8G6Z

JAK2 crystal structure in complex with Compound 13


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.45 Å
  • R-Value Free: 0.281 
  • R-Value Work: 0.225 
  • R-Value Observed: 0.228 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.3 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 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
YSI (Subject of Investigation/LOI)
Query on YSI

Download Ideal Coordinates CCD File 
C [auth A],
D [auth B]
(3R)-3-cyclopentyl-3-[(4M)-4-{5-methyl-2-[(1-methyl-1H-pyrazol-4-yl)amino]pyrimidin-4-yl}-1H-pyrazol-1-yl]propanenitrile
C20 H24 N8
FEQOESZUGZISHK-GOSISDBHSA-N
EDO
Query on EDO

Download Ideal Coordinates CCD File 
E [auth B]1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-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: 2.45 Å
  • R-Value Free: 0.281 
  • R-Value Work: 0.225 
  • R-Value Observed: 0.228 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 98.09α = 90
b = 36.46β = 94.02
c = 183.73γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
xia2data reduction
XDSdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


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