8G6Z | pdb_00008g6z

JAK2 crystal structure in complex with Compound 13


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.45 Å
  • R-Value Free: 
    0.281 (Depositor), 0.285 (DCC) 
  • R-Value Work: 
    0.225 (Depositor), 0.231 (DCC) 
  • R-Value Observed: 
    0.228 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 8G6Z

Ligand Structure Quality Assessment 


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 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.

Macromolecule Content 

  • Total Structure Weight: 75.6 kDa 
  • Atom Count: 4,884 
  • Modeled Residue Count: 561 
  • Deposited Residue Count: 636 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  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
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Reference Sequence

Small Molecules

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 (Depositor), 0.285 (DCC) 
  • R-Value Work:  0.225 (Depositor), 0.231 (DCC) 
  • R-Value Observed: 0.228 (Depositor) 
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
  • Version 1.4: 2024-10-16
    Changes: Structure summary