4RIO | pdb_00004rio

Crystal structure of JAK3 kinase domain in complex with a pyrrolopyridazine carboxamide inhibitor


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.69 Å
  • R-Value Free: 
    0.281 (Depositor), 0.280 (DCC) 
  • R-Value Work: 
    0.215 (Depositor), 0.220 (DCC) 
  • R-Value Observed: 
    0.218 (Depositor) 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 

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This is version 1.1 of the entry. See complete history


Literature

Discovery of pyrrolo[1,2-b]pyridazine-3-carboxamides as Janus kinase (JAK) inhibitors.

Duan, J.J.Lu, Z.Jiang, B.Yang, B.V.Doweyko, L.M.Nirschl, D.S.Haque, L.E.Lin, S.Brown, G.Hynes, J.Tokarski, J.S.Sack, J.S.Khan, J.Lippy, J.S.Zhang, R.F.Pitt, S.Shen, G.Pitts, W.J.Carter, P.H.Barrish, J.C.Nadler, S.G.Salter-Cid, L.M.McKinnon, M.Fura, A.Schieven, G.L.Wrobleski, S.T.

(2014) Bioorg Med Chem Lett 24: 5721-5726

  • DOI: https://doi.org/10.1016/j.bmcl.2014.10.061
  • Primary Citation of Related Structures:  
    4RIO

  • PubMed Abstract: 

    A new class of Janus kinase (JAK) inhibitors was discovered using a rationally designed pyrrolo[1,2-b]pyridazine-3-carboxamide scaffold. Preliminary studies identified (R)-(2,2-dimethylcyclopentyl)amine as a preferred C4 substituent on the pyrrolopyridazine core (3b). Incorporation of amino group to 3-position of the cyclopentane ring resulted in a series of JAK3 inhibitors (4g-4j) that potently inhibited IFNγ production in an IL2-induced whole blood assay and displayed high functional selectivity for JAK3-JAK1 pathway relative to JAK2. Further modifications led to the discovery of an orally bioavailable (2-fluoro-2-methylcyclopentyl)amino analogue 5g which is a nanomolar inhibitor of both JAK3 and TYK2, functionally selective for the JAK3-JAK1 pathway versus JAK2, and active in a human whole blood assay.


  • Organizational Affiliation

    Research and Development, Bristol-Myers Squibb Company, Princeton, NJ 08543-4000, USA. Electronic address: james.duan@bms.com.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Tyrosine-protein kinase JAK3293Homo sapiensMutation(s): 3 
Gene Names: JAK3
EC: 2.7.10.2
UniProt & NIH Common Fund Data Resources
Find proteins for P52333 (Homo sapiens)
Explore P52333 
Go to UniProtKB:  P52333
PHAROS:  P52333
GTEx:  ENSG00000105639 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP52333
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
3QX
Query on 3QX

Download Ideal Coordinates CCD File 
B [auth A]4-{[(1R,2S)-2-fluoro-2-methylcyclopentyl]amino}pyrrolo[1,2-b]pyridazine-3-carboxamide
C14 H17 F N4 O
UPBRYBJZTWHUQK-RISCZKNCSA-N
Binding Affinity Annotations 
IDSourceBinding Affinity
3QX BindingDB:  4RIO IC50: 1 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.69 Å
  • R-Value Free:  0.281 (Depositor), 0.280 (DCC) 
  • R-Value Work:  0.215 (Depositor), 0.220 (DCC) 
  • R-Value Observed: 0.218 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 47.54α = 90
b = 75.44β = 90
c = 87.98γ = 90
Software Package:
Software NamePurpose
BUSTERrefinement
HKL-2000data reduction
HKL-2000data scaling

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 3QXClick on this verticalbar to view details

Entry History 

Deposition Data

  • Released Date: 2014-12-24 
  • Deposition Author(s): Sack, J.S.

Revision History  (Full details and data files)

  • Version 1.0: 2014-12-24
    Type: Initial release
  • Version 1.1: 2024-02-28
    Changes: Data collection, Database references, Derived calculations