-efficient (LE) JAK inhibitor series, amenable to aqueous solubility. Subsequent in vitro analysis indicated the potential for off-target toxicity. A KINOME scan selectivity profile of 5 substantiated the likelihood of widespread series affinity across the human kinome. An sp 2 -to-sp 3 drug design strategy was undertaken to attenuate off-target kinase activity while driving JAK-STAT potency and aqueous solubility. Tactics to reduce aromatic character, increase fraction sp 3 (Fsp 3 ), and bolster molecular complexity led to the azetidin-3-amino bridging scaffold in 31 .


  • Organizational Affiliation

    Alcon Research, LLC, Durham, North Carolina 27703, United States.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Tyrosine-protein kinase JAK2
A, B
318Homo sapiensMutation(s): 2 
Gene Names: JAK2
EC: 2.7.10.2
UniProt & NIH Common Fund Data Resources
Find proteins for O60674 (Homo sapiens)
Explore O60674 
Go to UniProtKB:  O60674
PHAROS:  O60674
GTEx:  ENSG00000096968 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO60674
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
YT8 (Subject of Investigation/LOI)
Query on YT8

Download Ideal Coordinates CCD File 
C [auth A],
D [auth B]
3-cyclopropyl-1-{5-methyl-2-[(3-methyl-1,2-thiazol-5-yl)amino]pyrimidin-4-yl}azetidin-3-ol
C15 H19 N5 O S
AYYRUOOCJNTWHJ-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: 1.97 Å
  • R-Value Free:  0.236 (Depositor), 0.240 (DCC) 
  • R-Value Work:  0.195 (Depositor), 0.200 (DCC) 
  • R-Value Observed: 0.197 (Depositor) 
Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 36.65α = 90
b = 172.56β = 110.6
c = 52.48γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
xia2data reduction
XDSdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted YT8Click on this verticalbar to view details

Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Not funded--

Revision History  (Full details and data files)

  • Version 1.0: 2023-06-21
    Type: Initial release
  • Version 1.1: 2023-07-26
    Changes: Database references
  • Version 1.2: 2023-10-25
    Changes: Data collection
  • Version 1.3: 2023-11-15
    Changes: Data collection
  • Version 1.4: 2024-10-16
    Changes: Structure summary