5KHX

Crystal structure of JAK1 in complex with PF-4950736

• PDB DOI: https://doi.org/10.2210/pdb5KHX/pdb

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


• Deposited: 2016-06-16 Released: 2016-11-09 
• Deposition Author(s): Han, S., Caspers, N.L.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free: 0.242 
• R-Value Work: 0.170 
• R-Value Observed: 0.173 

Literature

Development of a high-throughput crystal structure-determination platform for JAK1 using a novel metal-chelator soaking system.

Caspers, N.L., Han, S., Rajamohan, F., Hoth, L.R., Geoghegan, K.F., Subashi, T.A., Vazquez, M.L., Kaila, N., Cronin, C.N., Johnson, E., Kurumbail, R.G.

(2016) Acta Crystallogr F Struct Biol Commun 72: 840-845

• PubMed: 27827355 
• DOI: https://doi.org/10.1107/S2053230X16016356
• Primary Citation of Related Structures:  
  5KHW, 5KHX


• PubMed Abstract: 
  

  Crystals of phosphorylated JAK1 kinase domain were initially generated in complex with nucleotide (ADP) and magnesium. The tightly bound Mg ²⁺ -ADP at the ATP-binding site proved recalcitrant to ligand displacement. Addition of a molar excess of EDTA helped to dislodge the divalent metal ion, promoting the release of ADP and allowing facile exchange with ATP-competitive small-molecule ligands. Many kinases require the presence of a stabilizing ligand in the ATP site for crystallization. This procedure could be useful for developing co-crystallization systems with an exchangeable ligand to enable structure-based drug design of other protein kinases.

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Organizational Affiliation: 

Structural Biology, Pfizer Inc., Eastern Point Road, Groton, CT 06340, USA.

Biological Assembly 1  

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

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

Macromolecule Content

• Total Structure Weight: 36.71 kDa 
• Atom Count: 2,370 
• Modelled Residue Count: 278 
• Deposited Residue Count: 316 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Tyrosine-protein kinase JAK1	A	316	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 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
6TE	B [auth A]	~{N}-[3-[methyl(7~{H}-pyrrolo[2,3-d]pyrimidin-4-yl)amino]cyclobutyl]methanesulfonamide C12 H17 N5 O2 S QZOGHNDWZHFIJP-DTORHVGOSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
PTR	A	L-PEPTIDE LINKING	C9 H12 N O6 P		TYR

Binding Affinity Annotations
ID	Source	Binding Affinity
6TE	BindingDB:  5KHX	IC50: min: 90, max: 750 (nM) from 2 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free: 0.242 
• R-Value Work: 0.170 
• R-Value Observed: 0.173 
• Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 46.25	α = 90
b = 88.3	β = 90
c = 146.84	γ = 90

Software Package:

Software Name	Purpose
BUSTER	refinement
XDS	data reduction
SCALA	data scaling
BUSTER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2016-11-09 
Deposition Author(s): Han, S., Caspers, N.L.

Revision History  

• Version 1.0: 2016-11-09
  Type: Initial release
  
• Version 1.1: 2018-05-16
  Changes: Data collection, Database references, Derived calculations
• Version 1.2: 2024-10-16
  Changes: Data collection, Database references, Structure summary