6TPD

Fragment-based discovery of pyrazolopyridones as JAK1 inhibitors with excellent subtype selectivity


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.99 Å
  • R-Value Free: 0.278 
  • R-Value Work: 0.223 
  • R-Value Observed: 0.226 

Starting Model: experimental
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This is version 1.2 of the entry. See complete history


Literature

Fragment-Based Discovery of Pyrazolopyridones as JAK1 Inhibitors with Excellent Subtype Selectivity.

Hansen, B.B.Jepsen, T.H.Larsen, M.Sindet, R.Vifian, T.Burhardt, M.N.Larsen, J.Seitzberg, J.G.Carnerup, M.A.Jerre, A.Molck, C.Lovato, P.Rai, S.Nasipireddy, V.R.Ritzen, A.

(2020) J Med Chem 63: 7008-7032

  • DOI: https://doi.org/10.1021/acs.jmedchem.0c00359
  • Primary Citation of Related Structures:  
    6TPD, 6TPE, 6TPF

  • PubMed Abstract: 

    Herein, we report the discovery of a series of JAK1-selective kinase inhibitors with high potency and excellent JAK family subtype selectivity. A fragment screening hit 1 with a pyrazolopyridone core and a JAK1 bias was selected as the starting point for our fragment-based lead generation efforts. A two-stage strategy was chosen with the dual aims of improving potency and JAK1 selectivity: Optimization of the lipophilic ribose pocket-targeting substituent was followed by the introduction of a variety of P-loop-targeting functional groups. Combining the best moieties from both stages of the optimization afforded compound 40 , which showed excellent potency and selectivity. Metabolism studies in vitro and in vivo together with an in vitro safety evaluation suggest that 40 may be a viable lead compound for the development of highly subtype-selective JAK1 inhibitors.


  • Organizational Affiliation

    Medicinal Chemistry, GVK Biosciences Private Limited, 28 A, IDA Nacharam, Hyderabad 500076, India.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Tyrosine-protein kinase JAK2289Homo sapiensMutation(s): 0 
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
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
QZ8 (Subject of Investigation/LOI)
Query on QZ8

Download Ideal Coordinates CCD File 
B [auth A]3-methyl-4-phenyl-2,7-dihydropyrazolo[3,4-b]pyridin-6-one
C13 H11 N3 O
LDYQYDPPCHEKQY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.99 Å
  • R-Value Free: 0.278 
  • R-Value Work: 0.223 
  • R-Value Observed: 0.226 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 107.411α = 90
b = 69.669β = 98.45
c = 50.798γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
xia2data reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Revision History  (Full details and data files)

  • Version 1.0: 2020-06-10
    Type: Initial release
  • Version 1.1: 2020-07-22
    Changes: Database references
  • Version 1.2: 2024-01-24
    Changes: Data collection, Database references, Refinement description