4K6Z | pdb_00004k6z

The Jak1 kinase domain in complex with compound 37

• PDB DOI: https://doi.org/10.2210/pdb4K6Z/pdb

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


• Deposited: 2013-04-16 Released: 2013-10-02 
• Deposition Author(s): Fong, R., Lupardus, P.J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.73 Å
• R-Value Free: 
  0.297 (Depositor), 0.304 (DCC) 
• R-Value Work: 
  0.238 (Depositor), 0.240 (DCC) 
• R-Value Observed: 
  0.244 (Depositor) 

Literature

Design and evaluation of novel 8-oxo-pyridopyrimidine Jak1/2 inhibitors.

Labadie, S., Barrett, K., Blair, W.S., Chang, C., Deshmukh, G., Eigenbrot, C., Gibbons, P., Johnson, A., Kenny, J.R., Kohli, P.B., Liimatta, M., Lupardus, P.J., Shia, S., Steffek, M., Ubhayakar, S., Abbema, A.V., Zak, M.

(2013) Bioorg Med Chem Lett 23: 5923-5930

• PubMed: 24042009 
• DOI: https://doi.org/10.1016/j.bmcl.2013.08.082
• Primary Citation Related Structures: 
  4K6Z, 4K77


• PubMed Abstract: 
  

  A highly ligand efficient, novel 8-oxo-pyridopyrimidine containing inhibitor of Jak1 and Jak2 isoforms with a pyridone moiety as the hinge-binding motif was discovered. Structure-based design strategies were applied to significantly improve enzyme potency and the polarity of the molecule was adjusted to gain cellular activity. The crystal structures of two representative inhibitors bound to Jak1 were obtained to enable SAR exploration.

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Organizational Affiliation: 
• Genentech Inc., 1 DNA Way, South San Francisco, CA 94080, USA. Electronic address: [e-mail].

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: 35.07 kDa 
• Atom Count: 2,343 
• Modeled Residue Count: 281 
• Deposited Residue Count: 302 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Tyrosine-protein kinase JAK1	A	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 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
1Q3	B [auth A]	(1R,2S)-2-{[8-oxo-2-(1H-pyrazol-4-yl)-5,8-dihydropyrido[3,4-d]pyrimidin-4-yl]amino}cyclopentanecarbonitrile C16 H15 N7 O GGNYHYINELGWQU-CABZTGNLSA-N

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.73 Å
• R-Value Free:  0.297 (Depositor), 0.304 (DCC) 
• R-Value Work:  0.238 (Depositor), 0.240 (DCC) 
• R-Value Observed: 0.244 (Depositor) 

Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 168.574	α = 90
b = 42.701	β = 90
c = 44.301	γ = 90

Software Package:

Software Name	Purpose
BOS	data collection
PHASER	phasing
BUSTER	refinement
XDS	data reduction
SCALA	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2013-10-02 
Deposition Author(s): Fong, R., Lupardus, P.J.

Revision History  

• Version 1.0: 2013-10-02
  Type: Initial release
  
• Version 1.1: 2013-10-23
  Changes: Database references
• Version 1.2: 2024-11-27
  Changes: Data collection, Database references, Derived calculations, Structure summary