Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 70.21 kDa 
• Atom Count: 4,884 
• Modelled Residue Count: 573 
• Deposited Residue Count: 604 
• Unique protein chains: 1

 4FK6

JAK1 kinase (JH1 domain) in complex with compound 72

• PDB DOI:  https://doi.org/10.2210/pdb4FK6/pdb

• Classification: TRANSFERASE/TRANSFERASE INHIBITOR
• Organism(s): Homo sapiens
• Expression System: Spodoptera frugiperda
• Mutation(s): No 


• Deposited: 2012-06-12 Released: 2012-11-07 
• Deposition Author(s): Eigenbrot, C., Steffek, M.

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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 

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

• PubMed: 23107482 
• 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.

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Organizational Affiliation: 

Small Molecule Discovery Chemistry, Genentech, Inc., 1 DNA Way, South San Francisco, CA 94080, United States. [e-mail]

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Tyrosine-protein kinase JAK1	A, B	302	Homo sapiens	Mutation(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

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
0UJ	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
ID	Chains	Type	Formula	2D Diagram	Parent
PTR	A, B	L-PEPTIDE LINKING	C9 H12 N O6 P		TYR

Binding Affinity Annotations
ID	Source	Binding Affinity
0UJ	BindingDB:  4FK6	Ki: min: 0.2, max: 3.2 (nM) from 3 assay(s)
		IC50: 1 (nM) from 1 assay(s)
		EC50: min: 13, max: 355 (nM) from 4 assay(s)
	Binding MOAD:  4FK6	Ki: 0.2 (nM) from 1 assay(s)
	PDBBind:  4FK6	Ki: 0.2 (nM) from 1 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 = 43.248	α = 90
b = 169.966	β = 90.51
c = 43.805	γ = 90

Software Package:

Software Name	Purpose
Blu-Ice	data collection
PHASER	phasing
BUSTER	refinement
DENZO	data reduction
SCALEPACK	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2012-11-07 
Deposition Author(s): Eigenbrot, C., Steffek, M.

Revision History  

• Version 1.0: 2012-11-07
  Type: Initial release
  
• Version 1.1: 2012-12-12
  Changes: Database references