4FK6

JAK1 kinase (JH1 domain) in complex with compound 72

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.251 
  • R-Value Work: 0.209 
  • R-Value Observed: 0.211 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history. 


Literature

Structure-based discovery of C-2 substituted imidazo-pyrrolopyridine JAK1 inhibitors with improved selectivity over JAK2.

Labadie, S., Dragovich, P.S., Barrett, K., Blair, W.S., Bergeron, P., Chang, C., Deshmukh, G., Eigenbrot, C., Ghilardi, N., Gibbons, P., Hurley, C.A., Johnson, A., Kenny, J.R., Kohli, P.B., Kulagowski, J.J., Liimatta, M., Lupardus, P.J., Mendonca, R., Murray, J.M., Pulk, R., Shia, S., Steffek, M., Ubhayakar, S., Ultsch, M., van Abbema, A., Ward, S., Zak, M.

(2012) Bioorg Med Chem Lett 22: 7627-7633

  • DOI: https://doi.org/10.1016/j.bmcl.2012.10.008
  • Primary Citation of Related Structures:  
    4FK6

  • PubMed Abstract: 

    Herein we describe our successful efforts in obtaining C-2 substituted imidazo-pyrrolopyridines with improved JAK1 selectivity relative to JAK2 by targeting an amino acid residue that differs between the two isoforms (JAK1: E966; JAK2: D939). Efforts to improve cellular potency by reducing the polarity of the inhibitors are also detailed. The X-ray crystal structure of a representative inhibitor in complex with the JAK1 enzyme is also disclosed.

    • Organizational Affiliation: 

    Small Molecule Discovery Chemistry, Genentech, Inc., 1 DNA Way, South San Francisco, CA 94080, United States. sharadal@gene.com


Macromolecules
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Tyrosine-protein kinase JAK1
A, B
302Homo sapiensMutation(s): 0 
Gene Names: JAK1, JAK1A, JAK1B
EC: 2.7.10.2
UniProt & NIH Common Fund Data Resources
Find proteins for P23458 (Homo sapiens)
Explore P23458 
Go to UniProtKB:  P23458
PHAROS:  P23458
GTEx:  ENSG00000162434 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP23458
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
0UJ
Query on 0UJ
Download Ideal Coordinates CCD File 
C [auth A],
D [auth B]		N-({1-[(1R,2R,4S)-bicyclo[2.2.1]hept-2-yl]-1,6-dihydroimidazo[4,5-d]pyrrolo[2,3-b]pyridin-2-yl}methyl)methanesulfonamide
C17 H21 N5 O2 S
IQHKHGHDPGFXAV-MISXGVKJSA-N
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
PTR
Query on PTR
A, B
L-PEPTIDE LINKINGC9 H12 N O6 PTYR
Binding Affinity Annotations 
IDSourceBinding Affinity
0UJ PDBBind:  4FK6 Ki: 0.2 (nM) from 1 assay(s)
BindingDB:  4FK6 Ki: min: 0.2, max: 3.2 (nM) from 2 assay(s)
IC50: 1 (nM) from 1 assay(s)
EC50: min: 13, max: 355 (nM) from 3 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.251 
  • R-Value Work: 0.209 
  • R-Value Observed: 0.211 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 43.248α = 90
b = 169.966β = 90.51
c = 43.805γ = 90
Software Package:
Software NamePurpose
Blu-Icedata collection
PHASERphasing
BUSTERrefinement
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

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Ligand Structure Quality Assessment 


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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2012-11-07
    Type: Initial release
  • Version 1.1: 2012-12-12
    Changes: Database references
  • Version 1.2: 2023-09-13
    Changes: Data collection, Database references, Derived calculations, Refinement description
  • Version 1.3: 2023-12-06
    Changes: Data collection