4I5C | pdb_00004i5c

The Jak1 kinase domain in complex with inhibitor

• PDB DOI: https://doi.org/10.2210/pdb4I5C/pdb

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


• Deposited: 2012-11-28 Released: 2013-05-22 
• Deposition Author(s): Fong, R., Lupardus, P.J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 
  0.245 (Depositor), 0.255 (DCC) 
• R-Value Work: 
  0.190 (Depositor), 0.200 (DCC) 
• R-Value Observed: 
  0.193 (Depositor) 

Starting Model: experimental

Literature

Novel triazolo-pyrrolopyridines as inhibitors of Janus kinase 1.

Hurley, C.A., Blair, W.S., Bull, R.J., Chang, C., Crackett, P.H., Deshmukh, G., Dyke, H.J., Fong, R., Ghilardi, N., Gibbons, P., Hewitt, P.R., Johnson, A., Johnson, T., Kenny, J.R., Kohli, P.B., Kulagowski, J.J., Liimatta, M., Lupardus, P.J., Maxey, R.J., Mendonca, R., Narukulla, R., Pulk, R., Ubhayakar, S., van Abbema, A., Ward, S.I., Waszkowycz, B., Zak, M.

(2013) Bioorg Med Chem Lett 23: 3592-3598

• PubMed: 23642482 
• DOI: https://doi.org/10.1016/j.bmcl.2013.04.018
• Primary Citation Related Structures: 
  4I5C


• PubMed Abstract: 
  

  The identification of a novel fused triazolo-pyrrolopyridine scaffold, optimized derivatives of which display nanomolar inhibition of Janus kinase 1, is described. Prototypical example 3 demonstrated lower cell potency shift, better permeability in cells and higher oral exposure in rat than the corresponding, previously reported, imidazo-pyrrolopyridine analogue 2. Examples 6, 7 and 18 were subsequently identified from an optimization campaign and demonstrated modest selectivity over JAK2, moderate to good oral bioavailability in rat with overall pharmacokinetic profiles comparable to that reported for an approved pan-JAK inhibitor (tofacitinib).

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Organizational Affiliation: 
• Department of Medicinal Chemistry, Argenta, 8/9 Spire Green Centre, Harlow, Essex CM19 5TR, United Kingdom. [e-mail]

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: 70.36 kDa 
• Atom Count: 5,069 
• Modeled Residue Count: 574 
• Deposited Residue Count: 604 
• Unique protein chains: 1

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 GTEx:  ENSG00000162434

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
C5I	C [auth A], H [auth B]	3-oxo-3-[(3R)-3-(pyrrolo[2,3-b][1,2,3]triazolo[4,5-d]pyridin-1(6H)-yl)piperidin-1-yl]propanenitrile C15 H15 N7 O COGIAVJREKAVDL-SNVBAGLBSA-N
EDO	D [auth B], E [auth B], F [auth B], G [auth B]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-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
C5I	BindingDB:  4I5C	Ki: 1.5 (nM) from 1 assay(s)
		EC50: 114 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free:  0.245 (Depositor), 0.255 (DCC) 
• R-Value Work:  0.190 (Depositor), 0.200 (DCC) 
• R-Value Observed: 0.193 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 42.7	α = 90
b = 173.969	β = 94.11
c = 44.675	γ = 90

Software Package:

Software Name	Purpose
Blu-Ice	data collection
PHASER	phasing
BUSTER	refinement
XDS	data reduction
SCALA	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2013-05-22 
Deposition Author(s): Fong, R., Lupardus, P.J.

Revision History  

• Version 1.0: 2013-05-22
  Type: Initial release
  
• Version 1.1: 2013-06-12
  Changes: Database references
• Version 1.2: 2023-09-20
  Changes: Data collection, Database references, Derived calculations, Refinement description
• Version 1.3: 2023-12-06
  Changes: Data collection
• Version 1.4: 2024-10-30
  Changes: Structure summary